Starting phenix.real_space_refine on Tue Jul 29 19:44:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kna_22937/07_2025/7kna_22937.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kna_22937/07_2025/7kna_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_22937/07_2025/7kna_22937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kna_22937/07_2025/7kna_22937.map" model { file = "/net/cci-nas-00/data/ceres_data/7kna_22937/07_2025/7kna_22937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kna_22937/07_2025/7kna_22937.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 5} 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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 5} 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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 5} 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: 6.74, per 1000 atoms: 0.58 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: 3.25 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.83 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: 3.82 Time building geometry restraints manager: 3.78 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 or resid 901 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: 1.030 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.150 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (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 TRP 0.017 0.004 TRP A 133 HIS 0.004 0.001 HIS C 635 PHE 0.023 0.004 PHE C 209 TYR 0.035 0.006 TYR B 587 ARG 0.005 0.001 ARG C 599 Details of bonding type rmsd link_NAG-ASN : bond 0.06944 ( 18) link_NAG-ASN : angle 2.45076 ( 54) link_BETA1-4 : bond 0.07257 ( 6) link_BETA1-4 : angle 4.16596 ( 18) hydrogen bonds : bond 0.15912 ( 468) hydrogen bonds : angle 7.59117 ( 1368) SS BOND : bond 0.01400 ( 18) SS BOND : angle 3.93858 ( 36) covalent geometry : bond 0.01593 (11860) covalent geometry : angle 1.47213 (16105) *********************** 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 : 1.285 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: 0.2873 time to fit residues: 56.9604 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 : 1.241 ------------------------------------------------------------------------------- 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 121 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.117092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094690 restraints weight = 18805.599| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.57 r_work: 0.3056 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11902 Z= 0.167 Angle : 0.616 6.472 16213 Z= 0.324 Chirality : 0.047 0.288 1836 Planarity : 0.004 0.039 2043 Dihedral : 5.198 28.234 2067 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.26 % Allowed : 3.69 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1437 helix: 1.60 (0.26), residues: 357 sheet: 0.62 (0.29), residues: 288 loop : 0.15 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 514 HIS 0.003 0.001 HIS C 635 PHE 0.016 0.002 PHE B 631 TYR 0.023 0.002 TYR A 650 ARG 0.005 0.000 ARG C 599 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 18) link_NAG-ASN : angle 2.52699 ( 54) link_BETA1-4 : bond 0.00304 ( 6) link_BETA1-4 : angle 1.57589 ( 18) hydrogen bonds : bond 0.05327 ( 468) hydrogen bonds : angle 5.50623 ( 1368) SS BOND : bond 0.00451 ( 18) SS BOND : angle 1.30193 ( 36) covalent geometry : bond 0.00372 (11860) covalent geometry : angle 0.59529 (16105) *********************** 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: 15 poor density : 67 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 266 MET cc_start: 0.8399 (pp-130) cc_final: 0.7661 (ptt) REVERT: B 266 MET cc_start: 0.8366 (pp-130) cc_final: 0.7596 (ptt) REVERT: C 104 ASP cc_start: 0.7697 (m-30) cc_final: 0.7445 (m-30) REVERT: C 110 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8045 (mm-30) REVERT: C 266 MET cc_start: 0.8418 (pp-130) cc_final: 0.7750 (ptt) REVERT: C 595 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7571 (mp) outliers start: 15 outliers final: 4 residues processed: 81 average time/residue: 0.2320 time to fit residues: 28.3413 Evaluate side-chains 46 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 136 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.110957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.088054 restraints weight = 19511.820| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.58 r_work: 0.2946 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2563 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= 0.290 Angle : 0.660 10.886 16213 Z= 0.338 Chirality : 0.048 0.275 1836 Planarity : 0.004 0.068 2043 Dihedral : 5.108 28.906 2061 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.34 % Allowed : 5.96 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1437 helix: 1.15 (0.26), residues: 378 sheet: -0.04 (0.30), residues: 300 loop : -0.16 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 159 HIS 0.006 0.002 HIS B 18 PHE 0.016 0.002 PHE C 127 TYR 0.027 0.002 TYR A 650 ARG 0.003 0.000 ARG B 599 Details of bonding type rmsd link_NAG-ASN : bond 0.01206 ( 18) link_NAG-ASN : angle 3.11627 ( 54) link_BETA1-4 : bond 0.00298 ( 6) link_BETA1-4 : angle 1.38326 ( 18) hydrogen bonds : bond 0.04878 ( 468) hydrogen bonds : angle 5.38408 ( 1368) SS BOND : bond 0.00564 ( 18) SS BOND : angle 1.36944 ( 36) covalent geometry : bond 0.00685 (11860) covalent geometry : angle 0.63260 (16105) *********************** 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 63 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 1.280 Fit side-chains REVERT: A 266 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8275 (ptt) REVERT: B 266 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7986 (ptt) REVERT: C 104 ASP cc_start: 0.7805 (m-30) cc_final: 0.7529 (m-30) REVERT: C 266 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8005 (ptt) REVERT: C 595 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7892 (mp) REVERT: C 650 TYR cc_start: 0.7419 (t80) cc_final: 0.7203 (t80) outliers start: 16 outliers final: 4 residues processed: 57 average time/residue: 0.1681 time to fit residues: 17.1813 Evaluate side-chains 45 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 266 MET Chi-restraints excluded: chain B residue 275 ILE 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 106 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.113630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.090870 restraints weight = 19047.404| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.56 r_work: 0.2985 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11902 Z= 0.133 Angle : 0.544 12.558 16213 Z= 0.272 Chirality : 0.044 0.259 1836 Planarity : 0.004 0.037 2043 Dihedral : 4.777 40.031 2061 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.26 % Allowed : 6.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1437 helix: 1.61 (0.27), residues: 375 sheet: -0.08 (0.30), residues: 300 loop : -0.15 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 514 HIS 0.005 0.001 HIS C 18 PHE 0.011 0.001 PHE A 631 TYR 0.022 0.001 TYR A 650 ARG 0.002 0.000 ARG C 599 Details of bonding type rmsd link_NAG-ASN : bond 0.00877 ( 18) link_NAG-ASN : angle 3.71570 ( 54) link_BETA1-4 : bond 0.00370 ( 6) link_BETA1-4 : angle 1.11837 ( 18) hydrogen bonds : bond 0.04166 ( 468) hydrogen bonds : angle 5.03520 ( 1368) SS BOND : bond 0.00244 ( 18) SS BOND : angle 0.89936 ( 36) covalent geometry : bond 0.00296 (11860) covalent geometry : angle 0.49846 (16105) *********************** 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 60 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 1.284 Fit side-chains REVERT: A 110 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8061 (mm-30) REVERT: A 266 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7870 (ptt) REVERT: B 266 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7966 (ptt) REVERT: C 266 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8012 (ptt) outliers start: 15 outliers final: 4 residues processed: 55 average time/residue: 0.1855 time to fit residues: 17.1055 Evaluate side-chains 45 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 595 LEU 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 266 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 65 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.113802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.091103 restraints weight = 18902.616| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.54 r_work: 0.2988 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2955 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= 0.128 Angle : 0.533 12.842 16213 Z= 0.267 Chirality : 0.044 0.262 1836 Planarity : 0.004 0.036 2043 Dihedral : 4.524 29.923 2061 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.09 % Allowed : 6.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1437 helix: 1.85 (0.27), residues: 378 sheet: -0.27 (0.32), residues: 270 loop : -0.06 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 159 HIS 0.004 0.001 HIS C 18 PHE 0.008 0.001 PHE B 121 TYR 0.026 0.001 TYR C 650 ARG 0.001 0.000 ARG B 599 Details of bonding type rmsd link_NAG-ASN : bond 0.00909 ( 18) link_NAG-ASN : angle 3.84274 ( 54) link_BETA1-4 : bond 0.00302 ( 6) link_BETA1-4 : angle 1.12304 ( 18) hydrogen bonds : bond 0.03933 ( 468) hydrogen bonds : angle 4.88883 ( 1368) SS BOND : bond 0.00231 ( 18) SS BOND : angle 1.24865 ( 36) covalent geometry : bond 0.00292 (11860) covalent geometry : angle 0.48141 (16105) *********************** 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 59 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 1.363 Fit side-chains REVERT: A 110 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8070 (mm-30) REVERT: A 266 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7807 (ptt) REVERT: B 266 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8004 (ptt) REVERT: C 266 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7980 (ptt) outliers start: 13 outliers final: 5 residues processed: 51 average time/residue: 0.1827 time to fit residues: 16.1961 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 : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 0.0000 chunk 94 optimal weight: 7.9990 chunk 16 optimal weight: 0.0370 chunk 124 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 overall best weight: 0.4462 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.115352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.092737 restraints weight = 18989.196| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.53 r_work: 0.3014 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11902 Z= 0.100 Angle : 0.501 12.679 16213 Z= 0.249 Chirality : 0.043 0.263 1836 Planarity : 0.003 0.037 2043 Dihedral : 4.102 29.520 2061 