Starting phenix.real_space_refine on Sat May 2 12:44:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ufy_64126/05_2026/9ufy_64126.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ufy_64126/05_2026/9ufy_64126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ufy_64126/05_2026/9ufy_64126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ufy_64126/05_2026/9ufy_64126.map" model { file = "/net/cci-nas-00/data/ceres_data/9ufy_64126/05_2026/9ufy_64126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ufy_64126/05_2026/9ufy_64126.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 3360 2.51 5 N 864 2.21 5 O 1048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5272 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "D" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "E" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "F" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "B" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "C" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "J" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "K" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "L" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "H" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "I" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'GO3': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'GO3': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'GO3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'GO3': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'GO3': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'GO3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.57, per 1000 atoms: 0.30 Number of scatterers: 5272 At special positions: 0 Unit cell: (91.16, 104.94, 47.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1048 8.00 N 864 7.00 C 3360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 158.6 milliseconds 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1224 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 46 through 53 removed outlier: 7.553A pdb=" N GLY A 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N HIS D 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL A 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N VAL D 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY A 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL E 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N HIS A 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY E 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL E 48 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL J 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS E 50 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY J 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLY G 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N HIS J 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VAL G 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N VAL J 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY G 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL G 48 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL K 49 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N HIS G 50 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY K 51 " --> pdb=" O HIS G 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 64 through 65 removed outlier: 6.055A pdb=" N THR A 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N THR G 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 69 through 80 removed outlier: 6.950A pdb=" N VAL A 70 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL D 71 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR A 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY D 73 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL D 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA A 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN D 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS A 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N ALA A 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N THR E 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N VAL A 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N VAL E 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY A 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA E 76 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N THR A 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA E 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N VAL A 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N LYS E 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLN A 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N ALA E 69 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N THR J 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N VAL E 71 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N