Starting phenix.real_space_refine on Sun Apr 5 20:39:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kf9_22847/04_2026/7kf9_22847.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kf9_22847/04_2026/7kf9_22847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kf9_22847/04_2026/7kf9_22847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kf9_22847/04_2026/7kf9_22847.map" model { file = "/net/cci-nas-00/data/ceres_data/7kf9_22847/04_2026/7kf9_22847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kf9_22847/04_2026/7kf9_22847.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.072 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 42 5.16 5 C 8331 2.51 5 N 2214 2.21 5 O 2574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13161 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1724 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "I" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "C" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1724 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "F" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "B" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1724 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "E" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "M" 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: "N" 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: "O" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.04, per 1000 atoms: 0.23 Number of scatterers: 13161 At special positions: 0 Unit cell: (148.35, 148.35, 106.95, 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 42 16.00 O 2574 8.00 N 2214 7.00 C 8331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 89 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.02 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 M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 401 " - " ASN A 257 " " NAG A 402 " - " ASN A 268 " " NAG A 403 " - " ASN A 228 " " NAG B 401 " - " ASN B 257 " " NAG B 402 " - " ASN B 268 " " NAG B 403 " - " ASN B 228 " " NAG C 401 " - " ASN C 257 " " NAG C 402 " - " ASN C 268 " " NAG C 403 " - " ASN C 228 " " NAG M 1 " - " ASN D 563 " " NAG N 1 " - " ASN F 563 " " NAG O 1 " - " ASN E 563 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 493.0 milliseconds 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 27 sheets defined 16.8% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'G' and resid 63 through 66 Processing helix chain 'G' and resid 88 through 92 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 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.787A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'D' and resid 528 through 532 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.033A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.908A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'I' and resid 63 through 66 Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.785A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'F' and resid 528 through 532 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.033A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.908A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 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 71 through 74 Processing helix chain 'B' and resid 78 through 84 removed outlier: 3.787A pdb=" N LYS B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'E' and resid 528 through 532 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.032A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 598 removed outlier: 3.908A pdb=" N ARG E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.217A pdb=" N TYR G 35 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP G 36 " --> pdb=" O PHE G 52 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE G 52 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP G 38 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.755A pdb=" N VAL G 120 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 45 removed outlier: 5.260A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 13.553A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 14.582A pdb=" N THR A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ASP A 237 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 98 removed outlier: 8.433A pdb=" N ALA A 101 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 65 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N GLU A 103 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY A 67 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA7, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA J 10 " --> pdb=" O THR J 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA J 10 " --> pdb=" O THR J 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 17 through 23 Processing sheet with id=AB1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.215A pdb=" N TYR I 35 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP I 36 " --> pdb=" O PHE I 52 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE I 52 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP I 38 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.757A pdb=" N VAL I 120 