Starting phenix.real_space_refine on Sun Aug 24 14:58:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hla_34859/08_2025/8hla_34859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hla_34859/08_2025/8hla_34859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hla_34859/08_2025/8hla_34859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hla_34859/08_2025/8hla_34859.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hla_34859/08_2025/8hla_34859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hla_34859/08_2025/8hla_34859.map" } resolution = 2.81 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 13596 2.51 5 N 3372 2.21 5 O 3840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20868 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "B" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "C" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "D" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "E" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "F" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "G" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "H" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "I" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "J" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "K" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "L" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'FL3': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'FL3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'FL3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'FL3': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'FL3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'FL3': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'FL3': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'FL3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.50, per 1000 atoms: 0.22 Number of scatterers: 20868 At special positions: 0 Unit cell: (163.777, 160.485, 71.601, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 3840 8.00 N 3372 7.00 C 13596 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 661.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4824 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 25 sheets defined 37.9% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 4.038A pdb=" N ALA A 27 " --> pdb=" O PRO A 23 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN A 29 " --> pdb=" O TYR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 74 through 89 Processing helix chain 'A' and resid 103 through 109 Processing helix chain 'A' and resid 145 through 162 Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.119A pdb=" N GLN B 29 " --> pdb=" O TYR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.596A pdb=" N PHE B 60 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 90 removed outlier: 5.960A pdb=" N LYS B 80 " --> pdb=" O CYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 109 Processing helix chain 'B' and resid 145 through 163 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'C' and resid 22 through 28 removed outlier: 4.338A pdb=" N PHE C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.726A pdb=" N LEU C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 89 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 145 through 163 Processing helix chain 'C' and resid 187 through 201 Processing helix chain 'D' and resid 22 through 26 removed outlier: 3.883A pdb=" N PHE D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 26' Processing helix chain 'D' and resid 42 through 63 removed outlier: 4.884A pdb=" N ASP D 58 " --> pdb=" O GLN D 54 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLN D 59 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 89 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 145 through 163 removed outlier: 3.707A pdb=" N ASP D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 removed outlier: 3.584A pdb=" N GLU D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 26 removed outlier: 4.319A pdb=" N PHE E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 22 through 26' Processing helix chain 'E' and resid 43 through 56 Processing helix chain 'E' and resid 56 through 62 Processing helix chain 'E' and resid 78 through 89 Processing helix chain 'E' and resid 103 through 109 Processing helix chain 'E' and resid 145 through 163 Processing helix chain 'E' and resid 187 through 199 Processing helix chain 'F' and resid 22 through 29 removed outlier: 3.795A pdb=" N PHE F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA F 27 " --> pdb=" O PRO F 23 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 56 Processing helix chain 'F' and resid 56 through 62 Processing helix chain 'F' and resid 74 through 89 Processing helix chain 'F' and resid 104 through 109 Processing helix chain 'F' and resid 145 through 163 Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'G' and resid 22 through 29 removed outlier: 3.947A pdb=" N PHE G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA G 27 " --> pdb=" O PRO G 23 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN G 29 " --> pdb=" O TYR G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 56 Processing helix chain 'G' and resid 56 through 63 removed outlier: 3.579A pdb=" N LEU G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 89 removed outlier: 3.733A pdb=" N GLU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 145 through 162 removed outlier: 3.515A pdb=" N ASP G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 194 Processing helix chain 'H' and resid 22 through 26 removed outlier: 4.185A pdb=" N PHE H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 22 through 26' Processing helix chain 'H' and resid 27 through 30 Processing helix chain 'H' and resid 43 through 56 Processing helix chain 'H' and resid 56 through 63 Processing helix chain 'H' and resid 74 through 89 Processing helix chain 'H' and resid 103 through 109 Processing helix chain 'H' and resid 145 through 163 Processing helix chain 'H' and resid 187 through 201 Processing helix chain 'I' and resid 22 through 26 removed outlier: 3.916A pdb=" N PHE I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 22 through 26' Processing helix chain 'I' and resid 43 through 56 Processing helix chain 'I' and resid 56 through 62 Processing helix chain 'I' and resid 74 through 89 removed outlier: 6.182A pdb=" N LYS I 80 " --> pdb=" O CYS I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 110 Processing helix chain 'I' and resid 145 through 162 Processing helix chain 'I' and resid 187 through 201 Processing helix chain 'J' and resid 24 through 29 Processing helix chain 'J' and resid 43 through 56 Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'J' and resid 74 through 89 removed outlier: 5.937A pdb=" N LYS J 80 " --> pdb=" O CYS J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 109 Processing helix chain 'J' and resid 145 through 162 Processing helix chain 'J' and resid 187 through 199 removed outlier: 3.540A pdb=" N ALA J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 26 removed outlier: 4.227A pdb=" N PHE K 26 " --> pdb=" O LEU K 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 22 through 26' Processing helix chain 'K' and resid 43 through 56 Processing helix chain 'K' and resid 56 through 63 removed outlier: 3.894A pdb=" N LEU K 63 " --> pdb=" O GLN K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 89 Processing helix chain 'K' and resid 103 through 109 removed outlier: 3.571A pdb=" N LYS K 108 " --> pdb=" O GLU K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 163 Processing helix chain 'K' and resid 187 through 200 Processing helix chain 'L' and resid 22 through 26 