Starting phenix.real_space_refine on Thu Feb 5 01:14:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p6x_71328/02_2026/9p6x_71328.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p6x_71328/02_2026/9p6x_71328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p6x_71328/02_2026/9p6x_71328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p6x_71328/02_2026/9p6x_71328.map" model { file = "/net/cci-nas-00/data/ceres_data/9p6x_71328/02_2026/9p6x_71328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p6x_71328/02_2026/9p6x_71328.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 60 5.16 5 C 8784 2.51 5 N 2392 2.21 5 O 2712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 13948 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2734 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 19, 'TRANS': 329} Chain breaks: 2 Chain: "B" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2748 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 19, 'TRANS': 331} Chain breaks: 2 Chain: "C" Number of atoms: 2651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2651 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Chain breaks: 3 Chain: "D" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 927 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "E" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 927 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "F" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 927 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "G" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.92, per 1000 atoms: 0.21 Number of scatterers: 13948 At special positions: 0 Unit cell: (173.525, 162.901, 102.699, 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 60 16.00 O 2712 8.00 N 2392 7.00 C 8784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 609 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 556 " distance=2.03 Simple disulfide: pdb=" SG CYS A 601 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 609 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.04 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 609 " distance=2.02 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 511 " - pdb=" SG CYS C 556 " distance=2.04 Simple disulfide: pdb=" SG CYS C 601 " - pdb=" SG CYS C 608 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " 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 J 3 " - " MAN J 6 " " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 701 " - " ASN A 257 " " NAG B 701 " - " ASN B 257 " " NAG C 701 " - " ASN C 257 " " NAG J 1 " - " ASN A 563 " " NAG K 1 " - " ASN C 563 " " NAG L 1 " - " ASN B 563 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 439.9 milliseconds 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3206 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 34 sheets defined 15.0% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 249 through 264 removed outlier: 3.595A pdb=" N THR A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 576 removed outlier: 3.746A pdb=" N ASN A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLN A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 596 removed outlier: 3.700A pdb=" N ARG A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 69 through 74 removed outlier: 3.850A pdb=" N GLY B 72 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 552 through 565 Processing helix chain 'B' and resid 565 through 576 Processing helix chain 'B' and resid 583 through 597 removed outlier: 3.715A pdb=" N ARG B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 56 removed outlier: 3.805A pdb=" N LYS C 56 " --> pdb=" O CYS C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.557A pdb=" N GLY C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 249 through 261 removed outlier: 3.781A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 565 Processing helix chain 'C' and resid 565 through 576 removed outlier: 3.868A pdb=" N LEU C 571 " --> pdb=" O GLN C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 597 removed outlier: 3.671A pdb=" N ARG C 587 " --> pdb=" O SER C 583 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.946A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 74 through 77 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.017A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.908A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.658A pdb=" N THR F 91 " --> pdb=" O PRO F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.012A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 110 removed outlier: 3.629A pdb=" N THR G 109 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR G 110 " --> pdb=" O ALA G 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 106 through 110' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.652A pdb=" N THR H 91 " --> pdb=" O PRO H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.645A pdb=" N THR H 109 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR H 110 " --> pdb=" O ALA H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.705A pdb=" N THR I 91 " --> pdb=" O PRO I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 110 removed outlier: 3.572A pdb=" N THR I 109 " --> pdb=" O LEU I 106 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR I 110 " --> pdb=" O ALA I 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 106 through 110' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.390A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.390A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 177 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.362A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL A 277 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 276 " --> pdb=" O ALA E 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.493A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AA8, first strand: chain 'B' and resid 177 through 179 removed outlier: 7.132A pdb=" N VAL B 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 105 through 114 removed outlier: 6.331A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG B 136 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 14.223A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 236 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL B 277 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 276 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 518 through 519 Processing sheet with id=AB2, first strand: chain 'C' and resid 42 through 46 removed outlier: 3.519A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 42 through 46 removed outlier: 3.519A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 177 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL C 96 " --> pdb=" O THR C 581 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB5, first strand: chain 'C' and resid 101 through 103 removed outlier: 3.529A pdb=" N TRP C 518 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 519 " --> pdb=" O ILE C 544 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.438A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL C 277 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 276 " --> pdb=" O ALA F 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.951A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET D 83 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS D 22 " --> pdb=" O MET D 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 11 through 13 removed outlier: 3.536A pdb=" N ALA D 33 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN D 59 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 5 through 7 removed outlier: 4.054A pdb=" N LEU E 18 " --> pdb=" O MET E 83 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET E 83 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP E 73 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.750A pdb=" N ALA E 92 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN E 59 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.750A pdb=" N ALA E 92 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 98 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR E 111 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 2 through 7 removed outlier: 3.730A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU F 81 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS F 22 " --> pdb=" O MET F 79 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.309A pdb=" N GLY F 10 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N SER F 121 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 12 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR F 116 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY F 35 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.516A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.530A pdb=" N SER G 122 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.775A pdb=" N TRP G 36 " --> pdb=" O ALA G 48 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER G 112 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.775A pdb=" N TRP G 36 " --> pdb=" O ALA G 48 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.694A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN H 5 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 11 through 13 removed outlier: 7.050A pdb=" N VAL H 12 " --> pdb=" O SER H 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.784A pdb=" N TRP H 36 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 112 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.784A pdb=" N TRP H 36 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.560A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 11 through 13 removed outlier: 7.050A pdb=" N VAL I 12 " --> pdb=" O SER I 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'I' and resid 59 through 60 removed outlier: 3.670A pdb=" N ALA I 59 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP I 36 " --> pdb=" O ALA I 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER I 112 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 59 through 60 removed outlier: 3.670A pdb=" N ALA I 59 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP I 36 " --> pdb=" O ALA I 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1212 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: 2.20 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4306 1.34 - 1.46: 3566 1.46 - 1.58: 6312 1.58 - 1.71: 0 1.71 - 1.83: 78 Bond restraints: 14262 Sorted by residual: bond pdb=" N ILE C 527 " pdb=" CA ILE C 527 