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.259A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 13.553A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 14.583A pdb=" N THR C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ASP C 237 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 98 removed outlier: 5.968A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.216A pdb=" N TYR H 35 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP H 36 " --> pdb=" O PHE H 52 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.756A pdb=" N VAL H 120 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 43 through 45 removed outlier: 5.260A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 13.554A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 11.527A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG B 136 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 14.583A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 10.545A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 96 through 98 removed outlier: 5.968A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AC7, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA K 10 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA K 10 " --> pdb=" O THR K 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 17 through 23 516 hydrogen bonds defined for protein. 1263 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: 2.23 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2727 1.32 - 1.46: 4619 1.46 - 1.59: 6025 1.59 - 1.73: 48 1.73 - 1.87: 45 Bond restraints: 13464 Sorted by residual: bond pdb=" CB HIS A 154 " pdb=" CG HIS A 154 " ideal model delta sigma weight residual 1.497 1.383 0.114 1.40e-02 5.10e+03 6.68e+01 bond pdb=" CB HIS B 154 " pdb=" CG HIS B 154 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.57e+01 bond pdb=" CB HIS C 154 " pdb=" CG HIS C 154 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.47e+01 bond pdb=" CB LEU L 111 " pdb=" CG LEU L 111 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" CB LEU J 111 " pdb=" CG LEU J 111 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.45e+01 ... (remaining 13459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 16440 3.01 - 6.01: 1660 6.01 - 9.02: 192 9.02 - 12.02: 8 12.02 - 15.03: 3 Bond angle restraints: 18303 Sorted by residual: angle pdb=" C ALA C 125 " pdb=" N PRO C 126 " pdb=" CA PRO C 126 " ideal model delta sigma weight residual 120.21 128.35 -8.14 9.60e-01 1.09e+00 7.19e+01 angle pdb=" C ALA B 125 " pdb=" N PRO B 126 " pdb=" CA PRO B 126 " ideal model delta sigma weight residual 120.21 128.24 -8.03 9.60e-01 1.09e+00 7.00e+01 angle pdb=" C ALA A 125 " pdb=" N PRO A 126 " pdb=" CA PRO A 126 " ideal model delta sigma weight residual 120.21 128.20 -7.99 9.60e-01 1.09e+00 6.93e+01 angle pdb=" C GLY D 536 " pdb=" N PRO D 537 " pdb=" CA PRO D 537 " ideal model delta sigma weight residual 120.03 127.22 -7.19 9.90e-01 1.02e+00 5.27e+01 angle pdb=" C GLY F 536 " pdb=" N PRO F 537 " pdb=" CA PRO F 537 " ideal model delta sigma weight residual 120.03 127.19 -7.16 9.90e-01 1.02e+00 5.23e+01 ... (remaining 18298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 7926 21.36 - 42.72: 156 42.72 - 64.07: 45 64.07 - 85.43: 33 85.43 - 106.79: 18 Dihedral angle restraints: 8178 sinusoidal: 3474 harmonic: 4704 Sorted by residual: dihedral pdb=" O4 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C5 BMA O 3 " pdb=" O5 BMA O 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.08 106.79 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.01 106.72 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.95 106.66 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 8175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1374 0.097 - 0.194: 515 0.194 - 0.291: 138 0.291 - 0.388: 42 0.388 - 0.484: 22 Chirality restraints: 2091 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 ... (remaining 2088 not shown) Planarity restraints: 2325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 113 " 0.070 2.00e-02 2.50e+03 3.62e-02 2.62e+01 pdb=" CG TYR I 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR I 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR I 113 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR I 113 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR I 113 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR I 113 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR I 113 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 113 " 0.070 2.00e-02 2.50e+03 3.59e-02 2.58e+01 pdb=" CG TYR H 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR H 113 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR H 113 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR H 113 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR H 113 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR H 113 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR H 113 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 113 " -0.070 2.00e-02 2.50e+03 3.59e-02 2.57e+01 pdb=" CG TYR G 113 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR G 113 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR G 113 