Starting phenix.real_space_refine on Wed Feb 4 19:54:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nps_49631/02_2026/9nps_49631.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nps_49631/02_2026/9nps_49631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nps_49631/02_2026/9nps_49631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nps_49631/02_2026/9nps_49631.map" model { file = "/net/cci-nas-00/data/ceres_data/9nps_49631/02_2026/9nps_49631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nps_49631/02_2026/9nps_49631.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 51 5.16 5 C 7882 2.51 5 N 2089 2.21 5 O 2469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12491 Number of models: 1 Model: "" Number of chains: 24 Chain: "K" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "L" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 2 Chain: "G" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1168 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain breaks: 1 Chain: "H" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 844 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 2 Chain: "I" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "J" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 2 Chain: "E" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "F" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 837 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain breaks: 2 Chain: "C" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1118 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 2 Chain: "A" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1188 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain breaks: 1 Chain: "B" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.76, per 1000 atoms: 0.22 Number of scatterers: 12491 At special positions: 0 Unit cell: (87.648, 89.4186, 159.36, 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 51 16.00 O 2469 8.00 N 2089 7.00 C 7882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS K 92 " - pdb=" SG CYS K 119 " distance=2.03 Simple disulfide: pdb=" SG CYS L 512 " - pdb=" SG CYS L 557 " distance=2.03 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 119 " distance=2.03 Simple disulfide: pdb=" SG CYS H 512 " - pdb=" SG CYS H 557 " distance=2.03 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 119 " distance=2.03 Simple disulfide: pdb=" SG CYS J 512 " - pdb=" SG CYS J 557 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 119 " distance=2.03 Simple disulfide: pdb=" SG CYS F 512 " - pdb=" SG CYS F 557 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 119 " distance=2.03 Simple disulfide: pdb=" SG CYS D 512 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 557 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 5 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG O 1 " - " ASN K 94 " " NAG P 1 " - " ASN G 94 " " NAG Q 1 " - " ASN I 94 " " NAG R 1 " - " ASN E 94 " " NAG S 1 " - " ASN C 94 " " NAG T 1 " - " ASN A 94 " " NAG U 1 " - " ASN L 564 " " NAG V 1 " - " ASN H 564 " " NAG W 1 " - " ASN J 564 " " NAG X 1 " - " ASN F 564 " " NAG Y 1 " - " ASN D 564 " " NAG Z 1 " - " ASN B 564 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 530.7 milliseconds 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2798 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 23 sheets defined 24.2% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'K' and resid 43 through 45 No H-bonds generated for 'chain 'K' and resid 43 through 45' Processing helix chain 'K' and resid 55 through 58 removed outlier: 3.829A pdb=" N LYS K 58 " --> pdb=" O SER K 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 55 through 58' Processing helix chain 'K' and resid 66 through 68 No H-bonds generated for 'chain 'K' and resid 66 through 68' Processing helix chain 'K' and resid 171 through 179 removed outlier: 3.677A pdb=" N MET K 177 " --> pdb=" O THR K 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 523 through 528 removed outlier: 4.317A pdb=" N LEU L 526 " --> pdb=" O GLU L 523 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA L 527 " --> pdb=" O ASP L 524 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 542 No H-bonds generated for 'chain 'L' and resid 540 through 542' Processing helix chain 'L' and resid 555 through 577 removed outlier: 3.578A pdb=" N ASN L 564 " --> pdb=" O ARG L 560 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN L 565 " --> pdb=" O ARG L 561 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA L 567 " --> pdb=" O ALA L 563 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS L 568 " --> pdb=" O ASN L 564 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER L 569 " --> pdb=" O GLN L 565 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU L 572 " --> pdb=" O LYS L 568 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR L 577 " --> pdb=" O LEU L 573 " (cutoff:3.500A) Processing helix chain 'L' and resid 585 through 597 Processing helix chain 'G' and resid 55 through 58 removed outlier: 3.843A pdb=" N LYS G 58 " --> pdb=" O SER G 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 55 through 58' Processing helix chain 'G' and resid 65 through 68 removed outlier: 3.960A pdb=" N LYS G 68 " --> pdb=" O GLU G 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 65 through 68' Processing helix chain 'G' and resid 171 through 178 Processing helix chain 'H' and resid 522 through 527 removed outlier: 3.561A pdb=" N LEU H 526 " --> pdb=" O GLN H 522 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA H 527 " --> pdb=" O GLU H 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 522 through 527' Processing helix chain 'H' and resid 555 through 566 removed outlier: 3.786A pdb=" N ARG H 561 " --> pdb=" O CYS H 557 " (cutoff:3.500A) Processing helix chain 'H' and resid 566 through 577 removed outlier: 3.723A pdb=" N VAL H 576 " --> pdb=" O LEU H 572 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR H 577 " --> pdb=" O LEU H 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 585 through 598 removed outlier: 3.597A pdb=" N LEU H 594 " --> pdb=" O ALA H 590 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 45 No H-bonds generated for 'chain 'I' and resid 43 through 45' Processing helix chain 'I' and resid 55 through 58 removed outlier: 3.755A pdb=" N LYS I 58 " --> pdb=" O SER I 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 55 through 58' Processing helix chain 'I' and resid 62 through 67 removed outlier: 4.024A pdb=" N SER I 67 " --> pdb=" O PRO I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 178 Processing helix chain 'J' and resid 554 through 561 removed outlier: 3.585A pdb=" N ARG J 558 " --> pdb=" O ASN J 554 " (cutoff:3.500A) Processing helix chain 'J' and resid 561 through 577 removed outlier: 4.681A pdb=" N GLN J 565 " --> pdb=" O ARG J 561 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER J 569 " --> pdb=" O GLN J 565 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU J 571 " --> pdb=" O ALA J 567 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU J 572 " --> pdb=" O LYS J 568 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL J 576 " --> pdb=" O LEU J 572 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR J 577 " --> pdb=" O LEU J 573 " (cutoff:3.500A) Processing helix chain 'J' and resid 585 through 598 removed outlier: 3.671A pdb=" N LEU J 594 " --> pdb=" O ALA J 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 55 through 58 removed outlier: 3.813A pdb=" N LYS E 58 " --> pdb=" O SER E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 65 through 68 removed outlier: 4.021A pdb=" N LYS E 68 " --> pdb=" O GLU E 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 65 through 68' Processing helix chain 'E' and resid 174 through 179 removed outlier: 3.689A pdb=" N ILE E 178 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 Processing helix chain 'F' and resid 540 through 542 No H-bonds generated for 'chain 'F' and resid 540 through 542' Processing helix chain 'F' and resid 554 through 577 removed outlier: 3.540A pdb=" N ARG F 558 " --> pdb=" O ASN F 554 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS F 568 " --> pdb=" O ASN F 564 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER F 569 " --> pdb=" O GLN F 565 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU F 571 " --> pdb=" O ALA F 567 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU F 572 " --> pdb=" O LYS F 568 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 573 " --> pdb=" O SER F 569 