Processing helix chain 'L' and resid 44 through 56 Processing helix chain 'L' and resid 56 through 63 removed outlier: 3.684A pdb=" N PHE L 60 " --> pdb=" O ARG L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 89 Processing helix chain 'L' and resid 103 through 109 Processing helix chain 'L' and resid 145 through 162 Processing helix chain 'L' and resid 188 through 191 Processing helix chain 'L' and resid 192 through 197 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.528A pdb=" N TRP A 32 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A 68 " --> pdb=" O TRP A 32 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 34 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG A 121 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR A 137 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 123 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 135 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 125 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 125 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE B 135 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 123 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR B 137 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ARG B 121 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP B 32 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 68 " --> pdb=" O TRP B 32 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL B 34 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 70 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE B 36 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ILE B 98 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY B 69 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 181 removed outlier: 3.685A pdb=" N GLU A 204 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 12 through 15 Processing sheet with id=AA4, first strand: chain 'B' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'C' and resid 12 through 15 Processing sheet with id=AA6, first strand: chain 'C' and resid 97 through 98 removed outlier: 8.399A pdb=" N ILE C 98 " --> pdb=" O PRO C 67 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY C 69 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TRP C 32 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE C 68 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL C 34 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU C 70 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE C 36 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 122 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG C 121 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR C 137 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL C 123 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE C 135 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 125 " --> pdb=" O ARG C 133 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE D 125 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE D 135 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 123 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR D 137 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG D 121 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP D 32 " --> pdb=" O GLU D 66 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE D 68 " --> pdb=" O TRP D 32 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 34 " --> pdb=" O ILE D 68 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU D 70 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE D 36 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ILE D 98 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY D 69 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS D 14 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AA8, first strand: chain 'D' and resid 180 through 181 Processing sheet with id=AA9, first strand: chain 'E' and resid 12 through 15 removed outlier: 3.567A pdb=" N GLY E 18 " --> pdb=" O THR E 15 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 97 through 99 removed outlier: 7.908A pdb=" N ILE E 98 " --> pdb=" O PRO E 67 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY E 69 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TRP E 32 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE E 68 " --> pdb=" O TRP E 32 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL E 34 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU E 70 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE E 36 " --> pdb=" O LEU E 70 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG E 121 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR E 137 " --> pdb=" O ARG E 121 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 123 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE E 135 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE E 125 " --> pdb=" O ARG E 133 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA F 134 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP F 32 " --> pdb=" O GLU F 66 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE F 68 " --> pdb=" O TRP F 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL F 34 " --> pdb=" O ILE F 68 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU F 70 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE F 36 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE F 98 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY F 69 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS F 14 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 180 through 181 Processing sheet with id=AB3, first strand: chain 'F' and resid 203 through 205 Processing sheet with id=AB4, first strand: chain 'G' and resid 12 through 15 Processing sheet with id=AB5, first strand: chain 'G' and resid 97 through 99 removed outlier: 8.082A pdb=" N ILE G 98 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY G 69 " --> pdb=" O ILE G 98 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TRP G 32 " --> pdb=" O GLU G 66 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE G 68 " --> pdb=" O TRP G 32 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL G 34 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU G 70 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE G 36 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG G 121 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR G 137 " --> pdb=" O ARG G 121 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL G 123 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE G 135 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE G 125 " --> pdb=" O ARG G 133 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE H 125 " --> pdb=" O ARG H 133 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE H 135 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL H 123 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR H 137 " --> pdb=" O ARG H 121 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ARG H 121 " --> pdb=" O TYR H 137 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP H 32 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE H 68 " --> pdb=" O TRP H 32 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL H 34 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU H 70 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE H 36 " --> pdb=" O LEU H 70 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE H 98 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY H 69 " --> pdb=" O ILE H 98 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS H 14 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 204 through 205 Processing sheet with id=AB7, first strand: chain 'H' and resid 180 through 181 Processing sheet with id=AB8, first