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR G 113 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR G 113 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 113 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR G 113 " -0.044 2.00e-02 2.50e+03 ... (remaining 2322 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 6637 2.96 - 3.44: 12335 3.44 - 3.93: 23579 3.93 - 4.41: 27520 4.41 - 4.90: 42979 Nonbonded interactions: 113050 Sorted by model distance: nonbonded pdb=" N ASP K 61 " pdb=" OD1 ASP K 61 " model vdw 2.470 3.120 nonbonded pdb=" N ASP J 61 " pdb=" OD1 ASP J 61 " model vdw 2.471 3.120 nonbonded pdb=" N ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.471 3.120 nonbonded pdb=" N THR B 249 " pdb=" O THR B 249 " model vdw 2.480 2.496 nonbonded pdb=" N THR C 249 " pdb=" O THR C 249 " model vdw 2.480 2.496 ... (remaining 113045 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: 0.03 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'E' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 12.460 Find NCS groups from input model: 0.100 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- 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 : 0.022 0.148 13497 Z= 1.155 Angle : 1.890 15.027 18393 Z= 1.248 Chirality : 0.117 0.484 2091 Planarity : 0.009 0.053 2313 Dihedral : 12.391 106.789 5169 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.14 % 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: 0.37 (0.19), residues: 1626 helix: -0.35 (0.29), residues: 195 sheet: -0.12 (0.23), residues: 489 loop : 0.79 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 85 TYR 0.070 0.012 TYR I 113 PHE 0.038 0.006 PHE H 80 TRP 0.053 0.011 TRP H 49 HIS 0.008 0.003 HIS E 549 Details of bonding type rmsd covalent geometry : bond 0.02149 (13464) covalent geometry : angle 1.88005 (18303) SS BOND : bond 0.00771 ( 9) SS BOND : angle 2.02885 ( 18) hydrogen bonds : bond 0.16680 ( 489) hydrogen bonds : angle 8.52206 ( 1263) link_ALPHA1-3 : bond 0.08406 ( 3) link_ALPHA1-3 : angle 4.44207 ( 9) link_ALPHA1-6 : bond 0.05315 ( 3) link_ALPHA1-6 : angle 2.77680 ( 9) link_BETA1-4 : bond 0.07659 ( 6) link_BETA1-4 : angle 5.58955 ( 18) link_NAG-ASN : bond 0.08402 ( 12) link_NAG-ASN : angle 2.04855 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8740 (ttt) cc_final: 0.7477 (tmm) REVERT: A 171 TYR cc_start: 0.9332 (m-80) cc_final: 0.9104 (m-80) REVERT: A 237 ASP cc_start: 0.9043 (t0) cc_final: 0.8731 (m-30) REVERT: J 35 ASP cc_start: 0.9207 (m-30) cc_final: 0.8372 (p0) REVERT: J 53 ASP cc_start: 0.8865 (p0) cc_final: 0.7837 (t0) REVERT: I 118 MET cc_start: 0.8656 (ttt) cc_final: 0.7637 (tmm) REVERT: C 99 TYR cc_start: 0.7360 (m-80) cc_final: 0.6748 (m-80) REVERT: C 109 TYR cc_start: 0.8670 (m-80) cc_final: 0.8435 (m-10) REVERT: C 237 ASP cc_start: 0.9032 (t0) cc_final: 0.8662 (m-30) REVERT: L 35 ASP cc_start: 0.9168 (m-30) cc_final: 0.8444 (p0) REVERT: L 53 ASP cc_start: 0.8886 (p0) cc_final: 0.7881 (t0) REVERT: H 118 MET cc_start: 0.8807 (ttt) cc_final: 0.7805 (tmm) REVERT: B 127 ASP cc_start: 0.9447 (m-30) cc_final: 0.9211 (t0) REVERT: B 237 ASP cc_start: 0.9006 (t0) cc_final: 0.8605 (m-30) REVERT: K 35 ASP cc_start: 0.9210 (m-30) cc_final: 0.8461 (p0) REVERT: K 53 ASP cc_start: 0.8913 (p0) cc_final: 0.7985 (t0) outliers start: 6 outliers final: 0 residues processed: 227 average time/residue: 0.1182 time to fit residues: 38.0366 Evaluate side-chains 75 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN C 107 ASN L 28 ASN B 107 ASN K 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.036336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.030131 restraints weight = 149032.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.031296 restraints weight = 80517.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.032145 restraints weight = 51917.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.032753 restraints weight = 37067.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.033175 restraints weight = 28457.376| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13497 Z= 0.290 Angle : 0.851 7.522 18393 Z= 0.448 Chirality : 0.049 0.257 2091 Planarity : 0.005 0.033 2313 Dihedral : 9.395 70.126 2292 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.91 % Favored : 97.91 % Rotamer: Outliers : 0.07 % Allowed : 2.29 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.06 (0.20), residues: 1626 helix: -0.32 (0.32), residues: 195 sheet: -0.34 (0.20), residues: 606 loop : 0.66 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 266 TYR 0.017 0.002 TYR C 109 PHE 0.030 0.003 PHE A 252 TRP 0.020 0.003 TRP L 100 HIS 0.005 0.001 HIS E 516 Details of bonding type rmsd covalent geometry : bond 0.00602 (13464) covalent geometry : angle 0.83128 (18303) SS BOND : bond 0.00600 ( 9) SS BOND : angle 2.54537 ( 18) hydrogen bonds : bond 0.06090 ( 489) hydrogen bonds : angle 7.39064 ( 1263) link_ALPHA1-3 : bond 0.00761 ( 3) link_ALPHA1-3 : angle 3.65657 ( 9) link_ALPHA1-6 : bond 0.00152 ( 3) link_ALPHA1-6 : angle 2.06063 ( 9) link_BETA1-4 : bond 0.00447 ( 6) link_BETA1-4 : angle 3.61689 ( 18) link_NAG-ASN : bond 0.00852 ( 12) link_NAG-ASN : angle 2.09768 