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.70e+00 bond pdb=" N ILE A 603 " pdb=" CA ILE A 603 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.95e+00 bond pdb=" N GLN B 521 " pdb=" CA GLN B 521 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.29e-02 6.01e+03 8.44e+00 bond pdb=" N ASP B 522 " pdb=" CA ASP B 522 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.33e-02 5.65e+03 8.33e+00 bond pdb=" N ILE B 527 " pdb=" CA ILE B 527 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.38e-02 5.25e+03 7.69e+00 ... (remaining 14257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 18306 2.08 - 4.16: 884 4.16 - 6.24: 120 6.24 - 8.32: 36 8.32 - 10.39: 21 Bond angle restraints: 19367 Sorted by residual: angle pdb=" N PRO F 105 " pdb=" CA PRO F 105 " pdb=" C PRO F 105 " ideal model delta sigma weight residual 110.70 119.16 -8.46 1.22e+00 6.72e-01 4.80e+01 angle pdb=" N PRO D 105 " pdb=" CA PRO D 105 " pdb=" C PRO D 105 " ideal model delta sigma weight residual 110.70 118.75 -8.05 1.22e+00 6.72e-01 4.36e+01 angle pdb=" N PRO E 105 " pdb=" CA PRO E 105 " pdb=" C PRO E 105 " ideal model delta sigma weight residual 110.70 118.07 -7.37 1.22e+00 6.72e-01 3.65e+01 angle pdb=" C SER D 27 " pdb=" N THR D 28 " pdb=" CA THR D 28 " ideal model delta sigma weight residual 121.54 129.93 -8.39 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C ASP B 49 " pdb=" N LYS B 50 " pdb=" CA LYS B 50 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 ... (remaining 19362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.74: 8172 24.74 - 49.48: 376 49.48 - 74.22: 89 74.22 - 98.96: 24 98.96 - 123.70: 28 Dihedral angle restraints: 8689 sinusoidal: 3639 harmonic: 5050 Sorted by residual: dihedral pdb=" CB CYS B 601 " pdb=" SG CYS B 601 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual -86.00 1.15 -87.15 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS A 53 " pdb=" SG CYS A 53 " pdb=" SG CYS A 609 " pdb=" CB CYS A 609 " ideal model delta sinusoidal sigma weight residual 93.00 161.44 -68.44 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CA GLN F 39 " pdb=" C GLN F 39 " pdb=" N ALA F 40 " pdb=" CA ALA F 40 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 8686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1990 0.107 - 0.215: 157 0.215 - 0.322: 13 0.322 - 0.429: 3 0.429 - 0.537: 1 Chirality restraints: 2164 Sorted by residual: chirality pdb=" CB ILE H 103 " pdb=" CA ILE H 103 " pdb=" CG1 ILE H 103 " pdb=" CG2 ILE H 103 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" CB VAL A 52 " pdb=" CA VAL A 52 " pdb=" CG1 VAL A 52 " pdb=" CG2 VAL A 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL D 2 " pdb=" CA VAL D 2 " pdb=" CG1 VAL D 2 " pdb=" CG2 VAL D 2 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 2161 not shown) Planarity restraints: 2497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 597 " -0.028 2.00e-02 2.50e+03 2.58e-02 1.66e+01 pdb=" CG TRP B 597 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP B 597 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 597 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 597 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 597 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 597 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 597 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 597 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 597 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 519 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C THR B 519 " -0.066 2.00e-02 2.50e+03 pdb=" O THR B 519 " 0.025 2.00e-02 2.50e+03 pdb=" N THR B 520 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA H 40 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO H 41 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " -0.040 5.00e-02 4.00e+02 ... (remaining 2494 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2267 2.77 - 3.30: 11805 3.30 - 3.84: 22279 3.84 - 4.37: 25603 4.37 - 4.90: 45475 Nonbonded interactions: 107429 Sorted by model distance: nonbonded pdb=" O GLN C 255 " pdb=" OG1 THR C 259 " model vdw 2.238 3.040 nonbonded pdb=" OG SER A 263 " pdb=" OG SER E 29 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OH TYR B 543 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASP C 163 " pdb=" OH TYR C 543 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASP A 163 " pdb=" OH TYR A 543 " model vdw 2.288 3.040 ... (remaining 107424 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 32 through 262 or resid 271 through 279 or resid 503 throu \ gh 701)) selection = (chain 'B' and (resid 32 through 262 or resid 271 through 279 or resid 503 throu \ gh 701)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' } 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: 7.