strand: chain 'I' and resid 12 through 15 removed outlier: 3.984A pdb=" N GLY I 18 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 97 through 99 removed outlier: 6.565A pdb=" N GLY I 69 " --> pdb=" O ILE I 98 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL I 34 " --> pdb=" O ILE I 68 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU I 70 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE I 36 " --> pdb=" O LEU I 70 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG I 121 " --> pdb=" O TYR I 137 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR I 137 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL I 123 " --> pdb=" O ILE I 135 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE I 135 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE I 125 " --> pdb=" O ARG I 133 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA J 134 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP J 32 " --> pdb=" O GLU J 66 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE J 68 " --> pdb=" O TRP J 32 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL J 34 " --> pdb=" O ILE J 68 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU J 70 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE J 36 " --> pdb=" O LEU J 70 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE J 98 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY J 69 " --> pdb=" O ILE J 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 180 through 181 Processing sheet with id=AC2, first strand: chain 'J' and resid 12 through 15 Processing sheet with id=AC3, first strand: chain 'J' and resid 203 through 205 removed outlier: 3.736A pdb=" N GLU J 204 " --> pdb=" O TYR J 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.487A pdb=" N LYS K 14 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ILE K 98 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY K 69 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP K 32 " --> pdb=" O GLU K 66 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE K 68 " --> pdb=" O TRP K 32 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL K 34 " --> pdb=" O ILE K 68 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU K 70 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE K 36 " --> pdb=" O LEU K 70 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG K 121 " --> pdb=" O TYR K 137 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR K 137 " --> pdb=" O ARG K 121 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL K 123 " --> pdb=" O ILE K 135 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE K 135 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE K 125 " --> pdb=" O ARG K 133 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ARG K 133 " --> pdb=" O PRO L 139 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE L 125 " --> pdb=" O ARG L 133 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE L 135 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL L 123 " --> pdb=" O ILE L 135 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR L 137 " --> pdb=" O ARG L 121 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG L 121 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP L 32 " --> pdb=" O GLU L 66 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE L 68 " --> pdb=" O TRP L 32 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL L 34 " --> pdb=" O ILE L 68 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU L 70 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE L 36 " --> pdb=" O LEU L 70 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE L 98 " --> pdb=" O PRO L 67 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY L 69 " --> pdb=" O ILE L 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 180 through 181 Processing sheet with id=AC6, first strand: chain 'L' and resid 12 through 15 removed outlier: 3.980A pdb=" N GLY L 18 " --> pdb=" O THR L 15 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 181 through 182 removed outlier: 4.494A pdb=" N SER L 211 " --> pdb=" O VAL L 182 " (cutoff:3.500A) 797 hydrogen bonds defined for protein. 2292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6337 1.33 - 1.45: 3584 1.45 - 1.57: 11391 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 21420 Sorted by residual: bond pdb=" C TYR I 137 " pdb=" N TYR I 138 " ideal model delta sigma weight residual 1.331 1.287 0.044 1.48e-02 4.57e+03 8.79e+00 bond pdb=" C TYR A 137 " pdb=" N TYR A 138 " ideal model delta sigma weight residual 1.329 1.277 0.052 1.86e-02 2.89e+03 7.87e+00 bond pdb=" CA ARG B 121 " pdb=" CB ARG B 121 " ideal model delta sigma weight residual 1.536 1.433 0.103 4.10e-02 5.95e+02 6.29e+00 bond pdb=" CG1 ILE A 79 " pdb=" CD1 ILE A 79 " ideal model delta sigma weight residual 1.513 1.417 0.096 3.90e-02 6.57e+02 6.12e+00 bond pdb=" C TYR K 137 " pdb=" N TYR K 138 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.47e-02 4.63e+03 6.00e+00 ... (remaining 21415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 28258 2.56 - 5.11: 722 5.11 - 7.67: 66 7.67 - 10.22: 12 10.22 - 12.78: 6 Bond angle restraints: 29064 Sorted by residual: angle pdb=" C GLN A 193 " pdb=" N ARG A 194 " pdb=" CA ARG A 194 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.83e+01 angle pdb=" N GLY A 201 " pdb=" CA GLY A 201 " pdb=" C GLY A 201 " ideal model delta sigma weight residual 114.95 108.29 6.66 1.41e+00 5.03e-01 2.23e+01 angle pdb=" N LYS F 192 " pdb=" CA LYS F 192 " pdb=" C LYS F 192 " ideal model delta sigma weight residual 113.18 107.28 5.90 1.33e+00 5.65e-01 1.97e+01 angle pdb=" N ILE G 79 " pdb=" CA ILE G 79 " pdb=" C ILE G 79 " ideal model delta sigma weight residual 112.29 108.17 4.12 9.40e-01 1.13e+00 1.92e+01 angle pdb=" N ARG A 194 " pdb=" CA ARG A 194 " pdb=" C ARG A 194 " ideal model delta sigma weight residual 110.80 120.09 -9.29 2.13e+00 2.20e-01 1.90e+01 ... (remaining 29059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 11374 17.52 - 35.04: 1050 35.04 - 52.56: 198 52.56 - 70.08: 30 70.08 - 87.60: 20 Dihedral angle restraints: 12672 sinusoidal: 5208 harmonic: 7464 Sorted by residual: dihedral pdb=" CA GLN A 193 " pdb=" C GLN A 193 " pdb=" N ARG A 194 " pdb=" CA ARG A 194 " ideal model delta harmonic sigma weight residual -180.00 -129.59 -50.41 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA GLY A 103 " pdb=" C GLY A 103 " pdb=" N GLU A 104 " pdb=" CA GLU A 104 " ideal model delta harmonic sigma weight residual -180.00 -143.98 -36.02 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N PRO B 23 " pdb=" CA PRO B 23 " ideal model delta harmonic sigma weight residual 180.00 147.80 32.20 0 5.00e+00 4.00e-02 4.15e+01 ... (remaining 12669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2486 0.078 - 0.155: 606 0.155 - 0.233: 37 0.233 - 0.311: 13 0.311 - 0.388: 2 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CB ILE A 68 " pdb=" CA ILE A 68 " pdb=" CG1 ILE A 68 " pdb=" CG2 ILE A 68 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CB VAL E 164 " pdb=" CA VAL E 164 " pdb=" CG1 VAL E 164 " pdb=" CG2 VAL E 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB VAL F 136 " pdb=" CA VAL F 136 " pdb=" CG1 VAL F 136 " pdb=" CG2 VAL F 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 3141 not shown) Planarity restraints: 3684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 26 " -0.054 2.00e-02 2.50e+03 5.27e-02 4.86e+01 pdb=" CG PHE J 26 " 0.119 2.00e-02 2.50e+03 pdb=" CD1 PHE J 26 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE J 26 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE J 26 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE J 26 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE J 26 