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8760 (ttt) cc_final: 0.8254 (tmm) REVERT: A 171 TYR cc_start: 0.9248 (m-80) cc_final: 0.8677 (m-80) REVERT: A 237 ASP cc_start: 0.9046 (t0) cc_final: 0.8804 (m-30) REVERT: J 35 ASP cc_start: 0.9197 (m-30) cc_final: 0.8980 (m-30) REVERT: J 74 LEU cc_start: 0.9285 (tt) cc_final: 0.9085 (pp) REVERT: I 118 MET cc_start: 0.8652 (ttt) cc_final: 0.8082 (tmm) REVERT: C 161 LEU cc_start: 0.9274 (mt) cc_final: 0.9064 (mt) REVERT: C 171 TYR cc_start: 0.9426 (m-80) cc_final: 0.9141 (m-80) REVERT: C 237 ASP cc_start: 0.9086 (t0) cc_final: 0.8831 (m-30) REVERT: C 273 LEU cc_start: 0.9116 (mt) cc_final: 0.8912 (mt) REVERT: L 35 ASP cc_start: 0.9318 (m-30) cc_final: 0.9115 (m-30) REVERT: L 61 ASP cc_start: 0.9542 (p0) cc_final: 0.9334 (p0) REVERT: L 74 LEU cc_start: 0.9303 (tt) cc_final: 0.9082 (pp) REVERT: H 118 MET cc_start: 0.8652 (ttt) cc_final: 0.8402 (tmm) REVERT: B 109 TYR cc_start: 0.8661 (m-80) cc_final: 0.8307 (m-10) REVERT: B 171 TYR cc_start: 0.9347 (m-80) cc_final: 0.8962 (m-80) REVERT: B 237 ASP cc_start: 0.9024 (t0) cc_final: 0.8700 (m-30) REVERT: B 273 LEU cc_start: 0.9106 (mt) cc_final: 0.8855 (mt) REVERT: K 74 LEU cc_start: 0.9271 (tt) cc_final: 0.9069 (pp) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1136 time to fit residues: 19.1352 Evaluate side-chains 71 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 69 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.035680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.029432 restraints weight = 151359.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.030557 restraints weight = 82390.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.031375 restraints weight = 53550.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.031957 restraints weight = 38673.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.032394 restraints weight = 29920.174| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13497 Z= 0.211 Angle : 0.701 7.534 18393 Z= 0.366 Chirality : 0.045 0.247 2091 Planarity : 0.005 0.033 2313 Dihedral : 8.096 55.224 2292 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: 0.05 (0.21), residues: 1626 helix: -0.23 (0.32), residues: 195 sheet: -0.37 (0.19), residues: 657 loop : 0.74 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 73 TYR 0.017 0.002 TYR A 99 PHE 0.017 0.003 PHE B 234 TRP 0.016 0.003 TRP H 36 HIS 0.004 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00447 (13464) covalent geometry : angle 0.68761 (18303) SS BOND : bond 0.00216 ( 9) SS BOND : angle 2.18652 ( 18) hydrogen bonds : bond 0.04972 ( 489) hydrogen bonds : angle 6.89044 ( 1263) link_ALPHA1-3 : bond 0.00963 ( 3) link_ALPHA1-3 : angle 1.57041 ( 9) link_ALPHA1-6 : bond 0.00051 ( 3) link_ALPHA1-6 : angle 2.04047 ( 9) link_BETA1-4 : bond 0.00660 ( 6) link_BETA1-4 : angle 2.75745 ( 18) link_NAG-ASN : bond 0.00390 ( 12) link_NAG-ASN : angle 1.61764 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8843 (ttt) cc_final: 0.7987 (tmm) REVERT: G 121 TRP cc_start: 0.7978 (m100) cc_final: 0.7703 (m100) REVERT: A 171 TYR cc_start: 0.9279 (m-80) cc_final: 0.8632 (m-80) REVERT: A 237 ASP cc_start: 0.9160 (t0) cc_final: 0.8802 (m-30) REVERT: A 273 LEU cc_start: 0.9057 (mt) cc_final: 0.8784 (mt) REVERT: I 118 MET cc_start: 0.8703 (ttt) cc_final: 0.7872 (tmm) REVERT: C 171 TYR cc_start: 0.9380 (m-80) cc_final: 0.9130 (m-80) REVERT: C 237 ASP cc_start: 0.9086 (t0) cc_final: 0.8792 (m-30) REVERT: C 273 LEU cc_start: 0.9208 (mt) cc_final: 0.8919 (mt) REVERT: H 118 MET cc_start: 0.8776 (ttt) cc_final: 0.8140 (tmm) REVERT: B 109 TYR cc_start: 0.8759 (m-80) cc_final: 0.8391 (m-10) REVERT: B 171 TYR cc_start: 0.9277 (m-80) cc_final: 0.8875 (m-80) REVERT: B 237 ASP cc_start: 0.9149 (t0) cc_final: 0.8849 (m-30) REVERT: B 273 LEU cc_start: 0.9143 (mt) cc_final: 0.8714 (mt) REVERT: E 517 TYR cc_start: 0.7002 (m-10) cc_final: 0.6654 (m-10) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1280 time to fit residues: 18.7728 Evaluate side-chains 61 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 128 optimal weight: 0.0470 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 161 optimal weight: 30.0000 chunk 68 optimal weight: 8.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.035080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.029060 restraints weight = 147953.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.030116 restraints weight = 81626.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.030860 restraints weight = 53622.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.031396 restraints weight = 39153.