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.76 % Allowed : 7.05 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1437 helix: 2.10 (0.27), residues: 378 sheet: -0.28 (0.32), residues: 270 loop : -0.02 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 514 HIS 0.004 0.001 HIS B 18 PHE 0.008 0.001 PHE A 121 TYR 0.025 0.001 TYR C 650 ARG 0.001 0.000 ARG C 599 Details of bonding type rmsd link_NAG-ASN : bond 0.00867 ( 18) link_NAG-ASN : angle 3.74216 ( 54) link_BETA1-4 : bond 0.00348 ( 6) link_BETA1-4 : angle 1.03889 ( 18) hydrogen bonds : bond 0.03718 ( 468) hydrogen bonds : angle 4.72174 ( 1368) SS BOND : bond 0.00200 ( 18) SS BOND : angle 0.95358 ( 36) covalent geometry : bond 0.00217 (11860) covalent geometry : angle 0.44978 (16105) *********************** 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: 9 poor density : 50 time to evaluate : 1.344 Fit side-chains REVERT: A 110 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8004 (mm-30) REVERT: A 266 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7801 (ptt) REVERT: B 266 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8020 (ptt) REVERT: C 266 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7917 (ptt) outliers start: 9 outliers final: 3 residues processed: 54 average time/residue: 0.1654 time to fit residues: 16.0371 Evaluate side-chains 49 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 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 118 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 142 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 141 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.110964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.088411 restraints weight = 19402.176| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.51 r_work: 0.2936 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 11902 Z= 0.251 Angle : 0.595 12.980 16213 Z= 0.295 Chirality : 0.046 0.255 1836 Planarity : 0.004 0.033 2043 Dihedral : 4.750 32.108 2061 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.76 % Allowed : 7.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1437 helix: 1.93 (0.27), residues: 378 sheet: -0.66 (0.31), residues: 243 loop : -0.32 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 159 HIS 0.005 0.001 HIS B 18 PHE 0.011 0.002 PHE C 105 TYR 0.022 0.002 TYR A 650 ARG 0.002 0.000 ARG C 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00852 ( 18) link_NAG-ASN : angle 3.95334 ( 54) link_BETA1-4 : bond 0.00261 ( 6) link_BETA1-4 : angle 1.32194 ( 18) hydrogen bonds : bond 0.04136 ( 468) hydrogen bonds : angle 5.00131 ( 1368) SS BOND : bond 0.00414 ( 18) SS BOND : angle 1.33645 ( 36) covalent geometry : bond 0.00593 (11860) covalent geometry : angle 0.54587 (16105) *********************** 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 57 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 1.235 Fit side-chains REVERT: A 110 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8140 (mm-30) REVERT: A 266 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7918 (ptt) REVERT: B 266 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8129 (ptt) REVERT: C 266 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8107 (ptt) outliers start: 9 outliers final: 6 residues processed: 54 average time/residue: 0.1868 time to fit residues: 16.8374 Evaluate side-chains 54 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain C residue 531 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 79 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.0370 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.113400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090185 restraints weight = 19244.467| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.61 r_work: 0.2969 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11902 Z= 0.117 Angle : 0.516 12.680 16213 Z= 0.256 Chirality : 0.043 0.245 1836 Planarity : 0.003 0.037 2043 Dihedral : 4.448 32.303 2061 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.67 % Allowed : 7.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1437 helix: 2.13 (0.27), residues: 378 sheet: -0.89 (0.34), residues: 213 loop : -0.15 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 585 HIS 0.005 0.001 HIS B 18 PHE 0.008 0.001 PHE A 121 TYR 0.020 0.001 TYR A 650 ARG 0.001 0.000 ARG B 599 Details of bonding type rmsd link_NAG-ASN : bond 0.00836 ( 18) link_NAG-ASN : angle 3.80938 ( 54) link_BETA1-4 : bond 0.00368 ( 6) link_BETA1-4 : angle 1.04913 ( 18) hydrogen bonds : bond 0.03737 ( 468) hydrogen bonds : angle 4.77384 ( 1368) SS BOND : bond 0.00252 ( 18) SS BOND : angle 0.89565 ( 36) covalent geometry : bond 0.00265 (11860) covalent geometry : angle 0.46476 (16105) *********************** 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 54 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 1.358 Fit side-chains REVERT: A 110 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8068 (mm-30) REVERT: A 266 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7866 (ptt) REVERT: B 266 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8077 (ptt) REVERT: B 626 ILE cc_start: 0.7998 (pt) cc_final: 0.7682 (mp) REVERT: C 266 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8065 (ptt) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.1653 time to fit residues: 15.1619 Evaluate side-chains 51 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 