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 43 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO L 44 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 32 " 0.028 2.00e-02 2.50e+03 2.49e-02 1.55e+01 pdb=" CG TRP G 32 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP G 32 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP G 32 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 32 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 32 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 32 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 32 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP G 32 " 0.005 2.00e-02 2.50e+03 ... (remaining 3681 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 335 2.60 - 3.18: 19507 3.18 - 3.75: 35806 3.75 - 4.33: 52859 4.33 - 4.90: 84199 Nonbonded interactions: 192706 Sorted by model distance: nonbonded pdb=" OH TYR A 138 " pdb=" OE2 GLU B 148 " model vdw 2.027 3.040 nonbonded pdb=" OG1 THR I 187 " pdb=" OD1 ASP I 189 " model vdw 2.033 3.040 nonbonded pdb=" O PRO H 183 " pdb=" NH2 ARG H 194 " model vdw 2.044 3.120 nonbonded pdb=" OE2 GLU C 148 " pdb=" OH TYR D 138 " model vdw 2.083 3.040 nonbonded pdb=" OE2 GLU G 148 " pdb=" OH TYR H 138 " model vdw 2.111 3.040 ... (remaining 192701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'B' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'C' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'D' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'E' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'F' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'G' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'H' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'I' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'J' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'K' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'L' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) } 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: 5.880 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.580 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.011 0.106 21432 Z= 0.451 Angle : 0.955 12.780 29064 Z= 0.513 Chirality : 0.065 0.388 3144 Planarity : 0.006 0.105 3684 Dihedral : 14.251 87.604 7848 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.22 % Favored : 91.67 % Rotamer: Outliers : 0.09 % Allowed : 1.22 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -2.33 (0.15), residues: 2556 helix: -1.34 (0.16), residues: 858 sheet: -1.64 (0.27), residues: 353 loop : -1.61 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 61 TYR 0.027 0.003 TYR A 212 PHE 0.119 0.004 PHE J 26 TRP 0.066 0.003 TRP G 32 HIS 0.021 0.003 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.01067 (21420) covalent geometry : angle 0.95549 (29064) hydrogen bonds : bond 0.18104 ( 797) hydrogen bonds : angle 8.66657 ( 2292) Misc. bond : bond 0.04372 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 412 time to evaluate : 0.632 Fit side-chains REVERT: B 45 VAL cc_start: 0.7569 (p) cc_final: 0.7320 (t) REVERT: B 86 LYS cc_start: 0.7995 (tttm) cc_final: 0.7767 (tttp) REVERT: D 108 LYS cc_start: 0.7431 (mptt) cc_final: 0.6900 (mmtp) REVERT: E 88 ASN cc_start: 0.8710 (m110) cc_final: 0.8487 (m-40) REVERT: I 100 ASP cc_start: 0.8129 (t70) cc_final: 0.7762 (OUTLIER) REVERT: I 200 LYS cc_start: 0.7260 (ptpt) cc_final: 0.6879 (ptpt) REVERT: K 148 GLU cc_start: 0.7614 (mm-30) cc_final: 0.6629 (tp30) outliers start: 2 outliers final: 2 residues processed: 413 average time/residue: 0.5439 time to fit residues: 255.5642 Evaluate side-chains 301 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 136 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN C 173 ASN H 193 GLN I 17 HIS K 29 GLN K 54 GLN L 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.171063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140389 restraints weight = 23944.610| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.09 r_work: 0.3417 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21432 Z= 0.153 Angle : 0.698 13.116 29064 Z= 0.362 Chirality : 0.051 0.185 3144 Planarity : 0.005 0.093 3684 Dihedral : 6.172 47.775 2749 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.44 % Favored : 94.41 % Rotamer: Outliers : 1.85 % Allowed : 12.12 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.45 (0.16), residues: 2556 helix: -0.10 (0.17), residues: 858 sheet: -1.70 (0.28), residues: 345 loop : -1.29 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 56 TYR 0.021 0.002 TYR L 212 PHE 0.018 0.002 PHE L 33 TRP 0.017 0.001 TRP G 32 HIS 0.006 0.001 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00357 (21420) covalent geometry : angle 0.69841 (29064) hydrogen bonds : bond 0.04300 ( 797) hydrogen bonds : angle 6.10022 ( 2292) Misc. bond : bond 0.00055 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 379 time to evaluate : 0.670 Fit side-chains REVERT: A 63 LEU cc_start: 0.7853 (tt) cc_final: 0.7604 (mp) REVERT: A 154 LYS cc_start: 0.7709 (mtpp) cc_final: 0.7448 (mttt) REVERT: B 53 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.6918 (tpp) REVERT: C 7 LYS cc_start: 0.6867 (tppt) cc_final: 0.6346 (tptt) REVERT: C 24 ASP cc_start: 0.7714 (p0) cc_final: 0.6991 (m-30) REVERT: D 108 LYS cc_start: 0.7529 (mptt) cc_final: 0.7210 (mmtp) REVERT: D 192 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7627 (mmpt) REVERT: E 88 ASN cc_start: 0.8804 (m110) cc_final: 0.8579 (m-40) REVERT: F 7 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7532 (tptp) REVERT: F 73 ASP cc_start: 0.8022 (m-30) cc_final: 0.7792 (m-30) REVERT: G 49 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8052 (mt-10) REVERT: G 188 VAL cc_start: 0.7908 (t) cc_final: 0.7639 (m) REVERT: H 82 MET cc_start: 0.8440 (mtp) cc_final: 0.8233 (mtp) REVERT: I 100 ASP cc_start: 0.8295 (t70) cc_final: 0.7872 (OUTLIER) REVERT: I 200 LYS cc_start: 0.7234 (ptpt) cc_final: 0.6742 (ptpt) REVERT: J 1 MET cc_start: 0.6208 (tpp) cc_final: 0.5668 (tpt) REVERT: J 26 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.5317 (p90) REVERT: L 1 MET cc_start: 0.5573 (tpt) cc_final: 0.5239 (tpp) REVERT: L 49 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7573 (mt-10) REVERT: L 100 ASP cc_start: 0.7683 (p0) cc_final: 0.7331 (p0) REVERT: L 132 ILE cc_start: 0.8133 (mt) cc_final: 0.7876 (mt) outliers start: 41 outliers final: 14 residues processed: 403 average time/residue: 0.5172 time to fit residues: 238.7284 Evaluate side-chains 332 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 316 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 71 optimal weight: 5.9990 chunk 22 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN C 173 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN G 193 GLN H 193 GLN I 193 GLN K 54 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.172524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141880 restraints weight = 23909.425| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.18 r_work: 0.3414 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21432 Z= 0.139 Angle : 0.639 11.744 29064 Z= 0.328 Chirality : 0.049 0.187 3144 Planarity : 0.005 0.086 3684 Dihedral : 5.793 47.154 2749 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.59 % Favored : 94.29 % Rotamer: Outliers : 2.79 % Allowed : 16.08 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.98 (0.16), residues: 2556 helix: 0.54 (0.18), residues: 843 sheet: -1.76 (0.28), residues: 340 loop : -1.09 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 194 TYR 0.024 0.002 TYR L 212 PHE 0.017 0.002 PHE D 33 TRP 0.014 0.001 TRP L 208 HIS 0.004 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00329 (21420) covalent