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.031798 restraints weight = 30793.100| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13497 Z= 0.197 Angle : 0.686 8.345 18393 Z= 0.352 Chirality : 0.046 0.276 2091 Planarity : 0.004 0.032 2313 Dihedral : 6.996 42.792 2292 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 0.02 (0.21), residues: 1626 helix: -0.39 (0.32), residues: 198 sheet: -0.24 (0.20), residues: 633 loop : 0.58 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 559 TYR 0.014 0.002 TYR C 99 PHE 0.017 0.002 PHE H 80 TRP 0.034 0.002 TRP H 121 HIS 0.004 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00414 (13464) covalent geometry : angle 0.67265 (18303) SS BOND : bond 0.00766 ( 9) SS BOND : angle 2.30059 ( 18) hydrogen bonds : bond 0.04597 ( 489) hydrogen bonds : angle 6.84147 ( 1263) link_ALPHA1-3 : bond 0.00813 ( 3) link_ALPHA1-3 : angle 2.61578 ( 9) link_ALPHA1-6 : bond 0.00331 ( 3) link_ALPHA1-6 : angle 1.99885 ( 9) link_BETA1-4 : bond 0.00349 ( 6) link_BETA1-4 : angle 2.49389 ( 18) link_NAG-ASN : bond 0.00328 ( 12) link_NAG-ASN : angle 1.47543 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8821 (ttt) cc_final: 0.8051 (tmm) REVERT: A 171 TYR cc_start: 0.9304 (m-80) cc_final: 0.8712 (m-80) REVERT: A 234 PHE cc_start: 0.9219 (t80) cc_final: 0.8805 (t80) REVERT: A 236 VAL cc_start: 0.8588 (t) cc_final: 0.8201 (t) REVERT: A 237 ASP cc_start: 0.9130 (t0) cc_final: 0.8733 (m-30) REVERT: A 273 LEU cc_start: 0.9085 (mt) cc_final: 0.8734 (mt) REVERT: D 517 TYR cc_start: 0.7017 (m-10) cc_final: 0.6741 (m-10) REVERT: I 118 MET cc_start: 0.8717 (ttt) cc_final: 0.8094 (tmm) REVERT: I 121 TRP cc_start: 0.8092 (m100) cc_final: 0.7737 (m100) REVERT: C 99 TYR cc_start: 0.8368 (m-10) cc_final: 0.8142 (m-80) REVERT: C 171 TYR cc_start: 0.9338 (m-80) cc_final: 0.9057 (m-80) REVERT: C 237 ASP cc_start: 0.9137 (t0) cc_final: 0.8713 (m-30) REVERT: L 53 ASP cc_start: 0.9148 (p0) cc_final: 0.8470 (m-30) REVERT: H 118 MET cc_start: 0.8606 (ttt) cc_final: 0.8111 (tmm) REVERT: B 171 TYR cc_start: 0.9272 (m-80) cc_final: 0.8840 (m-80) REVERT: B 234 PHE cc_start: 0.9182 (t80) cc_final: 0.8957 (t80) REVERT: B 237 ASP cc_start: 0.9158 (t0) cc_final: 0.8771 (m-30) REVERT: K 35 ASP cc_start: 0.9324 (m-30) cc_final: 0.8986 (t70) REVERT: K 53 ASP cc_start: 0.9212 (p0) cc_final: 0.8497 (m-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1273 time to fit residues: 16.9558 Evaluate side-chains 58 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 118 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 147 optimal weight: 0.0870 chunk 122 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.035370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.029325 restraints weight = 147856.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.030396 restraints weight = 81458.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.031190 restraints weight = 53171.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.031747 restraints weight = 38328.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.032130 restraints weight = 29812.157| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13497 Z= 0.135 Angle : 0.618 9.470 18393 Z= 0.320 Chirality : 0.045 0.202 2091 Planarity : 0.004 0.031 2313 Dihedral : 6.398 38.361 2292 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 0.03 (0.21), residues: 1626 helix: -0.29 (0.33), residues: 198 sheet: -0.26 (0.20), residues: 633 loop : 0.59 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 99 TYR 0.013 0.001 TYR D 517 PHE 0.017 0.002 PHE G 80 TRP 0.044 0.002 TRP G 121 HIS 0.002 0.000 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00286 (13464) covalent geometry : angle 0.60759 (18303) SS BOND : bond 0.00544 ( 9) SS BOND : angle 1.83048 ( 18) hydrogen bonds : bond 0.04176 ( 489) hydrogen bonds : angle 6.61689 ( 1263) link_ALPHA1-3 : bond 0.01056 ( 3) link_ALPHA1-3 : angle 1.91715 ( 9) link_ALPHA1-6 : bond 0.00075 ( 3) link_ALPHA1-6 : angle 1.87688 ( 9) link_BETA1-4 : bond 0.00451 ( 6) link_BETA1-4 : angle 2.29156 ( 18) link_NAG-ASN : bond 0.00378 ( 12) link_NAG-ASN : angle 1.28242 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.9297 (m-80) cc_final: 0.8701 (m-80) REVERT: A 234 PHE cc_start: 0.9008 (t80) cc_final: 0.8777 (t80) REVERT: A 236 VAL cc_start: 0.8631 (t) cc_final: 0.8256 (t) REVERT: A 237 ASP cc_start: 0.9113 (t0) cc_final: 0.8647 (m-30) REVERT: A 273 LEU cc_start: 0.8898 (mt) cc_final: 0.8627 (mt) REVERT: I 118 MET cc_start: 0.8796 (ttt) cc_final: 0.8093 (tmm) REVERT: C 171 TYR cc_start: 0.9320 (m-80) cc_final: 0.8959 (m-80) REVERT: C 234 PHE cc_start: 0.9147 (t80) cc_final: 0.8840 (t80) REVERT: C 237 ASP cc_start: 0.9103 (t0) cc_final: 0.8646 (m-30) REVERT: H 118 MET cc_start: 0.8703 (ttt) cc_final: 0.8191 (tmm) REVERT: B 33 ILE cc_start: 0.8627 (tp) cc_final: 0.7550 (tp) REVERT: B 171 TYR cc_start: 0.9288 (m-80) cc_final: 0.8841 (m-80) REVERT: B 236 VAL cc_start: 0.8605 (t) cc_final: 0.8356 (t) REVERT: B 237 ASP cc_start: 0.9163 (t0) cc_final: 0.8773 (m-30) REVERT: K 35 ASP cc_start: 0.9300 (m-30) cc_final: 0.8963 (t70) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1168 time to fit residues: 16.2884 Evaluate side-chains 64 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 5 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 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 = 0.3130 r_free = 0.3130 target = 0.033926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.027844 restraints weight = 141810.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.028887 restraints weight = 78398.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.029656 restraints weight = 51268.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.030182 restraints weight = 37284.