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.670 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.006 0.069 14303 Z= 0.286 Angle : 1.043 10.395 19469 Z= 0.560 Chirality : 0.061 0.537 2164 Planarity : 0.008 0.082 2491 Dihedral : 16.894 123.704 5420 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.06 % Favored : 94.59 % Rotamer: Outliers : 0.35 % Allowed : 0.62 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.18), residues: 1738 helix: -1.44 (0.32), residues: 163 sheet: -0.44 (0.22), residues: 555 loop : -1.32 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 19 TYR 0.050 0.003 TYR E 111 PHE 0.026 0.003 PHE B 592 TRP 0.068 0.003 TRP B 597 HIS 0.015 0.002 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00551 (14262) covalent geometry : angle 1.02569 (19367) SS BOND : bond 0.00506 ( 21) SS BOND : angle 1.68301 ( 42) hydrogen bonds : bond 0.25819 ( 407) hydrogen bonds : angle 9.46599 ( 1212) link_ALPHA1-3 : bond 0.00716 ( 3) link_ALPHA1-3 : angle 3.08841 ( 9) link_ALPHA1-6 : bond 0.00724 ( 5) link_ALPHA1-6 : angle 2.29751 ( 15) link_BETA1-4 : bond 0.00453 ( 6) link_BETA1-4 : angle 3.36744 ( 18) link_NAG-ASN : bond 0.01685 ( 6) link_NAG-ASN : angle 4.31176 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 201 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: B 51 LEU cc_start: 0.9004 (tt) cc_final: 0.8796 (tt) REVERT: B 239 LEU cc_start: 0.9217 (mm) cc_final: 0.8952 (tm) REVERT: C 522 ASP cc_start: 0.8210 (t70) cc_final: 0.7983 (t0) outliers start: 5 outliers final: 1 residues processed: 204 average time/residue: 0.6249 time to fit residues: 138.1927 Evaluate side-chains 145 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 62 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN B 586 ASN C 61 ASN C 550 ASN F 3 GLN F 77 ASN G 39 GLN G 52 ASN G 105 ASN H 77 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.114965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067847 restraints weight = 28999.118| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.84 r_work: 0.2822 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 14303 Z= 0.277 Angle : 0.791 9.133 19469 Z= 0.394 Chirality : 0.048 0.214 2164 Planarity : 0.005 0.052 2491 Dihedral : 12.744 112.701 2339 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.03 % Favored : 95.68 % Rotamer: Outliers : 2.21 % Allowed : 8.71 % Favored : 89.08 % 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: -1.03 (0.19), residues: 1738 helix: 0.49 (0.38), residues: 177 sheet: -0.34 (0.21), residues: 616 loop : -1.13 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 19 TYR 0.034 0.002 TYR H 32 PHE 0.030 0.002 PHE F 68 TRP 0.024 0.002 TRP A 86 HIS 0.006 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00663 (14262) covalent geometry : angle 0.76931 (19367) SS BOND : bond 0.00556 ( 21) SS BOND : angle 1.72364 ( 42) hydrogen bonds : bond 0.05047 ( 407) hydrogen bonds : angle 6.02781 ( 1212) link_ALPHA1-3 : bond 0.00720 ( 3) link_ALPHA1-3 : angle 2.89570 ( 9) link_ALPHA1-6 : bond 0.00756 ( 5) link_ALPHA1-6 : angle 2.65012 ( 15) link_BETA1-4 : bond 0.00401 ( 6) link_BETA1-4 : angle 3.16065 ( 18) link_NAG-ASN : bond 0.00588 ( 6) link_NAG-ASN : angle 3.51425 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.9071 (p0) cc_final: 0.8806 (p0) REVERT: A 188 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8331 (tp40) REVERT: A 595 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 214 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: C 49 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7774 (p0) REVERT: C 50 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7612 (mppt) REVERT: G 65 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8775 (ttpp) REVERT: H 32 TYR cc_start: 0.6306 (m-10) cc_final: 0.6047 (m-10) REVERT: I 76 LYS cc_start: 0.9481 (mmmm) cc_final: 0.9275 (mmmm) outliers start: 32 outliers final: 4 residues processed: 155 average time/residue: 0.5726 time to fit residues: 97.1804 Evaluate side-chains 144 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 GLN D 5 GLN G 52 ASN G 105 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.116015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.069043 restraints weight = 29085.116| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.74 r_work: 0.2833 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14303 Z= 0.151 Angle : 0.646 7.999 19469 Z= 0.325 Chirality : 0.044 0.224 2164 Planarity : 0.005 0.052 2491 Dihedral : 10.049 108.577 2337 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.20 % Favored : 95.63 % Rotamer: Outliers : 2.14 % Allowed : 10.71 % Favored : 87.15 % 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: -0.66 (0.19), residues: 1738 helix: 1.34 (0.40), residues: 177 sheet: -0.15 (0.21), residues: 580 loop : -0.94 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 27 TYR 0.032 0.001 TYR H 32 PHE 0.021 0.001 PHE F 68 TRP 0.017 0.001 TRP C 597 HIS 0.003 0.001 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00352 (14262) covalent geometry : angle 0.62685 (19367) SS BOND : bond 0.00394 ( 21) SS BOND : angle 1.29724 ( 42) hydrogen bonds : bond 0.03978 ( 407) hydrogen bonds : angle 5.19592 ( 1212) link_ALPHA1-3 : bond 0.00877 ( 3) link_ALPHA1-3 : angle 2.73748 ( 9) link_ALPHA1-6 : bond 0.00723 ( 5) link_ALPHA1-6 : angle 2.64055 ( 15) link_BETA1-4 : bond 0.00308 ( 6) link_BETA1-4 : angle 2.79501 ( 18) link_NAG-ASN : bond 0.00550 ( 6) link_NAG-ASN : angle 2.80400 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 GLN cc_start: 0.8604 (mp10) cc_final: 0.8386 (mp10) REVERT: A 521 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8390 (pm20) REVERT: A 595 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7370 (tm-30) REVERT: B 214 