geometry : angle 0.63927 (29064) hydrogen bonds : bond 0.03735 ( 797) hydrogen bonds : angle 5.65505 ( 2292) Misc. bond : bond 0.00034 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 363 time to evaluate : 0.584 Fit side-chains REVERT: A 63 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7782 (tt) REVERT: A 154 LYS cc_start: 0.7586 (mtpp) cc_final: 0.7341 (mttt) REVERT: B 55 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8153 (tptt) REVERT: B 56 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7977 (ptm160) REVERT: B 73 ASP cc_start: 0.7302 (m-30) cc_final: 0.6981 (m-30) REVERT: C 7 LYS cc_start: 0.6777 (tppt) cc_final: 0.6301 (tptt) REVERT: C 24 ASP cc_start: 0.7668 (p0) cc_final: 0.6859 (m-30) REVERT: C 91 GLU cc_start: 0.7544 (tp30) cc_final: 0.7300 (tp30) REVERT: D 14 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7273 (pttp) REVERT: D 192 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7566 (mmpt) REVERT: E 57 VAL cc_start: 0.8667 (p) cc_final: 0.8425 (t) REVERT: E 88 ASN cc_start: 0.8774 (m110) cc_final: 0.8536 (m-40) REVERT: F 73 ASP cc_start: 0.8173 (m-30) cc_final: 0.7807 (m-30) REVERT: F 87 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: G 49 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8088 (mt-10) REVERT: G 188 VAL cc_start: 0.7969 (t) cc_final: 0.7670 (m) REVERT: H 82 MET cc_start: 0.8368 (mtp) cc_final: 0.8162 (mtp) REVERT: H 192 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7531 (tptp) REVERT: I 92 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: I 104 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6803 (pt0) REVERT: I 178 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8112 (p0) REVERT: I 200 LYS cc_start: 0.7274 (ptpt) cc_final: 0.6693 (ptpt) REVERT: J 104 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7059 (mt-10) REVERT: J 192 LYS cc_start: 0.8106 (tmtt) cc_final: 0.7758 (tmmm) REVERT: L 49 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7664 (mt-10) REVERT: L 100 ASP cc_start: 0.7708 (p0) cc_final: 0.7384 (p0) outliers start: 62 outliers final: 30 residues processed: 402 average time/residue: 0.5145 time to fit residues: 237.8072 Evaluate side-chains 366 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 328 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 TYR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 192 LYS Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 181 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 80 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 223 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN C 173 ASN D 193 GLN G 173 ASN G 193 GLN H 193 GLN I 193 GLN L 193 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.169604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138270 restraints weight = 24081.401| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.20 r_work: 0.3365 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 21432 Z= 0.196 Angle : 0.661 11.753 29064 Z= 0.341 Chirality : 0.050 0.181 3144 Planarity : 0.005 0.091 3684 Dihedral : 5.842 49.844 2749 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 3.20 % Allowed : 17.88 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.00 (0.16), residues: 2556 helix: 0.55 (0.18), residues: 847 sheet: -1.72 (0.28), residues: 345 loop : -1.14 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 151 TYR 0.022 0.002 TYR I 25 PHE 0.019 0.002 PHE D 33 TRP 0.014 0.001 TRP L 208 HIS 0.006 0.001 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00474 (21420) covalent geometry : angle 0.66090 (29064) hydrogen bonds : bond 0.03830 ( 797) hydrogen bonds : angle 5.65482 ( 2292) Misc. bond : bond 0.00038 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 327 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7331 (pm20) cc_final: 0.6616 (pt0) REVERT: A 63 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7832 (tt) REVERT: A 154 LYS cc_start: 0.7766 (mtpp) cc_final: 0.7520 (mttt) REVERT: B 56 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8062 (ptm160) REVERT: B 73 ASP cc_start: 0.7378 (m-30) cc_final: 0.7102 (m-30) REVERT: B 74 GLN cc_start: 0.6776 (mm-40) cc_final: 0.6112 (mt0) REVERT: C 24 ASP cc_start: 0.7715 (p0) cc_final: 0.6899 (m-30) REVERT: C 74 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7292 (mp10) REVERT: D 7 LYS cc_start: 0.7849 (mmtt) cc_final: 0.7248 (mmmm) REVERT: D 14 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7267 (pttp) REVERT: D 192 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7644 (mmpt) REVERT: E 14 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7665 (mtpt) REVERT: E 87 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: E 88 ASN cc_start: 0.8817 (m110) cc_final: 0.8568 (m-40) REVERT: F 63 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8127 (tt) REVERT: F 73 ASP cc_start: 0.8215 (m-30) cc_final: 0.7586 (m-30) REVERT: F 87 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: G 49 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8031 (mt-10) REVERT: G 74 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: G 188 VAL cc_start: 0.7976 (t) cc_final: 0.7666 (m) REVERT: H 76 PHE cc_start: 0.8649 (t80) cc_final: 0.8324 (t80) REVERT: H 82 MET cc_start: 0.8385 (mtp) cc_final: 0.8167 (mtp) REVERT: H 193 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7253 (pt0) REVERT: I 92 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: I 104 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6857 (mm-30) REVERT: I 111 MET cc_start: 0.9013 (mtm) cc_final: 0.8759 (mtp) REVERT: I 200 LYS cc_start: 0.7278 (ptpt) cc_final: 0.6599 (ptpt) REVERT: I 207 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8020 (t0) REVERT: J 104 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7165 (mt-10) REVERT: J 192 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7658 (tmmm) REVERT: L 49 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7605 (mt-10) REVERT: L 100 ASP cc_start: 0.7630 (p0) cc_final: 0.7308 (p0) outliers start: 71 outliers final: 40 residues processed: 374 average time/residue: 0.4929 time to fit residues: 213.6581 Evaluate side-chains 361 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 181 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 237 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 178 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN G 193 GLN H 193 GLN I 193 GLN L 193 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.173148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.143090 restraints weight = 23459.275| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.95 r_work: 0.3420 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21432 Z= 0.168 Angle : 0.641 11.691 29064 Z= 0.328 Chirality : 0.049 0.202 3144 Planarity : 0.005 0.090 3684 Dihedral : 5.754 50.922 2749 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.83 % Favored : 94.05 % Rotamer: Outliers : 3.33 % Allowed : 19.32 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.89 (0.16), residues: 2556 helix: 0.68 (0.18), residues: 854 sheet: -1.74 (0.28), residues: 340 loop : -1.08 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 151 TYR 0.023 0.002 TYR I 25 PHE 0.018 0.002 PHE D 33 TRP 0.014 0.001 TRP L 208 HIS 0.005 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00403 (21420) covalent geometry : angle 0.64054 (29064) hydrogen bonds : bond 0.03640 ( 797) hydrogen bonds : angle 5.56792 ( 2292) Misc. bond : bond 0.00033 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 332 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7287 (pm20) cc_final: 0.7025 (mt0) REVERT: A 63 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7856 (tt) REVERT: A 154 LYS cc_start: 