VAL J 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY E 73 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA J 76 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N THR E 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA J 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N VAL E 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N LYS J 80 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N GLN E 79 " --> pdb=" O LYS J 80 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL G 70 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL J 71 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR G 72 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY J 73 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL J 77 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA G 78 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN J 79 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS G 80 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ALA G 69 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N THR K 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N VAL G 71 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N VAL K 74 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY G 73 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA K 76 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N THR G 75 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ALA K 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N VAL G 77 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N LYS K 80 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLN G 79 " --> pdb=" O LYS K 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 94 through 95 removed outlier: 6.787A pdb=" N PHE A 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE G 94 " --> pdb=" O VAL J 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 53 removed outlier: 7.550A pdb=" N GLY F 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N HIS B 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N VAL F 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N VAL B 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY F 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL F 48 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS F 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C 48 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL H 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N HIS C 50 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY H 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLY L 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N HIS H 50 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N VAL L 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N VAL H 52 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY L 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL L 48 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL I 49 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N HIS L 50 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY I 51 " --> pdb=" O HIS L 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 64 through 65 removed outlier: 6.057A pdb=" N THR F 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR L 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 69 through 80 removed outlier: 6.950A pdb=" N VAL F 70 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B 71 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR F 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY B 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA F 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN B 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS F 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N ALA F 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 10.210A pdb=" N THR C 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N VAL F 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N VAL C 74 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY F 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA C 76 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N THR F 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ALA C 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N VAL F 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 10.679A pdb=" N LYS C 80 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N GLN F 79 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N ALA C 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N THR H 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N VAL C 71 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N VAL H 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLY C 73 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA H 76 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N THR C 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA H 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N VAL C 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N LYS H 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N GLN C 79 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL L 70 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL H 71 " --> pdb=" O VAL L 70 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR L 72 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY H 73 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL H 77 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA L 78 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN H 79 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS L 80 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ALA L 69 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N THR I 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N VAL L 71 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N VAL I 74 " --> pdb=" O VAL L 71 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY L 73 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA I 76 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR L 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA I 78 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N VAL L 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N LYS I 80 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N GLN L 79 " --> pdb=" O LYS I 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 95 removed outlier: 6.786A pdb=" N PHE F 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE L 94 " --> pdb=" O VAL H 95 " (cutoff:3.500A) 42 hydrogen bonds defined for protein. 126 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: 0.83 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 868 1.26 - 1.33: 368 1.33 - 1.40: 736 1.40 - 1.47: 928 1.47 - 1.54: 2420 Bond restraints: 5320 Sorted by residual: bond pdb=" C10 GO3 L 201 " pdb=" C9 GO3 L 201 " ideal model delta sigma weight residual 1.482 1.394 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C10 GO3 G 201 " pdb=" C9 GO3 G 201 " ideal model delta sigma weight residual 1.482 1.394 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C10 GO3 D 201 " pdb=" C9 GO3 D 201 " ideal model delta sigma weight residual 1.482 1.394 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C10 GO3 J 201 " pdb=" C9 GO3 J 201 " ideal model delta sigma weight residual 1.482 1.394 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C10 GO3 A 201 " pdb=" C9 GO3 A 201 " ideal model delta sigma weight residual 1.482 1.394 0.088 2.00e-02 2.50e+03 1.91e+01 ... (remaining 5315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 6551 1.60 - 3.19: 498 3.19 - 4.79: 93 4.79 - 6.38: 50 6.38 - 7.98: 64 Bond angle restraints: 7256 Sorted by residual: angle pdb=" C THR G 81 " pdb=" N VAL G 82 " pdb=" CA VAL G 82 " ideal model delta sigma weight residual 123.16 119.48 3.68 1.06e+00 8.90e-01 1.20e+01 angle pdb=" C THR A 81 " pdb=" N VAL A 82 " pdb=" CA VAL A 82 " ideal model delta sigma weight residual 123.16 119.51 3.65 1.06e+00 8.90e-01 1.18e+01 angle pdb=" C THR F 81 " pdb=" N VAL F 82 " pdb=" CA VAL F 82 " ideal model delta sigma weight residual 123.16 119.52 3.64 1.06e+00 8.90e-01 1.18e+01 angle pdb=" C THR L 81 " pdb=" N VAL L 82 " pdb=" CA VAL L 82 " ideal model delta sigma weight residual 123.16 119.53 3.63 1.06e+00 8.90e-01 1.17e+01 angle pdb=" C THR D 81 " pdb=" N VAL D 82 " pdb=" CA VAL D 82 " ideal model delta sigma weight residual 123.16 119.55 3.61 1.06e+00 8.90e-01 1.16e+01 ... (remaining 7251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 2676 17.72 - 35.45: 224 35.45 - 53.17: 84 53.17 - 70.89: 28 70.89 - 88.61: 32 Dihedral angle restraints: 3044 sinusoidal: 1100 harmonic: 1944 Sorted by residual: dihedral pdb=" CB GLU L 46 " pdb=" CG GLU L 46 " pdb=" CD GLU L 46 " pdb=" OE1 GLU L 46 " ideal model delta sinusoidal sigma weight residual 0.00 -66.55 66.55 1 3.00e+01 1.11e-03 6.42e+00 dihedral pdb=" CB GLU E 46 " pdb=" CG GLU E 46 " pdb=" CD GLU E 46 " pdb=" OE1 GLU E 46 " ideal model delta sinusoidal sigma weight residual 0.00 -66.55 66.55 1 3.00e+01 1.11e-03 6.42e+00 dihedral pdb=" CB GLU J 46 " pdb=" CG GLU J 46 " pdb=" CD GLU J 46 " pdb=" OE1 GLU J 46 " ideal model delta sinusoidal sigma weight residual 0.00 -66.54 66.54 1 3.00e+01 1.11e-03 6.42e+00 ... (remaining 3041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 338 0.027 - 0.054: 325 0.054 - 0.081: 90 0.081 - 0.108: 80 0.108 - 0.135: 55 Chirality restraints: 888 Sorted by residual: chirality pdb=" CA VAL K 55 " pdb=" N VAL K 55 " pdb=" C VAL K 55 " pdb=" CB VAL K 55 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA VAL B 55 " pdb=" N VAL B 55 " pdb=" C VAL B 55 " pdb=" CB VAL B 55 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA VAL J 55 " pdb=" N VAL J 55 " pdb=" C VAL J 55 " pdb=" CB