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F 576 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 600 removed outlier: 4.074A pdb=" N GLY F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY F 600 " --> pdb=" O THR F 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 55 through 58 removed outlier: 3.638A pdb=" N LYS C 58 " --> pdb=" O SER C 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 58' Processing helix chain 'C' and resid 171 through 180 removed outlier: 4.540A pdb=" N SER C 180 " --> pdb=" O ARG C 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 577 removed outlier: 3.509A pdb=" N GLN D 565 " --> pdb=" O ARG D 561 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA D 567 " --> pdb=" O ALA D 563 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LYS D 568 " --> pdb=" O ASN D 564 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER D 569 " --> pdb=" O GLN D 565 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 572 " --> pdb=" O LYS D 568 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 598 Processing helix chain 'A' and resid 55 through 58 removed outlier: 3.733A pdb=" N LYS A 58 " --> pdb=" O SER A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.658A pdb=" N SER A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 554 through 577 removed outlier: 3.785A pdb=" N ARG B 558 " --> pdb=" O ASN B 554 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS B 568 " --> pdb=" O ASN B 564 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER B 569 " --> pdb=" O GLN B 565 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 597 removed outlier: 4.002A pdb=" N ARG B 597 " --> pdb=" O PHE B 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 47 through 53 removed outlier: 3.666A pdb=" N VAL K 149 " --> pdb=" O TYR K 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 70 through 73 Processing sheet with id=AA3, first strand: chain 'K' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'K' and resid 89 through 98 removed outlier: 6.438A pdb=" N LYS K 90 " --> pdb=" O THR K 121 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N HIS K 123 " --> pdb=" O LYS K 90 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS K 92 " --> pdb=" O HIS K 123 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE K 125 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN K 94 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLY K 127 " --> pdb=" O ASN K 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER K 96 " --> pdb=" O GLY K 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 475 through 476 removed outlier: 3.509A pdb=" N ASN L 475 " --> pdb=" O THR L 491 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 547 through 549 removed outlier: 4.348A pdb=" N LEU H 516 " --> pdb=" O ILE H 549 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR G 53 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU G 82 " --> pdb=" O PHE H 583 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 70 through 73 Processing sheet with id=AA8, first strand: chain 'G' and resid 92 through 98 removed outlier: 5.113A pdb=" N GLN A 126 " --> pdb=" O HIS G 124 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLN G 126 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 11.078A pdb=" N GLN A 128 " --> pdb=" O GLN G 126 " (cutoff:3.500A) removed outlier: 16.009A pdb=" N GLN G 128 " --> pdb=" O GLN A 128 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LYS A 90 " --> pdb=" O CYS A 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 47 through 48 Processing sheet with id=AB1, first strand: chain 'I' and resid 80 through 82 Processing sheet with id=AB2, first strand: chain 'I' and resid 70 through 73 Processing sheet with id=AB3, first strand: chain 'I' and resid 89 through 98 removed outlier: 6.955A pdb=" N LYS I 90 " --> pdb=" O THR I 121 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N HIS I 123 " --> pdb=" O LYS I 90 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N CYS I 92 " --> pdb=" O HIS I 123 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE I 125 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASN I 94 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY I 127 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER I 96 " --> pdb=" O GLY I 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 475 through 476 Processing sheet with id=AB5, first strand: chain 'J' and resid 517 through 521 Processing sheet with id=AB6, first strand: chain 'F' and resid 544 through 549 removed outlier: 4.302A pdb=" N LEU F 516 " --> pdb=" O ILE F 549 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY E 86 " --> pdb=" O TRP F 519 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N GLU E 85 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU E 49 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLU E 87 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY E 51 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 70 through 73 Processing sheet with id=AB8, first strand: chain 'E' and resid 89 through 98 removed outlier: 7.382A pdb=" N LYS E 90 " --> pdb=" O CYS E 119 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 80 through 82 removed outlier: 8.095A pdb=" N GLU C 85 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU C 49 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLU C 87 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLY C 51 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY C 86 " --> pdb=" O TRP D 519 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU D 516 " --> pdb=" O ILE D 549 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AC2, first strand: chain 'C' and resid 89 through 98 removed outlier: 7.155A pdb=" N LYS C 90 " --> pdb=" O CYS C 119 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 98 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 47 through 48 removed outlier: 4.158A pdb=" N HIS A 48 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A 168 " --> pdb=" O HIS A 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 545 through 549 removed outlier: 3.803A pdb=" N LEU B 516 " --> pdb=" O ILE B 549 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 86 " --> pdb=" O TRP B 519 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLY A 51 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 82 " --> pdb=" O PHE B 583 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 70 through 73 339 hydrogen bonds defined for protein. 921 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: 1.53 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3854 1.34 - 1.46: 2846 1.46 - 1.58: 5969 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 12744 Sorted by residual: bond pdb=" N ILE A 214 " pdb=" CA ILE A 214 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.12e-02 7.97e+03 1.05e+01 bond pdb=" N ASP A 208 " pdb=" CA ASP A 208 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.21e-02 6.83e+03 6.76e+00 bond pdb=" N THR A 209 " pdb=" CA THR A 209 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.10e+00 bond pdb=" N CYS G 211 " pdb=" CA CYS G 211 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.32e-02 5.74e+03 6.06e+00 bond pdb=" N ASP G 208 " pdb=" CA ASP G 208 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 6.01e+00 ... (remaining 12739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 16766 2.69 - 5.37: 405 5.37 - 8.06: 69 8.06 - 10.75: 21 10.75 - 13.43: 3 Bond angle restraints: 17264 Sorted by residual: angle pdb=" C ASN B 553 " pdb=" N ASN B 554 " pdb=" CA ASN B 554 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.83e+01 angle pdb=" C2 NAG W 1 " pdb=" N2 NAG W 1 " pdb=" C7 NAG W 1 " ideal model delta sigma weight residual 124.56 137.99 -13.43 3.00e+00 1.11e-01 2.01e+01 angle pdb=" C ILE A 178 " pdb=" N PHE A 179 " pdb=" CA PHE A 179 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C ARG L 581 " pdb=" N THR L 582 " pdb=" CA THR L 582 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 angle pdb=" CB LYS G 172 " pdb=" CG LYS G 172 " pdb=" CD LYS G 172 " ideal model delta sigma weight residual 111.30 120.96 -9.66 2.30e+00 1.89e-01 1.76e+01 ... (remaining 17259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.06: 7640 24.06 - 48.11: 373 48.11 - 72.17: 81 72.17 - 96.22: 22 96.22 - 120.28: 75 Dihedral angle restraints: 8191 sinusoidal: 3866 harmonic: 4325 Sorted by residual: dihedral pdb=" CA ALA H 563 " pdb=" C ALA H 563 " pdb=" N ASN H 564 " pdb=" CA ASN H 564 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASN H 564 " pdb=" C ASN H 564 " pdb=" N GLN H 565 " pdb=" CA GLN H 565 " ideal model delta harmonic sigma weight residual -180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ARG L 581 " pdb=" C ARG L 581 " pdb=" N THR L 582 " pdb=" CA THR L 582 " ideal model delta harmonic sigma weight residual 180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 8188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 2078 0.206 - 0.413: 8 0.413 - 0.619: 0 0.619 - 0.825: 0 0.825 - 1.032: 1 Chirality restraints: 2087 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN H 564 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN D 564 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CB ILE D 533 " pdb=" CA ILE D 533 " pdb=" CG1 ILE D 533 " pdb=" CG2 ILE D 533 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 2084 not shown) Planarity restraints: 2138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 564 " -0.047 2.00e-02 2.50e+03 4.69e-02 2.75e+01 pdb=" CG ASN H 564 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN H 564 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN H 564 " 0.052 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 76 " 0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO G 77 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO G 77 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO G 77 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 109 " 0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO E 110 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO E 110 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 110 " 0.044 5.00e-02 4.00e+02 ... (remaining 2135 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 3344 2.82 - 3.34: 10334 3.34 - 3.86: 19801 3.86 - 4.38: 21877 4.38 - 4.90: 39213 Nonbonded interactions: 94569 Sorted by model distance: nonbonded pdb=" O GLU I 87 " pdb=" OH TYR I 116 " model vdw 2.294 3.040 nonbonded pdb=" OE2 GLU F 579 " pdb=" OG1 THR B 582 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR E 83 " pdb=" O TYR E 146 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR I 83 " pdb=" O TYR I 146 " model vdw 2.315 3.040 nonbonded pdb=" OD1 ASP K 147 " pdb=" OH TYR L 544 " model vdw 2.325 3.040 ... (remaining 94564 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 39 through 180) selection = (chain 'C' and resid 39 through 180) selection = chain 'E' selection = (chain 'G' and resid 39 through 180) selection = chain 'I' selection = chain 'K' } ncs_group { reference = (chain 'B' and (resid 471 through 477 or resid 490 through 600)) selection = (chain 'D' and (resid 471 through 477 or resid 490 through 600)) selection = (chain 'F' and resid 471 through 600) selection = (chain 'H' and (resid 471 through 477 or resid 490 through 494 or resid 510 thro \ ugh 600)) selection = (chain 'J' and (resid 471 through 477 or resid 490 through 600)) selection = (chain 'L' and (resid 471 through 477 or resid 490 through 600)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 2.670 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.630 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.005 0.055 12804 Z= 0.228 Angle : 1.050 15.571 17432 Z= 0.507 Chirality : 0.059 1.032 2087 Planarity : 0.010 0.082 2126 Dihedral : 19.189 120.277 5357 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.39 % Favored : 95.48 % Rotamer: Outliers : 0.15 % Allowed : 0.46 % Favored : 99.38 % 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: -2.52 (0.19), residues: 1459 helix: -2.96 (0.19), residues: 326 sheet: -0.02 (0.28), residues: 322 loop : -1.83 (0.19), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG J 575 TYR 0.020 0.002 TYR F 544 PHE 0.017 0.002 PHE B 593 TRP 0.026 0.003 TRP A 70 HIS 0.014 0.001 HIS I 123 Details of bonding type rmsd covalent geometry : bond 0.00476 (12744) covalent geometry : angle 1.01808 (17264) SS BOND : bond 0.00153 ( 12) SS BOND : angle 0.68891 ( 24) hydrogen bonds : bond 0.17448 ( 339) hydrogen bonds : angle 6.59029 ( 921) link_ALPHA1-3 : bond 0.01413 ( 6) link_ALPHA1-3 : angle 2.48530 ( 18) link_ALPHA1-6 : bond 0.00593 ( 6) link_ALPHA1-6 : angle 1.49051 ( 18) link_BETA1-4 : bond 0.00793 ( 24) link_BETA1-4 : angle 2.38130 ( 72) link_NAG-ASN : bond 0.00908 ( 12) link_NAG-ASN : angle 4.60885 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 366 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8462 (mp10) REVERT: K 50 MET cc_start: 0.6204 (mtt) cc_final: 0.5852 (mtt) REVERT: K 58 LYS cc_start: 0.9468 (mppt) cc_final: 0.9250 (mmtm) REVERT: K 61 ASP cc_start: 0.9217 (p0) cc_final: 0.8873 (p0) REVERT: L 515 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8408 (tm-30) REVERT: L 517 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8436 (ttm110) REVERT: G 43 LYS cc_start: 0.8502 (mttt) cc_final: 0.8127 (mtmm) REVERT: G 61 ASP cc_start: 0.8996 (p0) cc_final: 0.8606 (p0) REVERT: H 598 TRP cc_start: 0.6299 (t-100) cc_final: 0.6055 (t-100) REVERT: I 43 LYS cc_start: 0.8538 (ptpp) cc_final: 0.8005 (ptmm) REVERT: I 46 ASP cc_start: 0.9067 (m-30) cc_final: 0.8755 (m-30) REVERT: I 87 GLU cc_start: 0.6084 (tt0) cc_final: 0.5623 (tt0) REVERT: I 115 ASP cc_start: 0.8679 (m-30) cc_final: 0.8451 (m-30) REVERT: I 158 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8704 (mmmm) REVERT: I 172 LYS cc_start: 0.9472 (tmtt) cc_final: 0.9107 (tptt) REVERT: J 515 GLU cc_start: 0.8179 (pp20) cc_final: 0.7935 (tm-30) REVERT: J 553 ASN cc_start: 0.8445 (m110) cc_final: 0.8023 (m-40) REVERT: E 62 SER cc_start: 0.9221 (m) cc_final: 0.8916 (p) REVERT: E 65 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8299 (tm-30) REVERT: E 82 GLU cc_start: 0.8634 (tt0) cc_final: 0.8344 (tp30) REVERT: E 114 ARG cc_start: 0.8992 (mtm-85) cc_final: 0.8683 (mtm-85) REVERT: E 176 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8256 (mtm110) REVERT: F 552 GLN cc_start: 0.7716 (pp30) cc_final: 0.7396 (pp30) REVERT: F 553 ASN cc_start: 0.8957 (t0) cc_final: 0.8671 (t0) REVERT: F 561 ARG cc_start: 0.7773 (ptt180) cc_final: 0.7551 (ptt180) REVERT: F 597 ARG cc_start: 0.7978 (ttt-90) cc_final: 0.7774 (ttt180) REVERT: C 178 ILE cc_start: 0.8970 (tp) cc_final: 0.8702 (tp) REVERT: A 42 GLN cc_start: 0.8250 (mm110) cc_final: 0.7895 (mt0) REVERT: A 61 ASP cc_start: 0.9029 (p0) cc_final: 0.8517 (p0) REVERT: A 172 LYS cc_start: 0.9155 (tppt) cc_final: 0.8681 (tppt) outliers start: 2 outliers final: 0 residues processed: 368 average time/residue: 0.1375 time to fit residues: 67.2280 Evaluate side-chains 283 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 207 ASN E 80 ASN C 126 GLN C 131 HIS D 554 ASN A 175 HIS A 207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.099432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.071340 restraints weight = 30058.529| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.14 r_work: 0.2960 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12804 Z= 0.201 Angle : 0.767 9.899 17432 Z= 0.357 Chirality : 0.048 0.354 2087 Planarity : 0.007 0.064 2126 Dihedral : 13.718 110.860 2571 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.04 % Favored : 95.82 % Rotamer: Outliers : 1.93 % Allowed : 8.87 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.20), residues: 1459 helix: -1.37 (0.27), residues: 329 sheet: -0.07 (0.28), residues: 322 loop : -1.66 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 575 TYR 0.015 0.002 TYR F 544 PHE 0.017 0.001 PHE F 583 TRP 0.016 0.002 TRP F 598 HIS 0.009 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00466 (12744) covalent geometry : angle 0.73552 (17264) SS BOND : bond 0.00208 ( 12) SS BOND : angle 0.86245 ( 24) hydrogen bonds : bond 0.04482 ( 339) hydrogen bonds : angle 4.78367 ( 921) link_ALPHA1-3 : bond 0.01191 ( 6) link_ALPHA1-3 : angle 2.78607 ( 18) link_ALPHA1-6 : bond 0.00714 ( 6) link_ALPHA1-6 : angle 2.19296 ( 18) link_BETA1-4 : bond 0.00471 ( 24) link_BETA1-4 : angle 2.27775 ( 72) link_NAG-ASN : bond 0.00568 ( 12) link_NAG-ASN : angle 2.86394 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 285 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8390 (mp10) REVERT: K 61 ASP cc_start: 0.9248 (p0) cc_final: 0.8858 (p0) REVERT: L 552 GLN cc_start: 0.8803 (tp40) cc_final: 0.7907 (tp40) REVERT: G 43 LYS cc_start: 0.8751 (mttt) cc_final: 0.8352 (mtmm) REVERT: G 103 LYS cc_start: 0.9436 (ttpp) cc_final: 0.9085 (ptmm) REVERT: I 43 LYS cc_start: 0.8495 (ptpp) cc_final: 0.7694 (ptmm) REVERT: I 45 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8304 (tm-30) REVERT: I 46 ASP cc_start: 0.8912 (m-30) cc_final: 0.8510 (m-30) REVERT: I 87 GLU cc_start: 0.6556 (tt0) cc_final: 0.6004 (tt0) REVERT: I 115 ASP cc_start: 0.8965 (m-30) cc_final: 0.8753 (m-30) REVERT: I 158 LYS cc_start: 0.9237 (mmtt) cc_final: 0.8683 (mmmm) REVERT: I 168 MET cc_start: 0.7706 (ptm) cc_final: 0.7345 (ptp) REVERT: J 517 ARG cc_start: 0.8809 (mtm110) cc_final: 0.8579 (ptm-80) REVERT: E 62 SER cc_start: 0.9173 (m) cc_final: 0.8857 (p) REVERT: E 103 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8272 (pttt) REVERT: E 114 ARG cc_start: 0.9323 (mtm-85) cc_final: 0.9105 (mtm-85) REVERT: E 120 LYS cc_start: 0.9263 (tppt) cc_final: 0.8976 (tppp) REVERT: F 511 ASP cc_start: 0.8149 (p0) cc_final: 0.7880 (p0) REVERT: F 552 GLN cc_start: 0.8092 (pp30) cc_final: 0.7743 (pp30) REVERT: F 597 ARG cc_start: 0.8424 (ttt-90) cc_final: 0.8084 (ttt180) REVERT: C 43 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8175 (mtmm) REVERT: C 172 LYS cc_start: 0.8606 (tptt) cc_final: 0.8374 (tmtt) REVERT: D 580 GLU cc_start: 0.8499 (mp0) cc_final: 0.8297 (mp0) REVERT: A 61 ASP cc_start: 0.9207 (p0) cc_final: 0.8848 (p0) REVERT: A 65 GLU cc_start: 0.8018 (tp30) cc_final: 0.7737 (tm-30) REVERT: A 103 LYS cc_start: 0.8951 (ttpp) cc_final: 0.8748 (ptmm) REVERT: A 172 LYS cc_start: 0.8951 (tppt) cc_final: 0.8731 (tppt) REVERT: B 470 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: B 475 ASN cc_start: 0.8596 (p0) cc_final: 0.8362 (p0) REVERT: B 515 GLU cc_start: 0.8520 (tt0) cc_final: 0.8311 (pm20) REVERT: B 579 GLU cc_start: 0.7533 (tp30) cc_final: 0.7222 (tp30) outliers start: 25 outliers final: 17 residues processed: 297 average time/residue: 0.1417 time to fit residues: 55.0635 Evaluate side-chains 280 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 262 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 540 ILE Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 491 THR Chi-restraints excluded: chain H residue 564 ASN Chi-restraints excluded: chain J residue 491 THR Chi-restraints excluded: chain J residue 493 SER Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 473 SER Chi-restraints excluded: chain F residue 571 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain B residue 470 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 116 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 164 ASN E 48 HIS A 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.098033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.069790 restraints weight = 30131.699| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 4.20 r_work: 0.2960 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12804 Z= 0.184 Angle : 0.698 9.663 17432 Z= 0.330 Chirality : 0.047 0.490 2087 Planarity : 0.005 0.058 2126 Dihedral : 9.757 106.162 2571 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.32 % Favored : 95.54 % Rotamer: Outliers : 1.85 % Allowed : 10.10 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.21), residues: 1459 helix: -0.72 (0.28), residues: 335 sheet: -0.10 (0.28), residues: 322 loop : -1.52 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 558 TYR 0.011 0.001 TYR F 544 PHE 0.019 0.001 PHE L 492 TRP 0.014 0.001 TRP B 519 HIS 0.004 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00430 (12744) covalent geometry : angle 0.66808 (17264) SS BOND : bond 0.00207 ( 12) SS BOND : angle 0.59580 ( 24) hydrogen bonds : bond 0.04142 ( 339) hydrogen bonds : angle 4.55572 ( 921) link_ALPHA1-3 : bond 0.01197 ( 6) link_ALPHA1-3 : angle 2.56865 ( 18) link_ALPHA1-6 : bond 0.00856 ( 6) link_ALPHA1-6 : angle 2.25622 ( 18) link_BETA1-4 : bond 0.00511 ( 24) link_BETA1-4 : angle 2.06291 ( 72) link_NAG-ASN : bond 0.00482 ( 12) link_NAG-ASN : angle 2.69664 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 270 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8386 (mp10) REVERT: K 58 LYS cc_start: 0.9560 (mppt) cc_final: 0.9273 (mmtm) REVERT: K 61 ASP cc_start: 0.9259 (p0) cc_final: 0.8870 (p0) REVERT: K 177 MET cc_start: 0.9467 (tmm) cc_final: 0.9249 (tmm) REVERT: L 513 ASP cc_start: 0.8640 (t0) cc_final: 0.8356 (t0) REVERT: L 550 LYS cc_start: 0.8825 (ptmm) cc_final: 0.8599 (ptmm) REVERT: L 552 GLN cc_start: 0.8853 (tp40) cc_final: 0.8434 (tp-100) REVERT: G 43 LYS cc_start: 0.8585 (mttt) cc_final: 0.8224 (mtmm) REVERT: G 45 GLU cc_start: 0.8983 (pm20) cc_final: 0.8717 (pm20) REVERT: G 88 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: G 103 LYS cc_start: 0.9421 (ttpp) cc_final: 0.9083 (ptmm) REVERT: H 550 LYS cc_start: 0.8478 (mptt) cc_final: 0.8060 (mptt) REVERT: I 43 LYS cc_start: 0.8410 (ptpp) cc_final: 0.7745 (ptmm) REVERT: I 45 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8349 (tm-30) REVERT: I 46 ASP cc_start: 0.8851 (m-30) cc_final: 0.8443 (m-30) REVERT: I 50 MET cc_start: 0.5417 (mtt) cc_final: 0.4865 (mtt) REVERT: I 58 LYS cc_start: 0.8896 (mmtm) cc_final: 0.8619 (mmtm) REVERT: I 156 ARG cc_start: 0.8735 (mtp-110) cc_final: 0.8493 (mtm110) REVERT: I 158 LYS cc_start: 0.9205 (mmtt) cc_final: 0.8686 (mmmm) REVERT: J 549 ILE cc_start: 0.9354 (mm) cc_final: 0.9006 (tp) REVERT: J 550 LYS cc_start: 0.9143 (ptmm) cc_final: 0.8554 (tmmt) REVERT: E 62 SER cc_start: 0.9096 (m) cc_final: 0.8845 (p) REVERT: E 103 LYS cc_start: 0.8661 (ttpt) cc_final: 0.8254 (pttt) REVERT: E 114 ARG cc_start: 0.9284 (mtm-85) cc_final: 0.9075 (mtm-85) REVERT: E 120 LYS cc_start: 0.9247 (tppt) cc_final: 0.8982 (tppp) REVERT: E 172 LYS cc_start: 0.9609 (tppt) cc_final: 0.9202 (tptp) REVERT: F 552 GLN cc_start: 0.8176 (pp30) cc_final: 0.7854 (pp30) REVERT: F 565 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8461 (mt0) REVERT: F 597 ARG cc_start: 0.8454 (ttt-90) cc_final: 0.8077 (ttt180) REVERT: C 43 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8180 (mtmm) REVERT: C 45 GLU cc_start: 0.9063 (pm20) cc_final: 0.8829 (pm20) REVERT: D 598 TRP cc_start: 0.7446 (OUTLIER) cc_final: 0.5995 (m-10) REVERT: A 43 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8594 (pttp) REVERT: A 61 ASP cc_start: 0.9227 (p0) cc_final: 0.8855 (p0) REVERT: A 65 GLU cc_start: 0.8107 (tp30) cc_final: 0.7781 (tm-30) REVERT: A 103 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8678 (ptmm) REVERT: A 172 LYS cc_start: 0.8998 (tppt) cc_final: 0.8778 (tppt) REVERT: A 176 ARG cc_start: 0.7361 (mmp80) cc_final: 0.7110 (mmp80) REVERT: B 515 GLU cc_start: 0.8523 (tt0) cc_final: 0.8228 (pm20) REVERT: B 579 GLU cc_start: 0.7522 (tp30) cc_final: 0.7318 (tp30) REVERT: B 581 ARG cc_start: 0.7798 (ptt90) cc_final: 0.7285 (ptt90) outliers start: 24 outliers final: 15 residues processed: 283 average time/residue: 0.1452 time to fit residues: 53.8154 Evaluate side-chains 274 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 256 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain L residue 540 ILE Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 564 ASN Chi-restraints excluded: chain J residue 491 THR Chi-restraints excluded: chain J residue 493 SER Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain F residue 571 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 598 TRP Chi-restraints excluded: chain A residue 95 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 48 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 79 optimal weight: 0.0170 chunk 110 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 117 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 56 optimal weight: 0.2980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.097771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.069055 restraints weight = 29981.396| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.13 r_work: 0.2975 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12804 Z= 0.117 Angle : 0.673 15.603 17432 Z= 0.313 Chirality : 0.045 0.470 2087 Planarity : 0.005 0.055 2126 Dihedral : 8.898 104.696 2571 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.84 % Favored : 96.02 % Rotamer: Outliers : 1.39 % Allowed : 11.03 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.21), residues: 1459 helix: -0.36 (0.30), residues: 332 sheet: 0.04 (0.28), residues: 310 loop : -1.43 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 581 TYR 0.011 0.001 TYR C 83 PHE 0.015 0.001 PHE G 212 TRP 0.009 0.001 TRP B 519 HIS 0.003 0.000 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00260 (12744) covalent geometry : angle 0.64085 (17264) SS BOND : bond 0.00157 ( 12) SS BOND : angle 0.56112 ( 24) hydrogen bonds : bond 0.03429 ( 339) hydrogen bonds : angle 4.41806 ( 921) link_ALPHA1-3 : bond 0.01373 ( 6) link_ALPHA1-3 : angle 2.45945 ( 18) link_ALPHA1-6 : bond 0.00882 ( 6) link_ALPHA1-6 : angle 2.04224 ( 18) link_BETA1-4 : bond 0.00533 ( 24) link_BETA1-4 : angle 1.95146 ( 72) link_NAG-ASN : bond 0.00551 ( 12) link_NAG-ASN : angle 3.04435 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 272 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8412 (mp10) REVERT: K 58 LYS cc_start: 0.9563 (mppt) cc_final: 0.9299 (mmtm) REVERT: K 61 ASP cc_start: 0.9205 (p0) cc_final: 0.8810 (p0) REVERT: K 177 MET cc_start: 0.9406 (tmm) cc_final: 0.9183 (tmm) REVERT: L 513 ASP cc_start: 0.8685 (t0) cc_final: 0.8380 (t0) REVERT: L 550 LYS cc_start: 0.8832 (ptmm) cc_final: 0.8606 (ptmm) REVERT: L 552 GLN cc_start: 0.8761 (tp40) cc_final: 0.8368 (tp-100) REVERT: G 43 LYS cc_start: 0.8551 (mttt) cc_final: 0.8229 (mtmm) REVERT: G 45 GLU cc_start: 0.8873 (pm20) cc_final: 0.8658 (pm20) REVERT: G 88 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: G 103 LYS cc_start: 0.9411 (ttpp) cc_final: 0.9081 (ptmm) REVERT: G 172 LYS cc_start: 0.8935 (tppt) cc_final: 0.8534 (tppt) REVERT: G 176 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8045 (mmp80) REVERT: I 43 LYS cc_start: 0.8471 (ptpp) cc_final: 0.7744 (ptmm) REVERT: I 45 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8323 (tm-30) REVERT: I 46 ASP cc_start: 0.8933 (m-30) cc_final: 0.8478 (m-30) REVERT: I 50 MET cc_start: 0.5560 (mtt) cc_final: 0.5075 (mtt) REVERT: I 58 LYS cc_start: 0.8936 (mmtm) cc_final: 0.8573 (mmtm) REVERT: I 156 ARG cc_start: 0.8789 (mtp-110) cc_final: 0.8521 (mtm110) REVERT: I 158 LYS cc_start: 0.9176 (mmtt) cc_final: 0.8696 (mmmm) REVERT: I 172 LYS cc_start: 0.9129 (tptt) cc_final: 0.8922 (tptt) REVERT: J 549 ILE cc_start: 0.9367 (mm) cc_final: 0.9006 (tp) REVERT: J 550 LYS cc_start: 0.9122 (ptmm) cc_final: 0.8507 (tmmt) REVERT: E 62 SER cc_start: 0.9140 (m) cc_final: 0.8905 (p) REVERT: E 103 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8308 (pttt) REVERT: E 120 LYS cc_start: 0.9220 (tppt) cc_final: 0.8966 (tppp) REVERT: E 172 LYS cc_start: 0.9596 (tppt) cc_final: 0.8952 (tptp) REVERT: E 176 ARG cc_start: 0.8586 (mtm110) cc_final: 0.7772 (mtm110) REVERT: E 178 ILE cc_start: 0.9300 (mm) cc_final: 0.8924 (pt) REVERT: F 550 LYS cc_start: 0.8867 (mttp) cc_final: 0.8266 (mptt) REVERT: F 552 GLN cc_start: 0.8105 (pp30) cc_final: 0.7788 (pp30) REVERT: F 597 ARG cc_start: 0.8424 (ttt-90) cc_final: 0.8095 (ttt-90) REVERT: C 43 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8238 (mtmm) REVERT: D 580 GLU cc_start: 0.8434 (mp0) cc_final: 0.8216 (mp0) REVERT: D 598 TRP cc_start: 0.7440 (OUTLIER) cc_final: 0.6109 (m-10) REVERT: A 43 LYS cc_start: 0.8947 (mtmm) cc_final: 0.8715 (pttp) REVERT: A 50 MET cc_start: 0.8234 (mpp) cc_final: 0.7570 (mtm) REVERT: A 61 ASP cc_start: 0.9183 (p0) cc_final: 0.8810 (p0) REVERT: A 65 GLU cc_start: 0.8153 (tp30) cc_final: 0.7823 (tm-30) REVERT: B 470 GLU cc_start: 0.8514 (mp0) cc_final: 0.7298 (mm-30) outliers start: 18 outliers final: 12 residues processed: 283 average time/residue: 0.1493 time to fit residues: 55.2674 Evaluate side-chains 269 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 255 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 473 SER Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain H residue 491 THR Chi-restraints excluded: chain H residue 564 ASN Chi-restraints excluded: chain J residue 491 THR Chi-restraints excluded: chain J residue 493 SER Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 571 GLU Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 598 TRP Chi-restraints excluded: chain A residue 211 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 65 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.099332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.070652 restraints weight = 30086.740| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 4.22 r_work: 0.3001 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12804 Z= 0.120 Angle : 0.659 13.075 17432 Z= 0.309 Chirality : 0.045 0.472 2087 Planarity : 0.005 0.040 2126 Dihedral : 8.336 103.919 2571 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.18 % Favored : 95.68 % Rotamer: Outliers : 2.31 % Allowed : 11.18 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.21), residues: 1459 helix: -0.22 (0.30), residues: 339 sheet: 0.09 (0.28), residues: 310 loop : -1.39 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 517 TYR 0.009 0.001 TYR C 83 PHE 0.023 0.001 PHE L 492 TRP 0.008 0.001 TRP B 519 HIS 0.002 0.000 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00274 (12744) covalent geometry : angle 0.62243 (17264) SS BOND : bond 0.00125 ( 12) SS BOND : angle 0.56988 ( 24) hydrogen bonds : bond 0.03253 ( 339) hydrogen bonds : angle 4.25543 ( 921) link_ALPHA1-3 : bond 0.01338 ( 6) link_ALPHA1-3 : angle 2.50346 ( 18) link_ALPHA1-6 : bond 0.00932 ( 6) link_ALPHA1-6 : angle 2.00681 ( 18) link_BETA1-4 : bond 0.00547 ( 24) link_BETA1-4 : angle 1.90860 ( 72) link_NAG-ASN : bond 0.00585 ( 12) link_NAG-ASN : angle 3.45018 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 262 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8377 (mp10) REVERT: K 58 LYS cc_start: 0.9564 (mppt) cc_final: 0.9297 (mmtm) REVERT: K 61 ASP cc_start: 0.9219 (p0) cc_final: 0.8841 (p0) REVERT: K 177 MET cc_start: 0.9391 (tmm) cc_final: 0.8861 (tmm) REVERT: L 513 ASP cc_start: 0.8644 (t0) cc_final: 0.8309 (t0) REVERT: L 550 LYS cc_start: 0.8835 (ptmm) cc_final: 0.8603 (ptmm) REVERT: L 552 GLN cc_start: 0.8825 (tp40) cc_final: 0.8425 (tp-100) REVERT: G 43 LYS cc_start: 0.8522 (mttt) cc_final: 0.8169 (mtmm) REVERT: G 88 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: G 103 LYS cc_start: 0.9403 (ttpp) cc_final: 0.9069 (ptmm) REVERT: G 172 LYS cc_start: 0.8997 (tppt) cc_final: 0.8658 (tppt) REVERT: G 176 ARG cc_start: 0.8900 (mmm160) cc_final: 0.8075 (mmp80) REVERT: H 550 LYS cc_start: 0.8369 (mptt) cc_final: 0.8135 (mptt) REVERT: I 43 LYS cc_start: 0.8421 (ptpp) cc_final: 0.7507 (ptmm) REVERT: I 45 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8372 (tm-30) REVERT: I 46 ASP cc_start: 0.8929 (m-30) cc_final: 0.8321 (m-30) REVERT: I 50 MET cc_start: 0.5504 (mtt) cc_final: 0.5063 (mtt) REVERT: I 156 ARG cc_start: 0.8806 (mtp-110) cc_final: 0.8539 (mtm110) REVERT: I 158 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8698 (mmmm) REVERT: I 172 LYS cc_start: 0.9116 (tptt) cc_final: 0.8850 (tptt) REVERT: J 570 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8481 (tt) REVERT: E 62 SER cc_start: 0.9118 (m) cc_final: 0.8875 (p) REVERT: E 103 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8254 (pttp) REVERT: E 120 LYS cc_start: 0.9218 (tppt) cc_final: 0.8847 (tppp) REVERT: E 172 LYS cc_start: 0.9580 (tppt) cc_final: 0.8911 (tptp) REVERT: E 176 ARG cc_start: 0.8593 (mtm110) cc_final: 0.7763 (mtm110) REVERT: E 178 ILE cc_start: 0.9303 (mm) cc_final: 0.8909 (pt) REVERT: F 520 SER cc_start: 0.8695 (m) cc_final: 0.8471 (p) REVERT: F 550 LYS cc_start: 0.8881 (mttp) cc_final: 0.8203 (mptt) REVERT: F 552 GLN cc_start: 0.8172 (pp30) cc_final: 0.7908 (pp30) REVERT: F 565 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8443 (mt0) REVERT: F 581 ARG cc_start: 0.7882 (ptm160) cc_final: 0.7541 (ptm160) REVERT: F 597 ARG cc_start: 0.8459 (ttt-90) cc_final: 0.8024 (ttt180) REVERT: C 43 LYS cc_start: 0.8595 (mtmm) cc_final: 0.8239 (mtmm) REVERT: A 43 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8767 (pttp) REVERT: A 61 ASP cc_start: 0.9191 (p0) cc_final: 0.8807 (p0) REVERT: A 65 GLU cc_start: 0.8169 (tp30) cc_final: 0.7841 (tm-30) REVERT: B 470 GLU cc_start: 0.8563 (mp0) cc_final: 0.7310 (mm-30) outliers start: 30 outliers final: 14 residues processed: 277 average time/residue: 0.1402 time to fit residues: 51.2501 Evaluate side-chains 269 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 252 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain H residue 491 THR Chi-restraints excluded: chain H residue 564 ASN Chi-restraints excluded: chain J residue 491 THR Chi-restraints excluded: chain J residue 493 SER Chi-restraints excluded: chain J residue 570 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 598 TRP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 211 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 74 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 91 optimal weight: 0.0870 chunk 139 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 124 optimal weight: 5.9990 overall best weight: 2.