0.7731 (mtpp) cc_final: 0.7461 (mttt) REVERT: B 24 ASP cc_start: 0.3343 (OUTLIER) cc_final: 0.3040 (m-30) REVERT: B 56 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8034 (ptm160) REVERT: B 73 ASP cc_start: 0.7435 (m-30) cc_final: 0.7082 (m-30) REVERT: B 74 GLN cc_start: 0.6734 (mm-40) cc_final: 0.6121 (mt0) REVERT: C 7 LYS cc_start: 0.7265 (ttmt) cc_final: 0.6522 (tptt) REVERT: C 24 ASP cc_start: 0.7657 (p0) cc_final: 0.6818 (m-30) REVERT: C 74 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7397 (mp10) REVERT: D 7 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7341 (mmmm) REVERT: D 14 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7235 (pttp) REVERT: D 192 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7610 (mmpt) REVERT: E 14 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7647 (mtpt) REVERT: E 57 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8413 (t) REVERT: E 88 ASN cc_start: 0.8751 (m110) cc_final: 0.8467 (m-40) REVERT: F 12 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7312 (mm-30) REVERT: F 21 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.6231 (mmtp) REVERT: F 63 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8116 (tt) REVERT: F 73 ASP cc_start: 0.8090 (m-30) cc_final: 0.7613 (m-30) REVERT: F 87 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: G 49 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8027 (mt-10) REVERT: G 74 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.6931 (mp10) REVERT: G 188 VAL cc_start: 0.7925 (t) cc_final: 0.7618 (m) REVERT: H 76 PHE cc_start: 0.8635 (t80) cc_final: 0.8331 (t80) REVERT: H 82 MET cc_start: 0.8406 (mtp) cc_final: 0.8203 (mtp) REVERT: H 193 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7505 (pp30) REVERT: I 92 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: I 104 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6963 (mm-30) REVERT: I 200 LYS cc_start: 0.7193 (ptpt) cc_final: 0.6896 (pttt) REVERT: I 207 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.7951 (t0) REVERT: J 104 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7225 (mt-10) REVERT: J 192 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7679 (tmmm) REVERT: L 49 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7529 (mt-10) REVERT: L 129 LYS cc_start: 0.8086 (mppt) cc_final: 0.7762 (mptp) outliers start: 74 outliers final: 42 residues processed: 381 average time/residue: 0.4726 time to fit residues: 209.1969 Evaluate side-chains 367 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 309 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 78 HIS Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 181 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 86 optimal weight: 0.4980 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN G 173 ASN G 193 GLN H 193 GLN I 193 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.171910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141151 restraints weight = 23470.610| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.96 r_work: 0.3375 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 21432 Z= 0.199 Angle : 0.659 11.568 29064 Z= 0.337 Chirality : 0.050 0.184 3144 Planarity : 0.005 0.092 3684 Dihedral : 5.798 52.602 2749 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.06 % Favored : 93.82 % Rotamer: Outliers : 3.60 % Allowed : 20.14 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.96 (0.16), residues: 2556 helix: 0.58 (0.17), residues: 874 sheet: -1.80 (0.28), residues: 339 loop : -1.11 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 151 TYR 0.023 0.002 TYR I 25 PHE 0.021 0.002 PHE F 33 TRP 0.014 0.002 TRP F 32 HIS 0.004 0.001 HIS C 168 Details of bonding type rmsd covalent geometry : bond 0.00481 (21420) covalent geometry : angle 0.65901 (29064) hydrogen bonds : bond 0.03737 ( 797) hydrogen bonds : angle 5.59143 ( 2292) Misc. bond : bond 0.00038 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 333 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.5988 (tp30) cc_final: 0.5687 (mm-30) REVERT: A 29 GLN cc_start: 0.7337 (pm20) cc_final: 0.7081 (mt0) REVERT: A 63 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7904 (tt) REVERT: A 154 LYS cc_start: 0.7765 (mtpp) cc_final: 0.7530 (mttt) REVERT: B 56 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.8056 (ptm160) REVERT: B 73 ASP cc_start: 0.7529 (m-30) cc_final: 0.7146 (m-30) REVERT: B 74 GLN cc_start: 0.6852 (mm-40) cc_final: 0.6256 (mt0) REVERT: B 144 ARG cc_start: 0.8630 (mtm180) cc_final: 0.7911 (mtm180) REVERT: C 7 LYS cc_start: 0.7274 (ttmt) cc_final: 0.6500 (tptt) REVERT: C 24 ASP cc_start: 0.7701 (p0) cc_final: 0.6891 (m-30) REVERT: C 74 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: C 154 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8132 (mtmm) REVERT: D 7 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7366 (mmmm) REVERT: D 14 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7261 (pttp) REVERT: D 24 ASP cc_start: 0.7354 (p0) cc_final: 0.6250 (m-30) REVERT: D 192 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7657 (mmpt) REVERT: E 14 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7692 (mtpt) REVERT: E 57 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8437 (t) REVERT: E 88 ASN cc_start: 0.8759 (m110) cc_final: 0.8471 (m-40) REVERT: F 63 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8121 (tt) REVERT: F 73 ASP cc_start: 0.8213 (m-30) cc_final: 0.7717 (m-30) REVERT: F 87 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: G 49 GLU cc_start: 0.8844 (mt-10) cc_final: 0.7940 (mt-10) REVERT: G 74 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.6972 (mp10) REVERT: G 188 VAL cc_start: 0.8000 (t) cc_final: 0.7684 (m) REVERT: H 76 PHE cc_start: 0.8625 (t80) cc_final: 0.8295 (t80) REVERT: H 193 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7453 (pp30) REVERT: I 92 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: I 104 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7057 (mm-30) REVERT: I 200 LYS cc_start: 0.7167 (ptpt) cc_final: 0.6897 (pttt) REVERT: I 207 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.7999 (t0) REVERT: J 104 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7255 (mt-10) REVERT: J 192 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7690 (tmmm) REVERT: L 49 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7579 (mt-10) REVERT: L 129 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7507 (tppt) outliers start: 80 outliers final: 50 residues processed: 382 average time/residue: 0.4744 time to fit residues: 210.0609 Evaluate side-chains 379 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 314 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 193 GLN Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 181 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 141 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 98 optimal weight: 0.0020 chunk 62 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 201 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN H 193 GLN L 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.175136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144559 restraints weight = 23509.924| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.05 r_work: 0.3433 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21432 Z= 0.134 Angle : 0.624 11.622 29064 Z= 0.317 Chirality : 0.048 0.187 3144 Planarity : 0.004 0.087 3684 Dihedral : 5.599 52.110 2749 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.13 % Favored : 94.76 % Rotamer: Outliers : 3.38 % Allowed : 20.95 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.75 (0.17), residues: 2556 helix: 0.85 (0.18), residues: 