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.030589 restraints weight = 29279.829| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13497 Z= 0.210 Angle : 0.670 7.910 18393 Z= 0.344 Chirality : 0.045 0.249 2091 Planarity : 0.004 0.037 2313 Dihedral : 6.152 32.490 2292 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -0.13 (0.21), residues: 1626 helix: -0.42 (0.33), residues: 198 sheet: -0.31 (0.20), residues: 633 loop : 0.42 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 17 TYR 0.013 0.002 TYR A 99 PHE 0.016 0.002 PHE A 234 TRP 0.017 0.002 TRP G 121 HIS 0.005 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00444 (13464) covalent geometry : angle 0.65781 (18303) SS BOND : bond 0.00511 ( 9) SS BOND : angle 2.05850 ( 18) hydrogen bonds : bond 0.04364 ( 489) hydrogen bonds : angle 6.66767 ( 1263) link_ALPHA1-3 : bond 0.00939 ( 3) link_ALPHA1-3 : angle 2.45868 ( 9) link_ALPHA1-6 : bond 0.00278 ( 3) link_ALPHA1-6 : angle 1.84985 ( 9) link_BETA1-4 : bond 0.00285 ( 6) link_BETA1-4 : angle 2.22333 ( 18) link_NAG-ASN : bond 0.00215 ( 12) link_NAG-ASN : angle 1.50683 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8728 (tmm) cc_final: 0.8479 (tmm) REVERT: A 171 TYR cc_start: 0.9342 (m-80) cc_final: 0.8705 (m-80) REVERT: A 234 PHE cc_start: 0.9026 (t80) cc_final: 0.8824 (t80) REVERT: A 237 ASP cc_start: 0.9181 (t0) cc_final: 0.8696 (m-30) REVERT: D 517 TYR cc_start: 0.7958 (m-80) cc_final: 0.7642 (m-10) REVERT: D 548 MET cc_start: 0.7539 (mmt) cc_final: 0.6986 (mmt) REVERT: I 118 MET cc_start: 0.8691 (ttt) cc_final: 0.7961 (tmm) REVERT: I 121 TRP cc_start: 0.8193 (m100) cc_final: 0.7778 (m100) REVERT: C 171 TYR cc_start: 0.9348 (m-80) cc_final: 0.9112 (m-80) REVERT: C 234 PHE cc_start: 0.9196 (t80) cc_final: 0.8890 (t80) REVERT: C 237 ASP cc_start: 0.9181 (t0) cc_final: 0.8698 (m-30) REVERT: H 118 MET cc_start: 0.8762 (ttt) cc_final: 0.8083 (tmm) REVERT: B 43 LEU cc_start: 0.9011 (tp) cc_final: 0.8749 (tp) REVERT: B 171 TYR cc_start: 0.9318 (m-80) cc_final: 0.8908 (m-80) REVERT: B 236 VAL cc_start: 0.8680 (t) cc_final: 0.8457 (t) REVERT: B 237 ASP cc_start: 0.9178 (t0) cc_final: 0.8657 (m-30) REVERT: E 548 MET cc_start: 0.6455 (mtp) cc_final: 0.5156 (mtp) REVERT: E 561 LEU cc_start: 0.9805 (tp) cc_final: 0.9586 (mt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1073 time to fit residues: 13.6454 Evaluate side-chains 62 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 164 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 GLN ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 595 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.033599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.027355 restraints weight = 148976.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.028397 restraints weight = 83562.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.029152 restraints weight = 55327.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.029684 restraints weight = 40613.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.030077 restraints weight = 32123.953| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13497 Z= 0.171 Angle : 0.632 10.263 18393 Z= 0.326 Chirality : 0.045 0.237 2091 Planarity : 0.004 0.038 2313 Dihedral : 5.826 26.838 2292 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -0.19 (0.21), residues: 1626 helix: -0.33 (0.34), residues: 198 sheet: -0.25 (0.20), residues: 603 loop : 0.21 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 17 TYR 0.015 0.002 TYR A 99 PHE 0.019 0.002 PHE B 234 TRP 0.013 0.002 TRP A 275 HIS 0.002 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00359 (13464) covalent geometry : angle 0.62115 (18303) SS BOND : bond 0.00440 ( 9) SS BOND : angle 1.99400 ( 18) hydrogen bonds : bond 0.04083 ( 489) hydrogen bonds : angle 6.57773 ( 1263) link_ALPHA1-3 : bond 0.00960 ( 3) link_ALPHA1-3 : angle 1.77695 ( 9) link_ALPHA1-6 : bond 0.00048 ( 3) link_ALPHA1-6 : angle 1.72752 ( 9) link_BETA1-4 : bond 0.00272 ( 6) link_BETA1-4 : angle 2.10061 ( 18) link_NAG-ASN : bond 0.00250 ( 12) link_NAG-ASN : angle 1.53872 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8593 (tmm) cc_final: 0.8263 (tmm) REVERT: A 171 TYR cc_start: 0.9347 (m-80) cc_final: 0.8736 (m-80) REVERT: A 237 ASP cc_start: 0.9151 (t0) cc_final: 0.8719 (m-30) REVERT: D 517 TYR cc_start: 0.7859 (m-80) cc_final: 0.7460 (m-80) REVERT: D 548 MET cc_start: 0.7453 (mmt) cc_final: 0.6493 (mmt) REVERT: I 118 MET cc_start: 0.8653 (ttt) cc_final: 0.7897 (tmm) REVERT: I 121 TRP cc_start: 0.8190 (m100) cc_final: 0.7802 (m100) REVERT: C 171 TYR cc_start: 0.9363 (m-80) cc_final: 0.9067 (m-80) REVERT: C 234 PHE cc_start: 0.9275 (t80) cc_final: 0.8953 (t80) REVERT: C 237 ASP cc_start: 0.9172 (t0) cc_final: 0.8874 (m-30) REVERT: H 118 MET cc_start: 0.8663 (ttt) cc_final: 0.7992 (tmm) REVERT: B 99 TYR cc_start: 0.8280 (m-80) cc_final: 0.7925 (m-80) REVERT: B 171 TYR cc_start: 0.9322 (m-80) cc_final: 0.8934 (m-80) REVERT: B 234 PHE cc_start: 0.9229 (t80) cc_final: 0.8935 (t80) REVERT: B 237 ASP cc_start: 0.9175 (t0) cc_final: 0.8685 (m-30) REVERT: E 548 MET cc_start: 0.5913 (mtp) cc_final: 0.4542 (mtp) REVERT: E 564 GLU cc_start: 0.9679 (mm-30) cc_final: 0.9331 (mm-30) REVERT: K 35 ASP cc_start: 0.9442 (m-30) cc_final: 0.9199 (t0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1136 time to fit residues: 14.0738 Evaluate side-chains 56 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 30.0000 chunk 23 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 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 = 0.3072 r_free = 0.3072 target = 0.032679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.026610 restraints weight = 151411.