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 175 HIS E 124 HIS ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN B 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.095410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066438 restraints weight = 30380.593| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 4.19 r_work: 0.2921 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12804 Z= 0.219 Angle : 0.728 12.988 17432 Z= 0.345 Chirality : 0.048 0.537 2087 Planarity : 0.005 0.053 2126 Dihedral : 8.067 102.552 2571 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.52 % Favored : 95.34 % Rotamer: Outliers : 2.16 % Allowed : 13.65 % Favored : 84.19 % 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: -1.13 (0.21), residues: 1459 helix: -0.02 (0.30), residues: 332 sheet: -0.04 (0.28), residues: 320 loop : -1.39 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 517 TYR 0.014 0.001 TYR F 544 PHE 0.014 0.002 PHE J 535 TRP 0.013 0.001 TRP B 598 HIS 0.004 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00521 (12744) covalent geometry : angle 0.69424 (17264) SS BOND : bond 0.00232 ( 12) SS BOND : angle 0.70089 ( 24) hydrogen bonds : bond 0.04159 ( 339) hydrogen bonds : angle 4.34310 ( 921) link_ALPHA1-3 : bond 0.01137 ( 6) link_ALPHA1-3 : angle 2.38883 ( 18) link_ALPHA1-6 : bond 0.00615 ( 6) link_ALPHA1-6 : angle 1.89990 ( 18) link_BETA1-4 : bond 0.00492 ( 24) link_BETA1-4 : angle 1.99149 ( 72) link_NAG-ASN : bond 0.00554 ( 12) link_NAG-ASN : angle 3.54671 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8571 (mm-40) REVERT: K 45 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8665 (pm20) REVERT: K 58 LYS cc_start: 0.9575 (mppt) cc_final: 0.9272 (mmtm) REVERT: K 61 ASP cc_start: 0.9289 (p0) cc_final: 0.8916 (p0) REVERT: L 513 ASP cc_start: 0.8715 (t0) cc_final: 0.8312 (t0) REVERT: L 552 GLN cc_start: 0.8959 (tp40) cc_final: 0.8616 (tp-100) REVERT: G 43 LYS cc_start: 0.8670 (mttt) cc_final: 0.8302 (mtmm) REVERT: G 88 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: G 103 LYS cc_start: 0.9379 (ttpp) cc_final: 0.9023 (ptmm) REVERT: G 172 LYS cc_start: 0.9056 (tppt) cc_final: 0.8817 (tppt) REVERT: G 176 ARG cc_start: 0.8934 (mmm160) cc_final: 0.8175 (mmp80) REVERT: H 491 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8277 (p) REVERT: H 550 LYS cc_start: 0.8502 (mptt) cc_final: 0.8176 (mptt) REVERT: H 579 GLU cc_start: 0.8547 (pt0) cc_final: 0.8338 (pt0) REVERT: I 43 LYS cc_start: 0.8590 (ptpp) cc_final: 0.8244 (ptpp) REVERT: I 46 ASP cc_start: 0.8943 (m-30) cc_final: 0.8568 (m-30) REVERT: I 58 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8453 (mmtm) REVERT: I 108 ASP cc_start: 0.9253 (m-30) cc_final: 0.8931 (m-30) REVERT: I 158 LYS cc_start: 0.9222 (mmtt) cc_final: 0.8679 (mmmm) REVERT: J 550 LYS cc_start: 0.9179 (ptmm) cc_final: 0.8541 (tmmt) REVERT: J 570 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8547 (tt) REVERT: E 45 GLU cc_start: 0.9193 (pm20) cc_final: 0.8979 (pm20) REVERT: E 62 SER cc_start: 0.9129 (m) cc_final: 0.8867 (p) REVERT: E 103 LYS cc_start: 0.8723 (ttpt) cc_final: 0.8282 (pttp) REVERT: E 120 LYS cc_start: 0.9228 (tppt) cc_final: 0.8990 (tppp) REVERT: E 172 LYS cc_start: 0.9589 (tppt) cc_final: 0.9253 (tptp) REVERT: E 178 ILE cc_start: 0.9298 (mm) cc_final: 0.8986 (pt) REVERT: F 550 LYS cc_start: 0.8864 (mttp) cc_final: 0.8622 (mttp) REVERT: F 552 GLN cc_start: 0.8313 (pp30) cc_final: 0.7976 (pp30) REVERT: F 565 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8382 (mt0) REVERT: F 581 ARG cc_start: 0.7900 (ptm160) cc_final: 0.7564 (ptp-170) REVERT: F 597 ARG cc_start: 0.8476 (ttt-90) cc_final: 0.7936 (ttt180) REVERT: D 578 THR cc_start: 0.8707 (t) cc_final: 0.8386 (t) REVERT: D 579 GLU cc_start: 0.7846 (tp30) cc_final: 0.7588 (tp30) REVERT: D 580 GLU cc_start: 0.8496 (mp0) cc_final: 0.8267 (mp0) REVERT: A 43 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8663 (pttm) REVERT: A 61 ASP cc_start: 0.9225 (p0) cc_final: 0.8826 (p0) REVERT: A 65 GLU cc_start: 0.8157 (tp30) cc_final: 0.7841 (tm-30) REVERT: A 172 LYS cc_start: 0.8969 (tppt) cc_final: 0.8681 (tppt) REVERT: A 176 ARG cc_start: 0.7181 (mmp80) cc_final: 0.6862 (mmp80) REVERT: B 552 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.7000 (pm20) outliers start: 28 outliers final: 18 residues processed: 277 average time/residue: 0.1416 time to fit residues: 51.3080 Evaluate side-chains 269 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain H residue 491 THR Chi-restraints excluded: chain H residue 564 ASN Chi-restraints excluded: chain J residue 491 THR Chi-restraints excluded: chain J residue 493 SER Chi-restraints excluded: chain J residue 570 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 598 TRP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain B residue 552 GLN Chi-restraints excluded: chain B residue 596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 51 optimal weight: 0.0170 chunk 86 optimal weight: 0.0970 chunk 115 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 27 optimal weight: 0.0050 chunk 88 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 142 optimal weight: 0.8980 overall best weight: 0.2630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 175 HIS ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.098506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.069670 restraints weight = 29782.500| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.21 r_work: 0.2971 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12804 Z= 0.121 Angle : 0.695 12.237 17432 Z= 0.328 Chirality : 0.045 0.485 2087 Planarity : 0.004 0.041 2126 Dihedral : 7.712 101.269 2571 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.84 % Favored : 96.02 % Rotamer: Outliers : 1.23 % Allowed : 14.96 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.21), residues: 1459 helix: 0.10 (0.30), residues: 332 sheet: 0.09 (0.29), residues: 316 loop : -1.31 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 156 TYR 0.013 0.001 TYR C 83 PHE 0.024 0.001 PHE L 492 TRP 0.011 0.001 TRP L 598 HIS 0.003 0.000 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00272 (12744) covalent geometry : angle 0.66403 (17264) SS BOND : bond 0.00115 ( 12) SS BOND : angle 0.45101 ( 24) hydrogen bonds : bond 0.03124 ( 339) hydrogen bonds : angle 4.24283 ( 921) link_ALPHA1-3 : bond 0.01448 ( 6) link_ALPHA1-3 : angle 2.49337 ( 18) link_ALPHA1-6 : bond 0.00779 ( 6) link_ALPHA1-6 : angle 1.71072 ( 18) link_BETA1-4 : bond 0.00560 ( 24) link_BETA1-4 : angle 1.83889 ( 72) link_NAG-ASN : bond 0.00617 ( 12) link_NAG-ASN : angle 3.33117 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 255 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8403 (mp10) REVERT: K 45 GLU cc_start: 0.8966 (pm20) cc_final: 0.8654 (pm20) REVERT: K 58 LYS cc_start: 0.9555 (mppt) cc_final: 0.9284 (mmtm) REVERT: K 61 ASP cc_start: 0.9260 (p0) cc_final: 0.8890 (p0) REVERT: K 172 LYS cc_start: 0.9573 (mmmm) cc_final: 0.9320 (mmmm) REVERT: L 552 GLN cc_start: 0.8902 (tp40) cc_final: 0.8565 (tp-100) REVERT: L 565 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8600 (pm20) REVERT: L 568 LYS cc_start: 0.9306 (tptp) cc_final: 0.9063 (tptp) REVERT: G 88 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: G 103 LYS cc_start: 0.9383 (ttpp) cc_final: 0.8965 (ptmm) REVERT: G 176 ARG cc_start: 0.8910 (mmm160) cc_final: 0.8375 (mmp80) REVERT: H 491 THR cc_start: 0.8754 (m) cc_final: 0.8357 (p) REVERT: H 550 LYS cc_start: 0.8397 (mptt) cc_final: 0.7993 (mptt) REVERT: I 43 LYS cc_start: 0.8465 (ptpp) cc_final: 0.7672 (ptmm) REVERT: I 46 ASP cc_start: 0.8932 (m-30) cc_final: 0.8482 (m-30) REVERT: I 50 MET cc_start: 0.5655 (mtt) cc_final: 0.5180 (mtt) REVERT: I 158 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8709 (mmmm) REVERT: I 172 LYS cc_start: 0.9018 (tptt) cc_final: 0.8456 (tptt) REVERT: I 176 ARG cc_start: 0.8755 (ttp-110) cc_final: 0.8264 (ttm110) REVERT: J 550 LYS cc_start: 0.9161 (ptmm) cc_final: 0.8500 (tmmt) REVERT: J 570 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8519 (tt) REVERT: E 45 GLU cc_start: 0.9153 (pm20) cc_final: 0.8940 (pm20) REVERT: E 62 SER cc_start: 0.9085 (m) cc_final: 0.8838 (p) REVERT: E 103 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8299 (pttp) REVERT: E 120 LYS cc_start: 0.9232 (tppt) cc_final: 0.8901 (tppp) REVERT: E 172 LYS cc_start: 0.9582 (tppt) cc_final: 0.9267 (tptp) REVERT: E 178 ILE cc_start: 0.9313 (mm) cc_final: 0.8953 (pt) REVERT: F 550 LYS cc_start: 0.8856 (mttp) cc_final: 0.8214 (mptt) REVERT: F 552 GLN cc_start: 0.8258 (pp30) cc_final: 0.7927 (pp30) REVERT: F 565 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: F 579 GLU cc_start: 0.8363 (tp30) cc_final: 0.8155 (tp30) REVERT: F 597 ARG cc_start: 0.8474 (ttt-90) cc_final: 0.7885 (ttt180) REVERT: C 43 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8300 (mtmm) REVERT: C 168 MET cc_start: 0.8900 (ptp) cc_final: 0.8634 (ptp) REVERT: D 583 PHE cc_start: 0.8196 (t80) cc_final: 0.7862 (t80) REVERT: A 45 GLU cc_start: 0.8360 (pm20) cc_final: 0.8147 (pm20) REVERT: A 50 MET cc_start: 0.7299 (mtt) cc_final: 0.6822 (mtt) REVERT: A 61 ASP cc_start: 0.9194 (p0) cc_final: 0.8788 (p0) REVERT: A 65 GLU cc_start: 0.8179 (tp30) cc_final: 0.7867 (tm-30) REVERT: A 172 LYS cc_start: 0.8882 (tppt) cc_final: 0.8573 (tppt) REVERT: A 176 ARG cc_start: 0.7129 (mmp80) cc_final: 0.6777 (mmp80) REVERT: B 470 GLU cc_start: 0.8365 (pm20) cc_final: 0.7210 (mm-30) outliers start: 16 outliers final: 7 residues processed: 266 average time/residue: 0.1430 time to fit residues: 50.1482 Evaluate side-chains 253 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 242 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain L residue 473 SER Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain L residue 565 GLN Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain H residue 564 ASN Chi-restraints excluded: chain J residue 570 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain D residue 598 TRP Chi-restraints excluded: chain A residue 209 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 142 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.096801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.068283 restraints weight = 30073.481| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 4.13 r_work: 0.2939 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12804 Z= 0.154 Angle : 0.705 12.479 17432 Z= 0.333 Chirality : 0.046 0.508 2087 Planarity : 0.004 0.040 2126 Dihedral : 7.608 100.410 2571 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.25 % Favored : 95.54 % Rotamer: Outliers : 1.46 % Allowed : 15.42 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.97 (0.22), residues: 1459 helix: 0.10 (0.31), residues: 332 sheet: 0.13 (0.28), residues: 312 loop : -1.29 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 156 TYR 0.010 0.001 TYR E 83 PHE 0.014 0.001 PHE J 474 TRP 0.024 0.001 TRP L 598 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00368 (12744) covalent geometry : angle 0.67206 (17264) SS BOND : bond 0.00159 ( 12) SS BOND : angle 1.27183 ( 24) hydrogen bonds : bond 0.03463 ( 339) hydrogen bonds : angle 4.18537 ( 921) link_ALPHA1-3 : bond 0.01350 ( 6) link_ALPHA1-3 : angle 2.41779 ( 18) link_ALPHA1-6 : bond 0.00646 ( 6) link_ALPHA1-6 : angle 1.80717 ( 18) link_BETA1-4 : bond 0.00516 ( 24) link_BETA1-4 : angle 1.89364 ( 72) link_NAG-ASN : bond 0.00548 ( 12) link_NAG-ASN : angle 3.37681 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 249 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8543 (mm-40) REVERT: K 45 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8684 (pm20) REVERT: K 58 LYS cc_start: 0.9547 (mppt) cc_final: 0.9264 (mmtm) REVERT: K 61 ASP cc_start: 0.9293 (p0) cc_final: 0.8920 (p0) REVERT: K 172 LYS cc_start: 0.9594 (mmmm) cc_final: 0.9363 (mmmm) REVERT: L 565 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8843 (pm20) REVERT: L 568 LYS cc_start: 0.9307 (tptp) cc_final: 0.9054 (tptp) REVERT: G 88 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: G 103 LYS cc_start: 0.9374 (ttpp) cc_final: 0.8959 (ptmm) REVERT: G 172 LYS cc_start: 0.9121 (tppt) cc_final: 0.8576 (tppt) REVERT: G 176 ARG cc_start: 0.8924 (mmm160) cc_final: 0.8150 (mmp80) REVERT: H 491 THR cc_start: 0.8741 (m) cc_final: 0.8363 (p) REVERT: H 550 LYS cc_start: 0.8449 (mptt) cc_final: 0.8037 (mptt) REVERT: I 43 LYS cc_start: 0.8477 (ptpp) cc_final: 0.7699 (ptmm) REVERT: I 46 ASP cc_start: 0.8903 (m-30) cc_final: 0.8458 (m-30) REVERT: I 50 MET cc_start: 0.5588 (mtt) cc_final: 0.4811 (mtt) REVERT: I 156 ARG cc_start: 0.8986 (mtm110) cc_final: 0.8727 (mtm110) REVERT: I 158 LYS cc_start: 0.9194 (mmtt) cc_final: 0.8676 (mmmm) REVERT: I 176 ARG cc_start: 0.8753 (ttp-110) cc_final: 0.8491 (ttm110) REVERT: J 552 GLN cc_start: 0.8559 (tt0) cc_final: 0.8276 (tp40) REVERT: J 570 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8494 (tt) REVERT: E 45 GLU cc_start: 0.9189 (pm20) cc_final: 0.8959 (pm20) REVERT: E 62 SER cc_start: 0.9073 (m) cc_final: 0.8812 (p) REVERT: E 103 LYS cc_start: 0.8722 (ttpt) cc_final: 0.8283 (pttp) REVERT: E 120 LYS cc_start: 0.9219 (tppt) cc_final: 0.8874 (tppp) REVERT: E 172 LYS cc_start: 0.9595 (tppt) cc_final: 0.9122 (tptp) REVERT: E 176 ARG cc_start: 0.8614 (mtm110) cc_final: 0.7887 (mtm110) REVERT: E 178 ILE cc_start: 0.9297 (mm) cc_final: 0.9043 (pt) REVERT: F 550 LYS cc_start: 0.8880 (mttp) cc_final: 0.8678 (mttp) REVERT: F 552 GLN cc_start: 0.8360 (pp30) cc_final: 0.8021 (pp30) REVERT: F 565 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8351 (mt0) REVERT: F 597 ARG cc_start: 0.8501 (ttt-90) cc_final: 0.7905 (ttt180) REVERT: C 43 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8390 (mtmm) REVERT: D 578 THR cc_start: 0.8672 (t) cc_final: 0.8436 (t) REVERT: D 583 PHE cc_start: 0.8276 (t80) cc_final: 0.7957 (t80) REVERT: A 45 GLU cc_start: 0.8399 (pm20) cc_final: 0.8173 (pm20) REVERT: A 61 ASP cc_start: 0.9206 (p0) cc_final: 0.8796 (p0) REVERT: A 65 GLU cc_start: 0.8193 (tp30) cc_final: 0.7875 (tm-30) REVERT: A 172 LYS cc_start: 0.8936 (tppt) cc_final: 0.8652 (tppt) REVERT: A 176 ARG cc_start: 0.7218 (mmp80) cc_final: 0.6904 (mmp80) REVERT: B 470 GLU cc_start: 0.8407 (pm20) cc_final: 0.7150 (mm-30) outliers start: 19 outliers final: 11 residues processed: 260 average time/residue: 0.1421 time to fit residues: 48.5409 Evaluate side-chains 258 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain L residue 565 GLN Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain H residue 564 ASN Chi-restraints excluded: chain J residue 493 SER Chi-restraints excluded: chain J residue 570 LEU Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 598 TRP Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 211 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 90 optimal weight: 0.0970 chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 0.0370 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.097412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.068367 restraints weight = 30139.327| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 4.26 r_work: 0.2969 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 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 : 0.003 0.048 12804 Z= 0.124 Angle : 0.702 12.185 17432 Z= 0.332 Chirality : 0.045 0.485 2087 Planarity : 0.004 0.040 2126 Dihedral : 7.406 98.842 2571 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.11 % Favored : 95.68 % Rotamer: Outliers : 1.31 % Allowed : 16.04 % Favored : 82.65 % 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: -0.93 (0.22), residues: 1459 helix: 0.15 (0.30), residues: 333 sheet: 0.10 (0.28), residues: 316 loop : -1.25 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 156 TYR 0.010 0.001 TYR C 83 PHE 0.026 0.001 PHE L 492 TRP 0.025 0.001 TRP L 598 HIS 0.002 0.000 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00293 (12744) covalent geometry : angle 0.67120 (17264) SS BOND : bond 0.00180 ( 12) SS BOND : angle 0.57706 ( 24) hydrogen bonds : bond 0.03065 ( 339) hydrogen bonds : angle 4.19082 ( 921) link_ALPHA1-3 : bond 0.01534 ( 6) link_ALPHA1-3 : angle 2.48103 ( 18) link_ALPHA1-6 : bond 0.00749 ( 6) link_ALPHA1-6 : angle 1.76498 ( 18) link_BETA1-4 : bond 0.00562 ( 24) link_BETA1-4 : angle 1.85006 ( 72) link_NAG-ASN : bond 0.00589 ( 12) link_NAG-ASN : angle 3.30121 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 254 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8341 (mp10) REVERT: K 45 GLU cc_start: 0.9002 (pm20) cc_final: 0.8718 (pm20) REVERT: K 58 LYS cc_start: 0.9531 (mppt) cc_final: 0.9266 (mmtm) REVERT: K 61 ASP cc_start: 0.9296 (p0) cc_final: 0.8912 (p0) REVERT: K 172 LYS cc_start: 0.9602 (mmmm) cc_final: 0.9359 (mmmm) REVERT: L 565 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8827 (pm20) REVERT: L 568 LYS cc_start: 0.9306 (tptp) cc_final: 0.9054 (tptp) REVERT: L 581 ARG cc_start: 0.7213 (ppt170) cc_final: 0.6067 (ppt170) REVERT: G 88 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: G 103 LYS cc_start: 0.9379 (ttpp) cc_final: 0.8966 (ptmm) REVERT: G 172 LYS cc_start: 0.9132 (tppt) cc_final: 0.8656 (tppt) REVERT: G 176 ARG cc_start: 0.8941 (mmm160) cc_final: 0.8119 (mmp80) REVERT: H 491 THR cc_start: 0.8743 (m) cc_final: 0.8409 (p) REVERT: H 581 ARG cc_start: 0.8045 (ppt170) cc_final: 0.7803 (pmt-80) REVERT: I 43 LYS cc_start: 0.8376 (ptpp) cc_final: 0.7589 (ptmm) REVERT: I 46 ASP