874 sheet: -1.76 (0.28), residues: 334 loop : -1.04 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 56 TYR 0.030 0.002 TYR L 212 PHE 0.016 0.001 PHE J 33 TRP 0.014 0.001 TRP F 32 HIS 0.004 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00317 (21420) covalent geometry : angle 0.62376 (29064) hydrogen bonds : bond 0.03378 ( 797) hydrogen bonds : angle 5.46858 ( 2292) Misc. bond : bond 0.00025 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 346 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.7752 (mtpp) cc_final: 0.7494 (mttt) REVERT: B 56 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7988 (ptm160) REVERT: B 73 ASP cc_start: 0.7437 (m-30) cc_final: 0.7077 (m-30) REVERT: B 144 ARG cc_start: 0.8541 (mtm180) cc_final: 0.7988 (mtm180) REVERT: C 7 LYS cc_start: 0.7200 (ttmt) cc_final: 0.6495 (tptt) REVERT: C 10 GLU cc_start: 0.5986 (tp30) cc_final: 0.5782 (mm-30) REVERT: D 14 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7154 (pttp) REVERT: D 24 ASP cc_start: 0.7150 (p0) cc_final: 0.6130 (m-30) REVERT: D 192 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7593 (mmpt) REVERT: E 14 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7628 (mtpt) REVERT: E 57 VAL cc_start: 0.8656 (p) cc_final: 0.8406 (t) REVERT: E 59 GLN cc_start: 0.8532 (mt0) cc_final: 0.8190 (mt0) REVERT: F 63 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8024 (tt) REVERT: F 87 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: F 169 LYS cc_start: 0.8935 (tttp) cc_final: 0.8650 (tttp) REVERT: G 49 GLU cc_start: 0.8800 (mt-10) cc_final: 0.7861 (mt-10) REVERT: G 188 VAL cc_start: 0.7821 (t) cc_final: 0.7487 (m) REVERT: H 76 PHE cc_start: 0.8552 (t80) cc_final: 0.8255 (t80) REVERT: I 92 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: I 178 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7942 (p0) REVERT: I 200 LYS cc_start: 0.7154 (ptpt) cc_final: 0.6865 (pttt) REVERT: I 207 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.7955 (t0) REVERT: J 1 MET cc_start: 0.6331 (tpp) cc_final: 0.5718 (tpt) REVERT: J 104 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7192 (mt-10) REVERT: J 192 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7660 (tmmm) REVERT: L 49 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7495 (mt-10) REVERT: L 129 LYS cc_start: 0.8052 (mppt) cc_final: 0.7733 (mptp) REVERT: L 193 GLN cc_start: 0.5852 (mt0) cc_final: 0.5591 (mt0) outliers start: 75 outliers final: 41 residues processed: 394 average time/residue: 0.4767 time to fit residues: 217.3523 Evaluate side-chains 366 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 315 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 78 HIS Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 95 optimal weight: 2.9990 chunk 170 optimal weight: 0.0070 chunk 21 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 212 optimal weight: 0.0770 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN G 193 GLN H 193 GLN ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.174407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142736 restraints weight = 23506.278| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.19 r_work: 0.3420 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21432 Z= 0.154 Angle : 0.640 11.575 29064 Z= 0.323 Chirality : 0.049 0.187 3144 Planarity : 0.004 0.088 3684 Dihedral : 5.576 52.417 2749 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.56 % Favored : 94.33 % Rotamer: Outliers : 3.24 % Allowed : 22.39 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.69 (0.17), residues: 2556 helix: 0.90 (0.18), residues: 870 sheet: -1.70 (0.29), residues: 334 loop : -1.02 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 56 TYR 0.025 0.002 TYR A 25 PHE 0.018 0.002 PHE J 33 TRP 0.020 0.001 TRP F 32 HIS 0.004 0.001 HIS C 168 Details of bonding type rmsd covalent geometry : bond 0.00368 (21420) covalent geometry : angle 0.63977 (29064) hydrogen bonds : bond 0.03449 ( 797) hydrogen bonds : angle 5.45339 ( 2292) Misc. bond : bond 0.00029 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 326 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 119 THR cc_start: 0.8215 (p) cc_final: 0.7957 (p) REVERT: A 154 LYS cc_start: 0.7649 (mtpp) cc_final: 0.7424 (mttt) REVERT: A 176 ILE cc_start: 0.7731 (mm) cc_final: 0.7519 (mp) REVERT: B 56 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.8039 (ptm160) REVERT: B 73 ASP cc_start: 0.7427 (m-30) cc_final: 0.7031 (m-30) REVERT: B 144 ARG cc_start: 0.8594 (mtm180) cc_final: 0.8075 (mtm180) REVERT: C 7 LYS cc_start: 0.7208 (ttmt) cc_final: 0.6513 (tptt) REVERT: D 14 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7197 (pttp) REVERT: D 24 ASP cc_start: 0.7187 (p0) cc_final: 0.6199 (m-30) REVERT: D 49 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8004 (tt0) REVERT: D 111 MET cc_start: 0.6706 (ptp) cc_final: 0.6442 (ptp) REVERT: D 129 LYS cc_start: 0.7746 (mmpt) cc_final: 0.7507 (tptp) REVERT: D 192 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7617 (mmpt) REVERT: E 14 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7674 (mtpt) REVERT: E 57 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8401 (t) REVERT: E 59 GLN cc_start: 0.8600 (mt0) cc_final: 0.8338 (mt0) REVERT: F 87 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: F 169 LYS cc_start: 0.8959 (tttp) cc_final: 0.8689 (tttp) REVERT: G 49 GLU cc_start: 0.8812 (mt-10) cc_final: 0.7859 (mt-10) REVERT: G 188 VAL cc_start: 0.7867 (t) cc_final: 0.7583 (m) REVERT: H 76 PHE cc_start: 0.8560 (t80) cc_final: 0.8259 (t80) REVERT: H 192 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7497 (tptp) REVERT: I 92 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: I 104 GLU cc_start: 0.7341 (pt0) cc_final: 0.6784 (mm-30) REVERT: I 178 ASP cc_start: 0.8186 (p0) cc_final: 0.7962 (p0) REVERT: I 200 LYS cc_start: 0.7139 (ptpt) cc_final: 0.6879 (pttt) REVERT: I 207 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8003 (t0) REVERT: J 87 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: J 104 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7209 (mt-10) REVERT: J 192 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7684 (tmmm) REVERT: L 49 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7562 (mt-10) REVERT: L 112 ILE cc_start: 0.3117 (OUTLIER) cc_final: 0.2854 (tp) REVERT: L 129 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7709 (mptp) outliers start: 72 outliers final: 45 residues processed: 371 average time/residue: 0.4720 time to fit residues: 202.8783 Evaluate side-chains 364 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 306 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 192 LYS Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 78 HIS Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 153 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 123 optimal weight: 0.0980 chunk 137 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN H 193 GLN ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.176473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144814 restraints weight = 23444.486| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.21 r_work: 0.3437 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21432 Z= 0.134 Angle : 0.635 11.858 29064 Z= 0.320 Chirality : 0.049 0.251 3144 Planarity : 0.004 0.087 3684 Dihedral : 5.469 52.176 2749 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.16 % Favored : 94.72 % Rotamer: Outliers : 3.06 % Allowed : 22.84 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.63 (0.17), residues: 2556 helix: 1.01 (0.18), residues: 876 sheet: -1.67 (0.28), residues: 354 loop : -1.00 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 