VAL J 55 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 885 not shown) Planarity restraints: 844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 GO3 L 201 " -0.050 2.00e-02 2.50e+03 4.58e-02 8.92e+01 pdb=" C12 GO3 L 201 " 0.047 2.00e-02 2.50e+03 pdb=" C14 GO3 L 201 " 0.036 2.00e-02 2.50e+03 pdb=" C16 GO3 L 201 " 0.045 2.00e-02 2.50e+03 pdb=" C18 GO3 L 201 " -0.039 2.00e-02 2.50e+03 pdb=" C20 GO3 L 201 " -0.063 2.00e-02 2.50e+03 pdb=" C22 GO3 L 201 " -0.014 2.00e-02 2.50e+03 pdb=" C24 GO3 L 201 " 0.010 2.00e-02 2.50e+03 pdb=" C26 GO3 L 201 " 0.021 2.00e-02 2.50e+03 pdb=" C28 GO3 L 201 " 0.033 2.00e-02 2.50e+03 pdb=" C30 GO3 L 201 " 0.020 2.00e-02 2.50e+03 pdb=" C32 GO3 L 201 " 0.059 2.00e-02 2.50e+03 pdb=" C38 GO3 L 201 " 0.025 2.00e-02 2.50e+03 pdb=" C9 GO3 L 201 " -0.074 2.00e-02 2.50e+03 pdb=" O2 GO3 L 201 " 0.047 2.00e-02 2.50e+03 pdb=" O4 GO3 L 201 " -0.013 2.00e-02 2.50e+03 pdb=" O6 GO3 L 201 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 GO3 A 201 " 0.051 2.00e-02 2.50e+03 4.58e-02 8.91e+01 pdb=" C12 GO3 A 201 " -0.046 2.00e-02 2.50e+03 pdb=" C14 GO3 A 201 " -0.036 2.00e-02 2.50e+03 pdb=" C16 GO3 A 201 " -0.045 2.00e-02 2.50e+03 pdb=" C18 GO3 A 201 " 0.039 2.00e-02 2.50e+03 pdb=" C20 GO3 A 201 " 0.062 2.00e-02 2.50e+03 pdb=" C22 GO3 A 201 " 0.014 2.00e-02 2.50e+03 pdb=" C24 GO3 A 201 " -0.010 2.00e-02 2.50e+03 pdb=" C26 GO3 A 201 " -0.022 2.00e-02 2.50e+03 pdb=" C28 GO3 A 201 " -0.033 2.00e-02 2.50e+03 pdb=" C30 GO3 A 201 " -0.020 2.00e-02 2.50e+03 pdb=" C32 GO3 A 201 " -0.059 2.00e-02 2.50e+03 pdb=" C38 GO3 A 201 " -0.025 2.00e-02 2.50e+03 pdb=" C9 GO3 A 201 " 0.074 2.00e-02 2.50e+03 pdb=" O2 GO3 A 201 " -0.047 2.00e-02 2.50e+03 pdb=" O4 GO3 A 201 " 0.013 2.00e-02 2.50e+03 pdb=" O6 GO3 A 201 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 GO3 L 202 " 0.050 2.00e-02 2.50e+03 4.58e-02 8.90e+01 pdb=" C12 GO3 L 202 " -0.046 2.00e-02 2.50e+03 pdb=" C14 GO3 L 202 " -0.037 2.00e-02 2.50e+03 pdb=" C16 GO3 L 202 " -0.045 2.00e-02 2.50e+03 pdb=" C18 GO3 L 202 " 0.039 2.00e-02 2.50e+03 pdb=" C20 GO3 L 202 " 0.062 2.00e-02 2.50e+03 pdb=" C22 GO3 L 202 " 0.014 2.00e-02 2.50e+03 pdb=" C24 GO3 L 202 " -0.010 2.00e-02 2.50e+03 pdb=" C26 GO3 L 202 " -0.021 2.00e-02 2.50e+03 pdb=" C28 GO3 L 202 " -0.033 2.00e-02 2.50e+03 pdb=" C30 GO3 L 202 " -0.021 2.00e-02 2.50e+03 pdb=" C32 GO3 L 202 " -0.059 2.00e-02 2.50e+03 pdb=" C38 GO3 L 202 " -0.025 2.00e-02 2.50e+03 pdb=" C9 GO3 L 202 " 0.073 2.00e-02 2.50e+03 pdb=" O2 GO3 L 202 " -0.047 2.00e-02 2.50e+03 pdb=" O4 GO3 L 202 " 0.013 2.00e-02 2.50e+03 pdb=" O6 GO3 L 202 " 0.090 2.00e-02 2.50e+03 ... (remaining 841 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 88 2.49 - 3.10: 3826 3.10 - 3.70: 7131 3.70 - 4.30: 11104 4.30 - 4.90: 22001 Nonbonded interactions: 44150 Sorted by model distance: nonbonded pdb=" C31 GO3 G 201 " pdb=" O2 GO3 G 201 " model vdw 1.893 3.460 nonbonded pdb=" C31 GO3 L 202 " pdb=" O2 GO3 L 202 " model vdw 1.894 3.460 nonbonded pdb=" C31 GO3 F 201 " pdb=" O2 GO3 F 201 " model vdw 1.894 3.460 nonbonded pdb=" C31 GO3 L 201 " pdb=" O2 GO3 L 201 " model vdw 1.894 3.460 nonbonded pdb=" C31 GO3 D 201 " pdb=" O2 GO3 D 201 " model vdw 1.894 3.460 ... (remaining 44145 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'B' selection = chain 'C' selection = chain 'K' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.090 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 : 0.012 0.088 5320 Z= 0.564 Angle : 1.237 7.975 7256 Z= 0.591 Chirality : 0.055 0.135 888 Planarity : 0.007 0.046 844 Dihedral : 19.805 88.612 1820 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.65 (0.23), residues: 696 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.18), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR L 39 PHE 0.020 0.005 PHE F 94 HIS 0.010 0.006 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.01181 ( 5320) covalent geometry : angle 1.23657 ( 7256) hydrogen bonds : bond 0.19704 ( 42) hydrogen bonds : angle 8.48718 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.172 Fit side-chains REVERT: A 97 LYS cc_start: 0.7398 (mttm) cc_final: 0.7186 (mtpt) REVERT: E 45 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8517 (mttt) REVERT: C 45 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8714 (mtpt) REVERT: J 45 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8580 (mttt) REVERT: J 97 LYS cc_start: 0.7369 (mttm) cc_final: 0.7061 (mtpt) REVERT: I 97 LYS cc_start: 0.7647 (mttm) cc_final: 0.7353 (mtpt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1802 time to fit residues: 8.9312 Evaluate side-chains 41 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.118445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090795 restraints weight = 5935.878| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.89 r_work: 0.3252 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5320 