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 140 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.109989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.087075 restraints weight = 19412.575| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.57 r_work: 0.2918 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 11902 Z= 0.264 Angle : 0.595 12.963 16213 Z= 0.294 Chirality : 0.046 0.267 1836 Planarity : 0.004 0.034 2043 Dihedral : 5.032 34.862 2061 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.59 % Allowed : 7.97 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1437 helix: 1.94 (0.27), residues: 378 sheet: -0.77 (0.31), residues: 243 loop : -0.39 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 159 HIS 0.006 0.001 HIS B 18 PHE 0.010 0.002 PHE C 105 TYR 0.020 0.002 TYR A 650 ARG 0.002 0.000 ARG B 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 18) link_NAG-ASN : angle 3.96505 ( 54) link_BETA1-4 : bond 0.00286 ( 6) link_BETA1-4 : angle 1.28273 ( 18) hydrogen bonds : bond 0.04103 ( 468) hydrogen bonds : angle 5.01041 ( 1368) SS BOND : bond 0.00394 ( 18) SS BOND : angle 1.20914 ( 36) covalent geometry : bond 0.00629 (11860) covalent geometry : angle 0.54624 (16105) *********************** 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 54 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 1.350 Fit side-chains REVERT: A 110 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8163 (mm-30) REVERT: A 266 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7960 (ptt) REVERT: B 266 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8214 (ptt) REVERT: C 266 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8132 (ptt) outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 0.1766 time to fit residues: 15.9613 Evaluate side-chains 52 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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 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 104 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.112363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.089259 restraints weight = 19209.963| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.59 r_work: 0.2956 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3514 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= 0.136 Angle : 0.529 12.766 16213 Z= 0.262 Chirality : 0.044 0.252 1836 Planarity : 0.003 0.037 2043 Dihedral : 4.792 35.299 2061 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.22), residues: 1437 helix: 2.18 (0.27), residues: 372 sheet: -1.00 (0.34), residues: 213 loop : -0.25 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 514 HIS 0.005 0.001 HIS B 18 PHE 0.008 0.001 PHE A 121 TYR 0.020 0.001 TYR A 650 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00816 ( 18) link_NAG-ASN : angle 3.85375 ( 54) link_BETA1-4 : bond 0.00373 ( 6) link_BETA1-4 : angle 1.06918 ( 18) hydrogen bonds : bond 0.03765 ( 468) hydrogen bonds : angle 4.80342 ( 1368) SS BOND : bond 0.00258 ( 18) SS BOND : angle 0.91261 ( 36) covalent geometry : bond 0.00315 (11860) covalent geometry : angle 0.47792 (16105) ********************** 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 52 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 1.269 Fit side-chains REVERT: A 110 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8090 (mm-30) REVERT: A 266 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7934 (ptt) REVERT: B 266 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8140 (ptt) REVERT: C 57 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8389 (m) REVERT: C 266 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8110 (ptt) REVERT: C 626 ILE cc_start: 0.8002 (pt) cc_final: 0.7694 (mp) outliers start: 9 outliers final: 4 residues processed: 48 average time/residue: 0.1659 time to fit residues: 14.3342 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 : 1.253 ------------------------------------------------------------------------------- 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 266 MET 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 143 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 121 optimal weight: 0.0470 chunk 57 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.112531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.089436 restraints weight = 19304.914| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.59 r_work: 0.2957 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11902 Z= 0.137 Angle : 0.520 12.793 16213 Z= 0.257 Chirality : 0.044 0.249 1836 Planarity : 0.003 0.037 2043 Dihedral : 4.588 35.480 2061 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.22), residues: 1437 helix: 2.28 (0.27), residues: 372 sheet: -0.97 (0.34), residues: 213 loop : -0.24 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 514 HIS 0.005 0.001 HIS A 18 PHE 0.008 0.001 PHE A 121 TYR 0.020 0.001 TYR A 650 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00821 ( 18) link_NAG-ASN : angle 3.82995 ( 54) link_BETA1-4 : bond 0.00294 ( 6) link_BETA1-4 : angle 1.11904 ( 18) hydrogen bonds : bond 0.03673 ( 468) hydrogen bonds : angle 4.72780 ( 1368) SS BOND : bond 0.00264 ( 18) SS BOND : angle 0.89253 ( 36) covalent geometry : bond 0.00320 (11860) covalent geometry : angle 0.46893 (16105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4444.54 seconds wall clock time: 77 minutes 43.17 seconds (4663.17 seconds total)