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: B 527 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8672 (pp) REVERT: C 49 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7731 (p0) REVERT: C 50 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7638 (mppt) REVERT: C 53 CYS cc_start: 0.7521 (m) cc_final: 0.7287 (m) REVERT: C 523 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8244 (pp20) REVERT: D 83 MET cc_start: 0.2523 (ptm) cc_final: 0.2297 (mmm) REVERT: G 43 LYS cc_start: 0.8986 (mmmm) cc_final: 0.8713 (mppt) REVERT: G 65 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8829 (ttpp) REVERT: I 76 LYS cc_start: 0.9491 (mmmm) cc_final: 0.9263 (mmmm) outliers start: 31 outliers final: 11 residues processed: 148 average time/residue: 0.5498 time to fit residues: 89.3152 Evaluate side-chains 151 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 73 optimal weight: 0.5980 chunk 108 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN G 52 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.114048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066896 restraints weight = 28999.995| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.71 r_work: 0.2802 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14303 Z= 0.228 Angle : 0.676 7.105 19469 Z= 0.340 Chirality : 0.045 0.183 2164 Planarity : 0.005 0.058 2491 Dihedral : 9.744 114.162 2337 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.20 % Favored : 95.63 % Rotamer: Outliers : 2.35 % Allowed : 12.09 % Favored : 85.56 % 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: -0.51 (0.20), residues: 1738 helix: 1.88 (0.41), residues: 171 sheet: -0.03 (0.22), residues: 580 loop : -0.93 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 64 TYR 0.025 0.002 TYR B 162 PHE 0.019 0.002 PHE F 68 TRP 0.020 0.001 TRP C 597 HIS 0.004 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00545 (14262) covalent geometry : angle 0.65544 (19367) SS BOND : bond 0.00447 ( 21) SS BOND : angle 1.38411 ( 42) hydrogen bonds : bond 0.04131 ( 407) hydrogen bonds : angle 5.09329 ( 1212) link_ALPHA1-3 : bond 0.00707 ( 3) link_ALPHA1-3 : angle 2.66512 ( 9) link_ALPHA1-6 : bond 0.00679 ( 5) link_ALPHA1-6 : angle 2.87622 ( 15) link_BETA1-4 : bond 0.00306 ( 6) link_BETA1-4 : angle 3.07474 ( 18) link_NAG-ASN : bond 0.00288 ( 6) link_NAG-ASN : angle 2.68178 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 GLN cc_start: 0.8703 (mp10) cc_final: 0.8493 (mp10) REVERT: A 595 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 214 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.7102 (m-80) REVERT: C 49 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.8019 (p0) REVERT: C 50 LYS cc_start: 0.8441 (mmmt) cc_final: 0.7937 (mppt) REVERT: C 523 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8244 (pp20) REVERT: D 83 MET cc_start: 0.3470 (OUTLIER) cc_final: 0.3182 (mmm) REVERT: E 83 MET cc_start: 0.2296 (mmp) cc_final: 0.1051 (mpm) REVERT: G 43 LYS cc_start: 0.9076 (mmmm) cc_final: 0.8597 (mptt) REVERT: G 65 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8927 (ttpp) REVERT: H 32 TYR cc_start: 0.6322 (m-10) cc_final: 0.6105 (m-10) REVERT: I 46 GLU cc_start: 0.8308 (pt0) cc_final: 0.8099 (pt0) REVERT: I 76 LYS cc_start: 0.9526 (mmmm) cc_final: 0.9305 (mmmm) outliers start: 34 outliers final: 16 residues processed: 148 average time/residue: 0.5019 time to fit residues: 81.7523 Evaluate side-chains 153 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 61 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 167 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 107 optimal weight: 0.0070 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN B 595 GLN G 52 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.115648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.068811 restraints weight = 28845.952| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.85 r_work: 0.2828 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14303 Z= 0.123 Angle : 0.601 7.484 19469 Z= 0.305 Chirality : 0.043 0.225 2164 Planarity : 0.004 0.058 2491 Dihedral : 9.236 108.491 2337 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.37 % Favored : 95.45 % Rotamer: Outliers : 2.42 % Allowed : 12.92 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1738 helix: 2.13 (0.41), residues: 171 sheet: 0.12 (0.22), residues: 558 loop : -0.82 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 64 TYR 0.024 0.001 TYR B 162 PHE 0.015 0.001 PHE F 68 TRP 0.023 0.001 TRP C 597 HIS 0.002 0.000 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00284 (14262) covalent geometry : angle 0.58485 (19367) SS BOND : bond 0.00339 ( 21) SS BOND : angle 1.03448 ( 42) hydrogen bonds : bond 0.03363 ( 407) hydrogen bonds : angle 4.77944 ( 1212) link_ALPHA1-3 : bond 0.00765 ( 3) link_ALPHA1-3 : angle 2.60300 ( 9) link_ALPHA1-6 : bond 0.00649 ( 5) link_ALPHA1-6 : angle 2.34183 ( 15) link_BETA1-4 : bond 0.00342 ( 6) link_BETA1-4 : angle 2.74567 ( 18) link_NAG-ASN : bond 0.00467 ( 6) link_NAG-ASN : angle 2.25292 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 GLN cc_start: 0.8762 (mp10) cc_final: 0.8437 (mp10) REVERT: A 595 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 214 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.7088 (m-80) REVERT: B 239 LEU cc_start: 0.9066 (mm) cc_final: 0.8416 (tm) REVERT: B 251 GLN cc_start: 0.8752 (mp10) cc_final: 0.8516 (mp10) REVERT: B 527 ILE cc_start: 0.8945 (tp) cc_final: 0.8541 (pp) REVERT: B 595 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7323 (pp30) REVERT: C 35 LEU cc_start: 0.8193 (pt) cc_final: 0.7805 (pp) REVERT: C 50 LYS cc_start: 0.8378 (mmmt) cc_final: 0.7901 (mppt) REVERT: C 239 LEU cc_start: 0.9337 (mm) cc_final: 0.8726 (tm) REVERT: C 523 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8221 (pp20) REVERT: D 83 MET cc_start: 0.3510 (OUTLIER) cc_final: 0.3236 (mmm) REVERT: E 83 MET cc_start: 0.2439 (mmp) cc_final: 0.1245 (mpm) REVERT: G 43 LYS cc_start: 0.9066 (mmmm) cc_final: 0.8865 (mmmm) REVERT: G 65 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8846 (ttpp) REVERT: I 76 LYS cc_start: 0.9536 (mmmm) cc_final: 0.9317 (mmmm) outliers start: 35 outliers final: 12 residues processed: 158 average time/residue: 0.5384 time to fit residues: 93.2317 Evaluate side-chains 153 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 595 GLN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain I residue 62 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 GLN G 52 ASN H 105 ASN I 52 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.112727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.065586 restraints weight = 29099.256| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.85 r_work: 0.2769 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 14303 Z= 0.277 Angle : 0.704 7.250 19469 Z= 0.354 Chirality : 0.046 0.246 2164 Planarity : 0.005 0.063 2491 Dihedral : 9.540 110.763 2337 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.37 % Favored : 95.51 % Rotamer: Outliers : 2.90 % Allowed : 13.61 % Favored : 83.48 % 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: -0.40 (0.20), residues: 1738 helix: 2.03 (0.41), residues: 171 sheet: 0.05 (0.22), residues: 584 loop : -0.88 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 596 TYR 0.025 0.002 TYR B 162 PHE 0.017 0.002 PHE H 47 TRP 0.028 0.002 TRP C 597 HIS 0.005 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00665 (14262) covalent geometry : angle 0.68313 (19367) SS BOND : bond 0.00521 ( 21) SS BOND : angle 1.52070 ( 42) hydrogen bonds : bond 0.04194 ( 407) hydrogen bonds : angle 5.02506 ( 1212) link_ALPHA1-3 : bond 0.00683 ( 3) link_ALPHA1-3 : angle 2.71203 ( 9) link_ALPHA1-6 : bond 0.00628 ( 5) link_ALPHA1-6 : angle 3.04336 ( 15) link_BETA1-4 : bond 0.00390 ( 6) link_BETA1-4 : angle 3.19580 ( 18) link_NAG-ASN : bond 0.00266 ( 6) link_NAG-ASN : angle 2.56060 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 GLN cc_start: 0.8794 (mp10) cc_final: 0.8434 (mp10) REVERT: A 521 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: A 595 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7716 (tm-30) REVERT: B 214 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: B 251 GLN cc_start: 0.8760 (mp10) cc_final: 0.8545 (mp10) REVERT: C 50 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8090 (mppt) REVERT: C 523 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8270 (pp20) REVERT: C 595 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8227 (tm-30) REVERT: G 43 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8862 (mmmm) REVERT: G 56 GLU cc_start: 0.8221 (pt0) cc_final: 0.7848 (pt0) REVERT: G 65 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8935 (ttpp) REVERT: I 27 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7527 (ppt170) REVERT: I 76 LYS cc_start: 0.9568 (mmmm) cc_final: 0.9361 (mmmm) outliers start: 42 outliers final: 19 residues processed: 153 average time/residue: 0.6005 time to fit residues: 100.0335 Evaluate side-chains 158 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 596 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 595 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 119 optimal weight: 10.0000 chunk 38 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 GLN G 52 ASN H 105 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.114523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.067435 restraints weight = 28773.952| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.71 r_work: 0.2813 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14303 Z= 0.142 Angle : 0.621 7.471 19469 Z= 0.315 Chirality : 0.043 0.211 2164 Planarity : 0.005 0.067 2491 Dihedral : 9.115 105.078 2337 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.66 % Favored : 95.22 % Rotamer: Outliers : 2.28 % Allowed : 14.58 % Favored : 83.14 % 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: -0.29 (0.20), residues: 1738 helix: 2.12 (0.41), residues: 171 sheet: 0.17 (0.22), residues: 565 loop : -0.81 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 596 TYR 0.025 0.001 TYR B 162 PHE 0.029 0.001 PHE D 68 TRP 0.036 0.001 TRP C 597 HIS 0.002 0.000 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00332 (14262) covalent geometry : angle 0.60380 (19367) SS BOND : bond 0.00363 ( 21) SS BOND : angle 1.14138 ( 42) hydrogen bonds : bond 0.03458 ( 407) hydrogen bonds : angle 4.79835 ( 1212) link_ALPHA1-3 : bond 0.00703 ( 3) link_ALPHA1-3 : angle 2.71537 ( 9) link_ALPHA1-6 : bond 0.00622 ( 5) link_ALPHA1-6 : angle 2.43324 ( 15) link_BETA1-4 : bond 0.00255 ( 6) link_BETA1-4 : angle 2.78059 ( 18) link_NAG-ASN : bond 0.00436 ( 6) link_NAG-ASN : angle 2.28163 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 GLN cc_start: 0.8816 (mp10) cc_final: 0.8457 (mp10) REVERT: A 595 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 214 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.7020 (m-80) REVERT: B 239 LEU cc_start: 0.9043 (mm) cc_final: 0.8386 (tm) REVERT: B 251 GLN cc_start: 0.8834 (mp10) cc_final: 0.8623 (mp10) REVERT: C 35 LEU cc_start: 0.8329 (pt) cc_final: 0.7963 (pp) REVERT: C 50 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8053 (mppt) REVERT: C 239 LEU cc_start: 0.9382 (mm) cc_final: 0.8794 (tm) REVERT: C 523 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8275 (pp20) REVERT: C 595 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: D 83 MET cc_start: 0.2001 (mmm) cc_final: 0.1701 (mpt) REVERT: G 43 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8877 (mmmm) REVERT: G 56 GLU cc_start: 0.8195 (pt0) cc_final: 0.7872 (pt0) REVERT: G 65 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8862 (ttpp) REVERT: I 76 LYS cc_start: 0.9567 (mmmm) cc_final: 0.9367 (mmmm) outliers start: 33 outliers final: 13 residues processed: 150 average time/residue: 0.6327 time to fit residues: 103.0385 Evaluate side-chains 147 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 595 GLN Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 ASN G 52 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.113990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.066873 restraints weight = 28723.261| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.89 r_work: 0.2797 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14303 Z= 0.183 Angle : 0.645 8.698 19469 Z= 0.326 Chirality : 0.044 0.229 2164 Planarity : 0.005 0.069 2491 Dihedral : 9.010 104.401 2337 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.43 % Favored : 95.45 % Rotamer: Outliers : 2.21 % Allowed : 15.41 % Favored : 82.38 % 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: -0.29 (0.20), residues: 1738 helix: 2.20 (0.41), residues: 171 sheet: 0.19 (0.22), residues: 550 loop : -0.84 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 27 TYR 0.025 0.001 TYR B 162 PHE 0.019 0.002 PHE H 47 TRP 0.039 0.001 TRP C 597 HIS 0.003 0.000 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00438 (14262) covalent geometry : angle 0.62688 (19367) SS BOND : bond 0.00384 ( 21) SS BOND : angle 1.32419 ( 42) hydrogen bonds : bond 0.03579 ( 407) hydrogen bonds : angle 4.79516 ( 1212) link_ALPHA1-3 : bond 0.00636 ( 3) link_ALPHA1-3 : angle 2.62917 ( 9) link_ALPHA1-6 : bond 0.00563 ( 5) link_ALPHA1-6 : angle 2.62500 ( 15) link_BETA1-4 : bond 0.00270 ( 6) link_BETA1-4 : angle 2.94263 ( 18) link_NAG-ASN : bond 0.00497 ( 6) link_NAG-ASN : angle 2.17500 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 GLN cc_start: 0.8809 (mp10) cc_final: 0.8445 (mp10) REVERT: A 595 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7629 (tm-30) REVERT: B 214 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.7015 (m-80) REVERT: B 239 LEU cc_start: 0.9043 (mm) cc_final: 0.8381 (tm) REVERT: C 50 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8094 (mppt) REVERT: C 239 LEU cc_start: 0.9405 (mm) cc_final: 0.8793 (tm) REVERT: C 523 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8267 (pp20) REVERT: C 595 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: G 43 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8892 (mmmm) REVERT: G 65 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8851 (ttpp) outliers start: 32 outliers final: 16 residues processed: 147 average time/residue: 0.6047 time to fit residues: 96.9757 Evaluate side-chains 152 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 595 GLN Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 142 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 128 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 GLN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.114326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.067060 restraints weight = 29105.520| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.83 r_work: 0.2813 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14303 Z= 0.151 Angle : 0.640 8.882 19469 Z= 0.323 Chirality : 0.043 0.218 2164 Planarity : 0.005 0.072 2491 Dihedral : 8.782 101.411 2337 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.83 % Favored : 95.05 % Rotamer: Outliers : 1.73 % Allowed : 15.89 % Favored : 82.38 % 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: -0.27 (0.20), residues: 1738 helix: 2.22 (0.41), residues: 171 sheet: 0.21 (0.22), residues: 550 loop : -0.83 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 596 TYR 0.025 0.001 TYR B 162 PHE 0.040 0.002 PHE D 68 TRP 0.051 0.001 TRP C 597 HIS 0.003 0.000 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00360 (14262) covalent geometry : angle 0.62208 (19367) SS BOND : bond 0.00356 ( 21) SS BOND : angle 1.42200 ( 42) hydrogen bonds : bond 0.03419 ( 407) hydrogen bonds : angle 4.72234 ( 1212) link_ALPHA1-3 : bond 0.00668 ( 3) link_ALPHA1-3 : angle 2.64266 ( 9) link_ALPHA1-6 : bond 0.00623 ( 5) link_ALPHA1-6 : angle 