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.027596 restraints weight = 85008.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.028310 restraints weight = 56705.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.028819 restraints weight = 41991.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.029190 restraints weight = 33325.699| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13497 Z= 0.240 Angle : 0.708 8.912 18393 Z= 0.360 Chirality : 0.046 0.284 2091 Planarity : 0.005 0.041 2313 Dihedral : 5.931 24.579 2292 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: -0.37 (0.21), residues: 1626 helix: -0.28 (0.36), residues: 180 sheet: -0.48 (0.20), residues: 627 loop : 0.16 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 17 TYR 0.015 0.002 TYR D 517 PHE 0.018 0.002 PHE B 234 TRP 0.016 0.002 TRP A 275 HIS 0.004 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00508 (13464) covalent geometry : angle 0.69531 (18303) SS BOND : bond 0.00621 ( 9) SS BOND : angle 2.23202 ( 18) hydrogen bonds : bond 0.04329 ( 489) hydrogen bonds : angle 6.73702 ( 1263) link_ALPHA1-3 : bond 0.00782 ( 3) link_ALPHA1-3 : angle 2.18395 ( 9) link_ALPHA1-6 : bond 0.00209 ( 3) link_ALPHA1-6 : angle 1.86992 ( 9) link_BETA1-4 : bond 0.00290 ( 6) link_BETA1-4 : angle 2.05376 ( 18) link_NAG-ASN : bond 0.00461 ( 12) link_NAG-ASN : angle 1.82051 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8580 (tmm) cc_final: 0.8176 (tmm) REVERT: A 171 TYR cc_start: 0.9391 (m-80) cc_final: 0.8780 (m-80) REVERT: A 234 PHE cc_start: 0.9083 (t80) cc_final: 0.8782 (t80) REVERT: A 237 ASP cc_start: 0.9178 (t0) cc_final: 0.8749 (m-30) REVERT: C 171 TYR cc_start: 0.9365 (m-80) cc_final: 0.9129 (m-80) REVERT: C 237 ASP cc_start: 0.9278 (t0) cc_final: 0.8812 (m-30) REVERT: F 561 LEU cc_start: 0.9799 (mt) cc_final: 0.9464 (mt) REVERT: H 118 MET cc_start: 0.8696 (ttt) cc_final: 0.7943 (tmm) REVERT: B 171 TYR cc_start: 0.9356 (m-80) cc_final: 0.9037 (m-80) REVERT: B 234 PHE cc_start: 0.9217 (t80) cc_final: 0.8908 (t80) REVERT: B 237 ASP cc_start: 0.9175 (t0) cc_final: 0.8718 (m-30) REVERT: K 35 ASP cc_start: 0.9326 (m-30) cc_final: 0.8996 (t0) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1103 time to fit residues: 12.4708 Evaluate side-chains 57 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 118 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS ** E 506 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 = 0.3126 r_free = 0.3126 target = 0.033928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.027648 restraints weight = 144734.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.028697 restraints weight = 80802.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.029463 restraints weight = 53237.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.029989 restraints weight = 38940.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.030399 restraints weight = 30698.586| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13497 Z= 0.117 Angle : 0.601 8.910 18393 Z= 0.307 Chirality : 0.045 0.227 2091 Planarity : 0.004 0.036 2313 Dihedral : 5.529 23.971 2292 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.22), residues: 1626 helix: -0.10 (0.36), residues: 180 sheet: -0.42 (0.21), residues: 627 loop : 0.30 (0.24), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 17 TYR 0.016 0.001 TYR A 99 PHE 0.023 0.002 PHE C 234 TRP 0.014 0.002 TRP A 275 HIS 0.004 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00250 (13464) covalent geometry : angle 0.59079 (18303) SS BOND : bond 0.00506 ( 9) SS BOND : angle 2.00044 ( 18) hydrogen bonds : bond 0.03881 ( 489) hydrogen bonds : angle 6.41308 ( 1263) link_ALPHA1-3 : bond 0.00982 ( 3) link_ALPHA1-3 : angle 1.38631 ( 9) link_ALPHA1-6 : bond 0.00215 ( 3) link_ALPHA1-6 : angle 1.63508 ( 9) link_BETA1-4 : bond 0.00232 ( 6) link_BETA1-4 : angle 1.97885 ( 18) link_NAG-ASN : bond 0.00380 ( 12) link_NAG-ASN : angle 1.48044 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8482 (tmm) cc_final: 0.8154 (tmm) REVERT: A 171 TYR cc_start: 0.9377 (m-80) cc_final: 0.8744 (m-80) REVERT: A 220 TYR cc_start: 0.9350 (m-80) cc_final: 0.9089 (m-80) REVERT: A 234 PHE cc_start: 0.9184 (t80) cc_final: 0.8837 (t80) REVERT: D 548 MET cc_start: 0.7896 (mmp) cc_final: 0.7164 (mmt) REVERT: I 118 MET cc_start: 0.8594 (ttt) cc_final: 0.7860 (tmm) REVERT: I 121 TRP cc_start: 0.8136 (m100) cc_final: 0.7801 (m100) REVERT: C 161 LEU cc_start: 0.9552 (mt) cc_final: 0.9302 (mt) REVERT: C 171 TYR cc_start: 0.9298 (m-80) cc_final: 0.8983 (m-80) REVERT: C 234 PHE cc_start: 0.9260 (t80) cc_final: 0.8948 (t80) REVERT: C 237 ASP cc_start: 0.9243 (t0) cc_final: 0.8727 (m-30) REVERT: H 118 MET cc_start: 0.8657 (ttt) cc_final: 0.7960 (tmm) REVERT: B 171 TYR cc_start: 0.9359 (m-80) cc_final: 0.8912 (m-10) REVERT: B 234 PHE cc_start: 0.9258 (t80) cc_final: 0.8950 (t80) REVERT: B 237 ASP cc_start: 0.9038 (t0) cc_final: 0.8810 (m-30) REVERT: E 548 MET cc_start: 0.5689 (mtp) cc_final: 0.4376 (mtt) REVERT: E 564 GLU cc_start: 0.9670 (mm-30) cc_final: 0.9316 (mm-30) REVERT: K 35 ASP cc_start: 0.9425 (m-30) cc_final: 0.9096 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1110 time to fit residues: 14.5632 Evaluate side-chains 62 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 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 = 0.3081 r_free = 0.3081 target = 0.032988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.026887 restraints weight = 152979.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.027897 restraints weight = 85875.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.028625 restraints weight = 56932.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.029123 restraints weight = 41981.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.029512 restraints weight = 33461.632| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13497 Z= 0.214 Angle : 0.657 8.562 18393 Z= 0.338 Chirality : 0.045 0.277 2091 Planarity : 0.004 0.039 2313 Dihedral : 5.629 25.388 2292 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1626 helix: -0.56 (0.35), residues: 198 sheet: -0.40 (0.21), residues: 606 loop : 0.12 (0.24), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 17 TYR 0.012 0.002 TYR F 517 PHE 0.023 0.002 PHE C 234 TRP 0.020 0.002 TRP C 104 HIS 0.019 0.002 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00448 (13464) covalent geometry : angle 0.64510 (18303) SS BOND : bond 0.00604 ( 9) SS BOND : angle 1.94683 ( 18) hydrogen bonds : bond 0.04125 ( 489) hydrogen bonds : angle 6.66344 ( 1263) link_ALPHA1-3 : bond 0.00703 ( 3) link_ALPHA1-3 : angle 1.75291 ( 9) link_ALPHA1-6 : bond 0.00033 ( 3) link_ALPHA1-6 : angle 1.77189 ( 9) link_BETA1-4 : bond 0.00238 ( 6) link_BETA1-4 : angle 1.99630 ( 18) link_NAG-ASN : bond 0.00345 ( 12) link_NAG-ASN : angle 1.80948 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8507 (tmm) cc_final: 0.8114 (tmm) REVERT: A 161 LEU cc_start: 0.9479 (mt) cc_final: 0.9179 (mt) REVERT: A 171 TYR cc_start: 0.9425 (m-80) cc_final: 0.8817 (m-80) REVERT: A 220 TYR cc_start: 0.9402 (m-80) cc_final: 0.9114 (m-80) REVERT: A 234 PHE cc_start: 0.9103 (t80) cc_final: 0.8772 (t80) REVERT: D 517 TYR cc_start: 0.7870 (m-80) cc_final: 0.7528 (m-80) REVERT: D 548 MET cc_start: 0.8089 (mmp) cc_final: 0.6344 (mtm) REVERT: I 118 MET cc_start: 0.8624 (ttt) cc_final: 0.7844 (tmm) REVERT: I 121 TRP cc_start: 0.8305 (m100) cc_final: 0.7829 (m100) REVERT: C 161 LEU cc_start: 0.9469 (mt) cc_final: 0.9212 (mt) REVERT: C 171 TYR cc_start: 0.9323 (m-80) cc_final: 0.9122 (m-80) REVERT: C 234 PHE cc_start: 0.9190 (t80) cc_final: 0.8931 (t80) REVERT: C 237 ASP cc_start: 0.9282 (t0) cc_final: 0.8768 (m-30) REVERT: H 118 MET cc_start: 0.8726 (ttt) cc_final: 0.8006 (tmm) REVERT: B 171 TYR cc_start: 0.9391 (m-80) cc_final: 0.9075 (m-80) REVERT: B 234 PHE cc_start: 0.9193 (t80) cc_final: 0.8908 (t80) REVERT: B 237 ASP cc_start: 0.9310 (t0) cc_final: 0.8806 (m-30) REVERT: K 35 ASP cc_start: 0.9400 (m-30) cc_final: 0.9136 (t0) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1094 time to fit residues: 12.7500 Evaluate side-chains 57 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 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 = 0.3072 r_free = 0.3072 target = 0.032764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.026729 restraints weight = 153265.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.027722 restraints weight = 85620.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.028441 restraints weight = 56909.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.028939 restraints weight = 42094.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.029318 restraints weight = 33527.029| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13497 Z= 0.207 Angle : 0.660 8.083 18393 Z= 0.340 Chirality : 0.046 0.296 2091 Planarity : 0.005 0.041 2313 Dihedral : 5.683 26.441 2292 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: -0.56 (0.21), residues: 1626 helix: -0.81 (0.33), residues: 213 sheet: -0.53 (0.21), residues: 606 loop : 0.09 (0.24), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 26 TYR 0.013 0.002 TYR E 517 PHE 0.023 0.002 PHE C 234 TRP 0.018 0.002 TRP A 275 HIS 0.008 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00437 (13464) covalent geometry : angle 0.64824 (18303) SS BOND : bond 0.00579 ( 9) SS BOND : angle 1.91235 ( 18) hydrogen bonds : bond 0.04215 ( 489) hydrogen bonds : angle 6.67100 ( 1263) link_ALPHA1-3 : bond 0.00754 ( 3) link_ALPHA1-3 : angle 1.60007 ( 9) link_ALPHA1-6 : bond 0.00073 ( 3) link_ALPHA1-6 : angle 1.67493 ( 9) link_BETA1-4 : bond 0.00177 ( 6) link_BETA1-4 : angle 1.84595 ( 18) link_NAG-ASN : bond 0.00341 ( 12) link_NAG-ASN : angle 2.00223 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.92 seconds wall clock time: 30 minutes 14.27 seconds (1814.27 seconds total)