Z= 0.134 Angle : 0.621 5.295 7256 Z= 0.310 Chirality : 0.050 0.130 888 Planarity : 0.002 0.010 844 Dihedral : 14.020 78.767 848 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.20 % Allowed : 7.54 % Favored : 92.26 % 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: -3.96 (0.24), residues: 696 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.18), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 39 PHE 0.019 0.004 PHE E 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5320) covalent geometry : angle 0.62082 ( 7256) hydrogen bonds : bond 0.02354 ( 42) hydrogen bonds : angle 5.57349 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.194 Fit side-chains REVERT: A 97 LYS cc_start: 0.7158 (mttm) cc_final: 0.6876 (mtpt) REVERT: D 97 LYS cc_start: 0.6986 (mttm) cc_final: 0.6688 (mtpt) REVERT: E 45 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8392 (mttt) REVERT: F 97 LYS cc_start: 0.7271 (mtpt) cc_final: 0.6561 (tttp) REVERT: B 97 LYS cc_start: 0.7276 (mttm) cc_final: 0.6858 (mtmt) REVERT: C 97 LYS cc_start: 0.6993 (mttm) cc_final: 0.6764 (mtpt) REVERT: J 45 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8418 (mttt) REVERT: J 97 LYS cc_start: 0.7241 (mttm) cc_final: 0.6939 (mtpt) REVERT: I 97 LYS cc_start: 0.7796 (mttm) cc_final: 0.7430 (mtpt) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.1888 time to fit residues: 9.2947 Evaluate side-chains 41 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 0.0570 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 overall best weight: 2.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.115036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.089128 restraints weight = 5943.830| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.79 r_work: 0.3159 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5320 Z= 0.217 Angle : 0.613 4.159 7256 Z= 0.331 Chirality : 0.053 0.127 888 Planarity : 0.003 0.011 844 Dihedral : 13.497 77.167 848 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 1.19 % Allowed : 11.90 % Favored : 86.90 % 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: -3.65 (0.26), residues: 696 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR J 39 PHE 0.021 0.005 PHE E 94 HIS 0.010 0.005 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 5320) covalent geometry : angle 0.61308 ( 7256) hydrogen bonds : bond 0.03076 ( 42) hydrogen bonds : angle 5.15018 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.179 Fit side-chains REVERT: D 97 LYS cc_start: 0.6991 (mttm) cc_final: 0.6675 (mtmt) REVERT: E 45 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8465 (mttt) REVERT: F 97 LYS cc_start: 0.7156 (mtpt) cc_final: 0.6456 (tttp) REVERT: B 97 LYS cc_start: 0.7260 (mttm) cc_final: 0.6827 (mtpt) REVERT: C 97 LYS cc_start: 0.7030 (mttm) cc_final: 0.6821 (mtpt) REVERT: J 97 LYS cc_start: 0.7147 (mttm) cc_final: 0.6892 (mtpt) REVERT: L 97 LYS cc_start: 0.6900 (mttm) cc_final: 0.6620 (mtpt) REVERT: I 97 LYS cc_start: 0.7700 (mttm) cc_final: 0.7258 (mtpt) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.1526 time to fit residues: 9.3119 Evaluate side-chains 50 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 70 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.114813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.088364 restraints weight = 5822.026| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.85 r_work: 0.3135 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 5320 Z= 0.220 Angle : 0.610 3.669 7256 Z= 0.331 Chirality : 0.053 0.128 888 Planarity : 0.003 0.013 844 Dihedral : 13.593 79.516 848 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 2.78 % Allowed : 12.50 % Favored : 84.72 % 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: -3.48 (0.27), residues: 696 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR J 39 PHE 0.023 0.005 PHE E 94 HIS 0.010 0.005 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 5320) covalent geometry : angle 0.60985 ( 7256) hydrogen bonds : bond 0.02803 ( 42) hydrogen bonds : angle 4.81604 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.195 Fit side-chains REVERT: D 97 LYS cc_start: 0.6846 (mttm) cc_final: 0.6511 (mtmt) REVERT: E 45 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8508 (mttt) REVERT: F 97 LYS cc_start: 0.7107 (mtpt) cc_final: 0.6388 (tttp) REVERT: B 97 LYS cc_start: 0.7075 (mttm) cc_final: 0.6674 (mtpt) REVERT: J 97 LYS cc_start: 0.7108 (mttm) cc_final: 0.6847 (mtpt) REVERT: L 44 THR cc_start: 0.8992 (p) cc_final: 0.8740 (p) REVERT: L 97 LYS cc_start: 0.6783 (mttm) cc_final: 0.6537 (mtpt) REVERT: I 58 LYS cc_start: 0.8760 (ptpt) cc_final: 0.8489 (pttt) REVERT: I 97 LYS cc_start: 0.7780 (mttm) cc_final: 0.7317 (mtpt) outliers start: 14 outliers final: 11 residues processed: 59 average time/residue: 0.1496 time to fit residues: 10.3802 Evaluate side-chains 56 