151 TYR 0.026 0.002 TYR I 25 PHE 0.016 0.001 PHE J 33 TRP 0.025 0.001 TRP B 81 HIS 0.004 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00317 (21420) covalent geometry : angle 0.63498 (29064) hydrogen bonds : bond 0.03298 ( 797) hydrogen bonds : angle 5.39067 ( 2292) Misc. bond : bond 0.00025 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 330 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 119 THR cc_start: 0.8164 (p) cc_final: 0.7949 (p) REVERT: A 154 LYS cc_start: 0.7649 (mtpp) cc_final: 0.7401 (mttt) REVERT: A 176 ILE cc_start: 0.7694 (mm) cc_final: 0.7476 (mp) REVERT: B 73 ASP cc_start: 0.7359 (m-30) cc_final: 0.6974 (m-30) REVERT: B 144 ARG cc_start: 0.8566 (mtm180) cc_final: 0.8083 (mtm180) REVERT: B 192 LYS cc_start: 0.8129 (mmtp) cc_final: 0.7643 (mttp) REVERT: C 12 GLU cc_start: 0.7285 (tp30) cc_final: 0.7053 (mm-30) REVERT: C 21 LYS cc_start: 0.6623 (ttmm) cc_final: 0.6368 (ttmt) REVERT: D 7 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7704 (mmtt) REVERT: D 14 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7242 (ttpm) REVERT: D 24 ASP cc_start: 0.7192 (p0) cc_final: 0.6197 (m-30) REVERT: D 49 GLU cc_start: 0.8632 (mt-10) cc_final: 0.7975 (tt0) REVERT: D 192 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7603 (mmpt) REVERT: E 57 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8407 (t) REVERT: E 59 GLN cc_start: 0.8578 (mt0) cc_final: 0.8238 (mt0) REVERT: F 1 MET cc_start: 0.6453 (mmp) cc_final: 0.5977 (tpp) REVERT: F 87 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: F 169 LYS cc_start: 0.8925 (tttp) cc_final: 0.8664 (tttp) REVERT: G 49 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8042 (mt-10) REVERT: G 74 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7003 (mp10) REVERT: G 188 VAL cc_start: 0.7761 (t) cc_final: 0.7442 (m) REVERT: H 76 PHE cc_start: 0.8492 (t80) cc_final: 0.8214 (t80) REVERT: I 92 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: I 104 GLU cc_start: 0.7321 (pt0) cc_final: 0.6753 (mm-30) REVERT: I 111 MET cc_start: 0.8873 (mtm) cc_final: 0.8604 (mtp) REVERT: I 207 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8003 (t0) REVERT: J 1 MET cc_start: 0.6387 (tpp) cc_final: 0.5752 (tpt) REVERT: J 86 LYS cc_start: 0.8328 (ttmt) cc_final: 0.7945 (tptt) REVERT: J 87 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: J 104 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7101 (mt-10) REVERT: J 192 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7690 (tmmm) REVERT: L 49 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7401 (mt-10) REVERT: L 112 ILE cc_start: 0.2868 (OUTLIER) cc_final: 0.2597 (tp) REVERT: L 129 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7668 (mptp) outliers start: 68 outliers final: 45 residues processed: 373 average time/residue: 0.4748 time to fit residues: 205.7139 Evaluate side-chains 369 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 313 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 73 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN G 193 GLN H 193 GLN ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 GLN L 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.171150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.139096 restraints weight = 23644.629| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.21 r_work: 0.3369 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 21432 Z= 0.242 Angle : 0.711 11.191 29064 Z= 0.363 Chirality : 0.052 0.224 3144 Planarity : 0.005 0.091 3684 Dihedral : 5.788 54.551 2749 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.06 % Favored : 93.82 % Rotamer: Outliers : 2.75 % Allowed : 23.51 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.92 (0.16), residues: 2556 helix: 0.55 (0.17), residues: 888 sheet: -1.69 (0.28), residues: 337 loop : -1.08 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 194 TYR 0.025 0.002 TYR I 25 PHE 0.022 0.002 PHE F 33 TRP 0.031 0.002 TRP B 81 HIS 0.005 0.002 HIS C 168 Details of bonding type rmsd covalent geometry : bond 0.00588 (21420) covalent geometry : angle 0.71126 (29064) hydrogen bonds : bond 0.03889 ( 797) hydrogen bonds : angle 5.60704 ( 2292) Misc. bond : bond 0.00052 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 312 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7560 (mttt) REVERT: B 56 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7420 (ptm160) REVERT: B 73 ASP cc_start: 0.7453 (m-30) cc_final: 0.7063 (m-30) REVERT: B 144 ARG cc_start: 0.8682 (mtm180) cc_final: 0.8004 (mtm180) REVERT: B 192 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7731 (mttp) REVERT: C 7 LYS cc_start: 0.7298 (ttmt) cc_final: 0.6521 (tptt) REVERT: C 12 GLU cc_start: 0.7346 (tp30) cc_final: 0.7058 (mm-30) REVERT: C 21 LYS cc_start: 0.6769 (ttmm) cc_final: 0.6286 (ttpt) REVERT: D 24 ASP cc_start: 0.7300 (p0) cc_final: 0.6302 (m-30) REVERT: D 192 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7652 (mmpt) REVERT: E 57 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8380 (t) REVERT: F 87 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: F 125 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8700 (mm) REVERT: F 204 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7367 (mp0) REVERT: G 49 GLU cc_start: 0.8864 (mt-10) cc_final: 0.7929 (mt-10) REVERT: G 188 VAL cc_start: 0.7877 (t) cc_final: 0.7600 (m) REVERT: H 76 PHE cc_start: 0.8639 (t80) cc_final: 0.8327 (t80) REVERT: I 92 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: I 104 GLU cc_start: 0.7379 (pt0) cc_final: 0.6905 (mm-30) REVERT: I 200 LYS cc_start: 0.7106 (ptpt) cc_final: 0.6870 (pttt) REVERT: J 87 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: J 104 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7251 (mt-10) REVERT: J 192 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7693 (tmmm) REVERT: L 49 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7480 (mt-10) REVERT: L 112 ILE cc_start: 0.2904 (OUTLIER) cc_final: 0.2684 (tp) REVERT: L 129 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7484 (tppt) outliers start: 61 outliers final: 42 residues processed: 355 average time/residue: 0.4982 time to fit residues: 204.0093 Evaluate side-chains 351 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 299 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 136 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN B 38 HIS ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN G 193 GLN H 193 GLN ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 GLN L 74 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.175516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.143984 restraints weight = 23448.228| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.14 r_work: 0.3433 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21432 Z= 0.143 Angle : 0.655 11.575 29064 Z= 0.331 Chirality : 0.049 0.214 3144 Planarity : 0.004 0.087 3684 Dihedral : 5.567 54.188 2749 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.44 % Favored : 94.44 % Rotamer: Outliers : 2.48 % Allowed : 24.32 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.73 (0.17), residues: 2556 helix: 0.90 (0.18), residues: 874 sheet: -1.75 (0.28), residues: 346 loop : -1.04 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.025 0.002 TYR I 25 PHE 0.016 0.001 PHE L 33 TRP 0.032 0.001 TRP B 81 HIS 0.006 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00341 (21420) covalent geometry : angle 0.65465 (29064) hydrogen bonds : bond 0.03364 ( 797) hydrogen bonds : angle 5.44431 ( 2292) Misc. bond : bond 0.00030 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7252.78 seconds wall clock time: 124 minutes 16.69 seconds (7456.69 seconds total)