cc_start: 0.8872 (m-30) cc_final: 0.8409 (m-30) REVERT: I 158 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8706 (mmmm) REVERT: I 176 ARG cc_start: 0.8803 (ttp-110) cc_final: 0.8533 (ttm110) REVERT: J 552 GLN cc_start: 0.8569 (tt0) cc_final: 0.8310 (tp40) REVERT: J 570 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8457 (tt) REVERT: E 45 GLU cc_start: 0.9182 (pm20) cc_final: 0.8947 (pm20) REVERT: E 62 SER cc_start: 0.9059 (m) cc_final: 0.8799 (p) REVERT: E 103 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8311 (pttp) REVERT: E 120 LYS cc_start: 0.9218 (tppt) cc_final: 0.8881 (tppp) REVERT: E 172 LYS cc_start: 0.9591 (tppt) cc_final: 0.9051 (tptp) REVERT: E 176 ARG cc_start: 0.8600 (mtm110) cc_final: 0.7816 (mtm110) REVERT: E 178 ILE cc_start: 0.9282 (mm) cc_final: 0.9012 (pt) REVERT: F 552 GLN cc_start: 0.8381 (pp30) cc_final: 0.8029 (pp30) REVERT: F 565 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: F 597 ARG cc_start: 0.8469 (ttt-90) cc_final: 0.7872 (ttt180) REVERT: C 43 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8392 (mtmm) REVERT: C 168 MET cc_start: 0.8809 (ptp) cc_final: 0.8557 (ptp) REVERT: D 583 PHE cc_start: 0.8197 (t80) cc_final: 0.7858 (t80) REVERT: A 43 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8746 (mtmm) REVERT: A 50 MET cc_start: 0.7135 (mtt) cc_final: 0.6712 (mtt) REVERT: A 61 ASP cc_start: 0.9194 (p0) cc_final: 0.8776 (p0) REVERT: A 65 GLU cc_start: 0.8202 (tp30) cc_final: 0.7864 (tm-30) REVERT: A 172 LYS cc_start: 0.8908 (tppt) cc_final: 0.8598 (tppt) REVERT: A 176 ARG cc_start: 0.7183 (mmp80) cc_final: 0.6865 (mmp80) REVERT: B 470 GLU cc_start: 0.8423 (pm20) cc_final: 0.7178 (mm-30) outliers start: 17 outliers final: 11 residues processed: 265 average time/residue: 0.1444 time to fit residues: 50.3844 Evaluate side-chains 264 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 249 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain L residue 565 GLN Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain H residue 564 ASN Chi-restraints excluded: chain J residue 493 SER Chi-restraints excluded: chain J residue 512 CYS Chi-restraints excluded: chain J residue 570 LEU Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 598 TRP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 211 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 65 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.095780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.066926 restraints weight = 30287.741| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 4.16 r_work: 0.2931 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12804 Z= 0.179 Angle : 0.735 12.367 17432 Z= 0.349 Chirality : 0.047 0.522 2087 Planarity : 0.005 0.048 2126 Dihedral : 7.325 96.620 2571 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.80 % Favored : 95.00 % Rotamer: Outliers : 1.46 % Allowed : 16.04 % Favored : 82.50 % 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: -0.90 (0.22), residues: 1459 helix: 0.30 (0.31), residues: 327 sheet: -0.01 (0.28), residues: 322 loop : -1.23 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG L 581 TYR 0.010 0.001 TYR E 83 PHE 0.015 0.001 PHE J 474 TRP 0.025 0.001 TRP L 598 HIS 0.003 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00429 (12744) covalent geometry : angle 0.70472 (17264) SS BOND : bond 0.00224 ( 12) SS BOND : angle 0.62473 ( 24) hydrogen bonds : bond 0.03579 ( 339) hydrogen bonds : angle 4.19925 ( 921) link_ALPHA1-3 : bond 0.01402 ( 6) link_ALPHA1-3 : angle 2.44782 ( 18) link_ALPHA1-6 : bond 0.00641 ( 6) link_ALPHA1-6 : angle 1.85695 ( 18) link_BETA1-4 : bond 0.00510 ( 24) link_BETA1-4 : angle 1.91925 ( 72) link_NAG-ASN : bond 0.00517 ( 12) link_NAG-ASN : angle 3.36639 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 251 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8555 (mm-40) REVERT: K 58 LYS cc_start: 0.9541 (mppt) cc_final: 0.9282 (mmtm) REVERT: K 61 ASP cc_start: 0.9268 (p0) cc_final: 0.8905 (p0) REVERT: K 172 LYS cc_start: 0.9616 (mmmm) cc_final: 0.9336 (mmmm) REVERT: L 565 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8832 (pm20) REVERT: L 568 LYS cc_start: 0.9315 (tptp) cc_final: 0.9060 (tptp) REVERT: G 50 MET cc_start: 0.7138 (ptp) cc_final: 0.6853 (ptp) REVERT: G 88 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: G 103 LYS cc_start: 0.9371 (ttpp) cc_final: 0.8947 (ptmm) REVERT: G 172 LYS cc_start: 0.9158 (tppt) cc_final: 0.8701 (tppt) REVERT: G 176 ARG cc_start: 0.8926 (mmm160) cc_final: 0.8171 (mmp80) REVERT: H 491 THR cc_start: 0.8772 (m) cc_final: 0.8438 (p) REVERT: I 43 LYS cc_start: 0.8501 (ptpp) cc_final: 0.7701 (ptmm) REVERT: I 46 ASP cc_start: 0.8898 (m-30) cc_final: 0.8464 (m-30) REVERT: I 50 MET cc_start: 0.5351 (mtt) cc_final: 0.4518 (mtt) REVERT: I 58 LYS cc_start: 0.9016 (mmtm) cc_final: 0.8544 (mmtm) REVERT: I 158 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8755 (mmmm) REVERT: I 172 LYS cc_start: 0.8900 (tptt) cc_final: 0.8601 (tppt) REVERT: J 552 GLN cc_start: 0.8554 (tt0) cc_final: 0.8312 (tp40) REVERT: J 570 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8560 (tt) REVERT: E 62 SER cc_start: 0.9049 (m) cc_final: 0.8781 (p) REVERT: E 103 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8330 (pttp) REVERT: E 120 LYS cc_start: 0.9224 (tppt) cc_final: 0.8888 (tppp) REVERT: E 172 LYS cc_start: 0.9586 (tppt) cc_final: 0.9078 (tptp) REVERT: E 176 ARG cc_start: 0.8577 (mtm110) cc_final: 0.7755 (mtm110) REVERT: E 178 ILE cc_start: 0.9293 (mm) cc_final: 0.9001 (pt) REVERT: F 470 GLU cc_start: 0.8566 (mp0) cc_final: 0.7857 (mt-10) REVERT: F 552 GLN cc_start: 0.8427 (pp30) cc_final: 0.8090 (pp30) REVERT: F 565 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8347 (mt0) REVERT: F 597 ARG cc_start: 0.8554 (ttt-90) cc_final: 0.8276 (tmm-80) REVERT: C 43 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8446 (mtmm) REVERT: C 168 MET cc_start: 0.8817 (ptp) cc_final: 0.8609 (ptp) REVERT: D 583 PHE cc_start: 0.8357 (t80) cc_final: 0.8055 (t80) REVERT: A 43 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8697 (mtmm) REVERT: A 50 MET cc_start: 0.7354 (mtt) cc_final: 0.6809 (mtt) REVERT: A 61 ASP cc_start: 0.9217 (p0) cc_final: 0.8804 (p0) REVERT: A 65 GLU cc_start: 0.8230 (tp30) cc_final: 0.7905 (tm-30) REVERT: A 172 LYS cc_start: 0.8994 (tppt) cc_final: 0.8724 (tppt) REVERT: A 176 ARG cc_start: 0.7331 (mmp80) cc_final: 0.7084 (mmp80) outliers start: 19 outliers final: 14 residues processed: 263 average time/residue: 0.1399 time to fit residues: 48.4160 Evaluate side-chains 265 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain L residue 565 GLN Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain H residue 564 ASN Chi-restraints excluded: chain J residue 493 SER Chi-restraints excluded: chain J residue 512 CYS Chi-restraints excluded: chain J residue 570 LEU Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 598 TRP Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 211 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 175 HIS ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.096730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.068913 restraints weight = 30103.742| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.01 r_work: 0.2909 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12804 Z= 0.167 Angle : 0.742 10.182 17432 Z= 0.354 Chirality : 0.047 0.521 2087 Planarity : 0.004 0.040 2126 Dihedral : 7.229 94.030 2571 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.52 % Favored : 95.27 % Rotamer: Outliers : 1.46 % Allowed : 16.65 % Favored : 81.88 % 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: -0.97 (0.21), residues: 1459 helix: 0.05 (0.30), residues: 340 sheet: 0.12 (0.28), residues: 304 loop : -1.26 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 176 TYR 0.010 0.001 TYR E 83 PHE 0.026 0.001 PHE L 492 TRP 0.026 0.001 TRP L 598 HIS 0.004 0.001 HIS I 175 Details of bonding type rmsd covalent geometry : bond 0.00400 (12744) covalent geometry : angle 0.71379 (17264) SS BOND : bond 0.00216 ( 12) SS BOND : angle 0.55179 ( 24) hydrogen bonds : bond 0.03519 ( 339) hydrogen bonds : angle 4.23632 ( 921) link_ALPHA1-3 : bond 0.01469 ( 6) link_ALPHA1-3 : angle 2.48359 ( 18) link_ALPHA1-6 : bond 0.00747 ( 6) link_ALPHA1-6 : angle 1.85683 ( 18) link_BETA1-4 : bond 0.00534 ( 24) link_BETA1-4 : angle 1.92741 ( 72) link_NAG-ASN : bond 0.00463 ( 12) link_NAG-ASN : angle 3.10717 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2568.23 seconds wall clock time: 44 minutes 45.57 seconds (2685.57 seconds total)