2.48763 ( 15) link_BETA1-4 : bond 0.00261 ( 6) link_BETA1-4 : angle 2.83435 ( 18) link_NAG-ASN : bond 0.00497 ( 6) link_NAG-ASN : angle 2.16373 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 GLN cc_start: 0.8822 (mp10) cc_final: 0.8449 (mp10) REVERT: A 595 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7596 (tm-30) REVERT: B 214 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: B 239 LEU cc_start: 0.9048 (mm) cc_final: 0.8367 (tm) REVERT: C 35 LEU cc_start: 0.8324 (pt) cc_final: 0.7938 (pp) REVERT: C 50 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8068 (mppt) REVERT: C 239 LEU cc_start: 0.9401 (mm) cc_final: 0.8789 (tm) REVERT: C 523 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8280 (pp20) REVERT: C 595 GLN cc_start: 0.8560 (tp40) cc_final: 0.8188 (tm-30) REVERT: G 43 LYS cc_start: 0.9128 (mmmm) cc_final: 0.8901 (mmmm) REVERT: G 65 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8833 (ttpp) outliers start: 25 outliers final: 16 residues processed: 146 average time/residue: 0.5821 time to fit residues: 92.5604 Evaluate side-chains 149 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 107 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 105 ASN ** 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 = 0.3825 r_free = 0.3825 target = 0.114824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067617 restraints weight = 28887.748| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.91 r_work: 0.2814 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14303 Z= 0.150 Angle : 0.647 9.576 19469 Z= 0.327 Chirality : 0.043 0.169 2164 Planarity : 0.005 0.074 2491 Dihedral : 8.663 100.458 2337 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.17 % Rotamer: Outliers : 1.52 % Allowed : 16.17 % Favored : 82.31 % 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: -0.24 (0.20), residues: 1738 helix: 2.26 (0.41), residues: 171 sheet: 0.24 (0.22), residues: 550 loop : -0.82 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG H 27 TYR 0.024 0.001 TYR B 162 PHE 0.020 0.001 PHE D 68 TRP 0.059 0.001 TRP C 597 HIS 0.002 0.000 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00360 (14262) covalent geometry : angle 0.63007 (19367) SS BOND : bond 0.00333 ( 21) SS BOND : angle 1.46540 ( 42) hydrogen bonds : bond 0.03416 ( 407) hydrogen bonds : angle 4.67877 ( 1212) link_ALPHA1-3 : bond 0.00660 ( 3) link_ALPHA1-3 : angle 2.61552 ( 9) link_ALPHA1-6 : bond 0.00635 ( 5) link_ALPHA1-6 : angle 2.48936 ( 15) link_BETA1-4 : bond 0.00218 ( 6) link_BETA1-4 : angle 2.83447 ( 18) link_NAG-ASN : bond 0.00476 ( 6) link_NAG-ASN : angle 2.07124 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 GLN cc_start: 0.8821 (mp10) cc_final: 0.8446 (mp10) REVERT: A 595 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7592 (tm-30) REVERT: B 214 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.7015 (m-80) REVERT: B 239 LEU cc_start: 0.9036 (mm) cc_final: 0.8354 (tm) REVERT: C 35 LEU cc_start: 0.8303 (pt) cc_final: 0.7912 (pp) REVERT: C 50 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8052 (mppt) REVERT: C 239 LEU cc_start: 0.9388 (mm) cc_final: 0.8773 (tm) REVERT: C 523 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8287 (pp20) REVERT: C 595 GLN cc_start: 0.8524 (tp40) cc_final: 0.8158 (tm-30) REVERT: G 43 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8931 (mmmm) REVERT: G 65 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8828 (ttpp) outliers start: 22 outliers final: 13 residues processed: 142 average time/residue: 0.6279 time to fit residues: 96.8155 Evaluate side-chains 142 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 113 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 142 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 GLN C 506 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.115163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.068211 restraints weight = 28828.068| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.67 r_work: 0.2826 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14303 Z= 0.135 Angle : 0.630 8.020 19469 Z= 0.319 Chirality : 0.043 0.170 2164 Planarity : 0.005 0.076 2491 Dihedral : 8.388 98.182 2337 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.60 % Favored : 95.28 % Rotamer: Outliers : 1.59 % Allowed : 16.31 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.20), residues: 1738 helix: 2.20 (0.42), residues: 171 sheet: 0.29 (0.22), residues: 550 loop : -0.80 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 27 TYR 0.032 0.001 TYR H 32 PHE 0.034 0.001 PHE D 68 TRP 0.057 0.001 TRP C 597 HIS 0.002 0.000 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00322 (14262) covalent geometry : angle 0.61360 (19367) SS BOND : bond 0.00313 ( 21) SS BOND : angle 1.29475 ( 42) hydrogen bonds : bond 0.03327 ( 407) hydrogen bonds : angle 4.61066 ( 1212) link_ALPHA1-3 : bond 0.00614 ( 3) link_ALPHA1-3 : angle 2.58205 ( 9) link_ALPHA1-6 : bond 0.00644 ( 5) link_ALPHA1-6 : angle 2.44853 ( 15) link_BETA1-4 : bond 0.00277 ( 6) link_BETA1-4 : angle 2.79635 ( 18) link_NAG-ASN : bond 0.00474 ( 6) link_NAG-ASN : angle 2.08051 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5122.75 seconds wall clock time: 87 minutes 50.14 seconds (5270.14 seconds total)