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 81 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.113463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086663 restraints weight = 6046.873| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.86 r_work: 0.3190 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 5320 Z= 0.273 Angle : 0.653 3.676 7256 Z= 0.359 Chirality : 0.055 0.129 888 Planarity : 0.003 0.013 844 Dihedral : 13.744 80.130 848 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 2.38 % Allowed : 15.48 % Favored : 82.14 % 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: -3.50 (0.27), residues: 696 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR J 39 PHE 0.024 0.006 PHE E 94 HIS 0.011 0.006 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00659 ( 5320) covalent geometry : angle 0.65341 ( 7256) hydrogen bonds : bond 0.03102 ( 42) hydrogen bonds : angle 4.76246 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.158 Fit side-chains REVERT: D 97 LYS cc_start: 0.6913 (mttm) cc_final: 0.6560 (mtmt) REVERT: E 45 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8595 (mttt) REVERT: B 97 LYS cc_start: 0.7281 (mttm) cc_final: 0.6930 (mtpt) REVERT: J 97 LYS cc_start: 0.7234 (mttm) cc_final: 0.6946 (mtpt) REVERT: L 44 THR cc_start: 0.9083 (p) cc_final: 0.8833 (p) REVERT: I 97 LYS cc_start: 0.7686 (mttm) cc_final: 0.7391 (mtpt) outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.1365 time to fit residues: 9.5453 Evaluate side-chains 58 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 40 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.118113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092403 restraints weight = 6074.923| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.83 r_work: 0.3231 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 5320 Z= 0.121 Angle : 0.516 3.615 7256 Z= 0.275 Chirality : 0.051 0.131 888 Planarity : 0.002 0.014 844 Dihedral : 13.050 79.987 848 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 1.59 % Allowed : 17.46 % Favored : 80.95 % 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: -3.14 (0.28), residues: 696 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR A 39 PHE 0.016 0.004 PHE E 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 5320) covalent geometry : angle 0.51568 ( 7256) hydrogen bonds : bond 0.02021 ( 42) hydrogen bonds : angle 4.61811 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.152 Fit side-chains REVERT: D 97 LYS cc_start: 0.6926 (mttm) cc_final: 0.6568 (mtmt) REVERT: E 45 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8491 (mttt) REVERT: B 97 LYS cc_start: 0.7161 (mttm) cc_final: 0.6851 (mtpt) REVERT: J 97 LYS cc_start: 0.7198 (mttm) cc_final: 0.6953 (mtpt) REVERT: I 97 LYS cc_start: 0.7796 (mttm) cc_final: 0.7335 (mtpt) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.1456 time to fit residues: 8.6858 Evaluate side-chains 47 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.119108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093383 restraints weight = 6021.324| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.85 r_work: 0.3190 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 5320 Z= 0.159 Angle : 0.529 3.646 7256 Z= 0.286 Chirality : 0.051 0.126 888 Planarity : 0.002 0.014 844 Dihedral : 13.202 79.711 848 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 2.38 % Allowed : 17.06 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.28), residues: 696 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR A 39 PHE 0.019 0.004 PHE E 94 HIS 0.008 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 5320) covalent geometry : angle 0.52912 ( 7256) hydrogen bonds : bond 0.02303 ( 42) hydrogen bonds : angle 4.55902 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.185 Fit side-chains REVERT: D 97 LYS cc_start: 0.6724 (mttm) cc_final: 0.6379 (mtmt) REVERT: E 45 LYS cc_start: 0.8735 (mtpp) cc_final: 0.8485 (mttt) REVERT: B 97 LYS cc_start: 0.7092 (mttm) cc_final: 0.6786 (mtpt) REVERT: J 97 LYS cc_start: 0.7195 (mttm) cc_final: 0.6975 (mtpt) REVERT: I 97 LYS cc_start: 0.7605 (mttm) cc_final: 0.7220 (mtpt) outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 0.1491 time to fit residues: 9.5579 Evaluate side-chains 53 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 81 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 32 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 56 optimal weight: 0.2980 chunk 12 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.115687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.089852 restraints weight = 6014.865| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.84 r_work: 0.3161 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 5320 Z= 0.212 Angle : 0.581 3.557 7256 Z= 0.317 Chirality : 0.052 0.127 888 Planarity : 0.003 0.012 844 Dihedral : 13.403 80.910 848 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 2.98 % Allowed : 16.47 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.28), residues: 696 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR J 39 PHE 0.022 0.005 PHE E 94 HIS 0.009 0.005 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 5320) covalent geometry : angle 0.58072 ( 7256) hydrogen bonds : bond 0.02551 ( 42) hydrogen bonds : angle 4.55982 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.123 Fit side-chains REVERT: D 97 LYS cc_start: 0.6749 (mttm) cc_final: 0.6429 (mtmt) REVERT: E 45 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8506 (mttt) REVERT: B 97 LYS cc_start: 0.7083 (mttm) cc_final: 0.6787 (mtpt) REVERT: J 97 LYS cc_start: 0.7164 (mttm) cc_final: 0.6934 (mtpt) REVERT: I 97 LYS cc_start: 0.7583 (mttm) cc_final: 0.7207 (mtpt) outliers start: 15 outliers final: 12 residues processed: 59 average time/residue: 0.1437 time to fit residues: 9.9605 Evaluate side-chains 57 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 10.0000 chunk 69 optimal weight: 0.0670 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.115013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.089315 restraints weight = 6111.249| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.83 r_work: 0.3153 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 5320 Z= 0.259 Angle : 0.628 3.732 7256 Z= 0.345 Chirality : 0.054 0.129 888 Planarity : 0.003 0.012 844 Dihedral : 13.571 81.951 848 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 3.37 % Allowed : 15.87 % Favored : 80.75 % 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: -3.22 (0.28), residues: 696 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR J 39 PHE 0.024 0.006 PHE E 94 HIS 0.011 0.006 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 5320) covalent geometry : angle 0.62789 ( 7256) hydrogen bonds : bond 0.02769 ( 42) hydrogen bonds : angle 4.65521 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.195 Fit side-chains REVERT: D 97 LYS cc_start: 0.6885 (mttm) cc_final: 0.6540 (mtmt) REVERT: E 45 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8530 (mttt) REVERT: B 97 LYS cc_start: 0.6840 (mttm) cc_final: 0.6517 (mtpt) REVERT: J 97 LYS cc_start: 0.7147 (mttm) cc_final: 0.6929 (mtpt) REVERT: L 44 THR cc_start: 0.9051 (p) cc_final: 0.8820 (p) REVERT: I 97 LYS cc_start: 0.7592 (mttm) cc_final: 0.7228 (mtpt) outliers start: 17 outliers final: 16 residues processed: 61 average time/residue: 0.1350 time to fit residues: 9.6504 Evaluate side-chains 60 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.120860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.095584 restraints weight = 6034.460| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.81 r_work: 0.3318 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 5320 Z= 0.091 Angle : 0.472 3.621 7256 Z= 0.248 Chirality : 0.050 0.127 888 Planarity : 0.002 0.009 844 Dihedral : 12.782 80.166 848 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.39 % Allowed : 18.06 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.29), residues: 696 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 39 PHE 0.014 0.003 PHE E 94 HIS 0.006 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 5320) covalent geometry : angle 0.47202 ( 7256) hydrogen bonds : bond 0.01681 ( 42) hydrogen bonds : angle 4.50215 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.179 Fit side-chains REVERT: D 97 LYS cc_start: 0.6806 (mttm) cc_final: 0.6485 (mtmt) REVERT: E 45 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8508 (mttt) REVERT: B 97 LYS cc_start: 0.6865 (mttm) cc_final: 0.6543 (mtpt) REVERT: J 97 LYS cc_start: 0.7159 (mttm) cc_final: 0.6933 (mtpt) REVERT: I 97 LYS cc_start: 0.7371 (mttm) cc_final: 0.7074 (mtpt) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.1549 time to fit residues: 8.2618 Evaluate side-chains 45 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.116891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091203 restraints weight = 6157.713| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.86 r_work: 0.3150 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 5320 Z= 0.268 Angle : 0.618 3.715 7256 Z= 0.340 Chirality : 0.054 0.127 888 Planarity : 0.003 0.012 844 Dihedral : 13.489 81.189 848 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 2.18 % Allowed : 17.46 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.28), residues: 696 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR J 39 PHE 0.024 0.006 PHE E 94 HIS 0.010 0.006 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00650 ( 5320) covalent geometry : angle 0.61761 ( 7256) hydrogen bonds : bond 0.02810 ( 42) hydrogen bonds : angle 4.61536 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1423.25 seconds wall clock time: 25 minutes 15.39 seconds (1515.39 seconds total)