Starting phenix.real_space_refine on Wed Jun 18 04:44:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hla_34859/06_2025/8hla_34859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hla_34859/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hla_34859/06_2025/8hla_34859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hla_34859/06_2025/8hla_34859.map" model { file = "/net/cci-nas-00/data/ceres_data/8hla_34859/06_2025/8hla_34859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hla_34859/06_2025/8hla_34859.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.16, per 1000 atoms: 0.63 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: 5.23 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.66 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: 6.43 Time building geometry restraints manager: 6.13 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: 0.02 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: 3.320 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: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 47.760 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.080 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:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.250 ------------------------------------------------------------------------------- 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 : 19.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.066 0.003 TRP G 32 HIS 0.021 0.003 HIS D 78 PHE 0.119 0.004 PHE J 26 TYR 0.027 0.003 TYR A 212 ARG 0.007 0.001 ARG K 61 Details of bonding type rmsd hydrogen bonds : bond 0.18104 ( 797) hydrogen bonds : angle 8.66657 ( 2292) covalent geometry : bond 0.01067 (21420) covalent geometry : angle 0.95549 (29064) 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 : 2.491 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: 1.3100 time to fit residues: 616.6326 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 : 2.307 ------------------------------------------------------------------------------- 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 212 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 G 193 GLN H 193 GLN I 17 HIS K 29 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 = 0.170893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140107 restraints weight = 23870.365| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.09 r_work: 0.3413 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21432 Z= 0.160 Angle : 0.698 13.061 29064 Z= 0.361 Chirality : 0.051 0.182 3144 Planarity : 0.005 0.093 3684 Dihedral : 6.163 47.592 2749 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.40 % Favored : 94.48 % Rotamer: Outliers : 1.80 % Allowed : 12.34 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.16), residues: 2556 helix: -0.13 (0.17), residues: 858 sheet: -1.71 (0.28), residues: 345 loop : -1.29 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 32 HIS 0.007 0.001 HIS D 78 PHE 0.018 0.002 PHE C 210 TYR 0.022 0.002 TYR L 212 ARG 0.006 0.001 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 797) hydrogen bonds : angle 6.07743 ( 2292) covalent geometry : bond 0.00378 (21420) covalent geometry : angle 0.69812 (29064) Misc. bond : bond 0.00049 ( 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 422 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 382 time to evaluate : 2.234 Fit side-chains REVERT: A 63 LEU cc_start: 0.7861 (tt) cc_final: 0.7576 (mp) REVERT: A 154 LYS cc_start: 0.7710 (mtpp) cc_final: 0.7456 (mttt) REVERT: B 53 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7077 (tpp) REVERT: C 7 LYS cc_start: 0.6895 (tppt) cc_final: 0.6360 (tptt) REVERT: C 24 ASP cc_start: 0.7714 (p0) cc_final: 0.6995 (m-30) REVERT: D 4 ILE cc_start: 0.8069 (mm) cc_final: 0.7754 (mm) REVERT: D 108 LYS cc_start: 0.7544 (mptt) cc_final: 0.7241 (mmtp) REVERT: D 192 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7630 (mmpt) REVERT: E 88 ASN cc_start: 0.8809 (m110) cc_final: 0.8580 (m-40) REVERT: F 7 LYS cc_start: 0.7754 (mmmt) cc_final: 0.7506 (tptp) REVERT: G 49 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8008 (mt-10) REVERT: G 188 VAL cc_start: 0.7920 (t) cc_final: 0.7661 (m) REVERT: H 82 MET cc_start: 0.8443 (mtp) cc_final: 0.8233 (mtp) REVERT: I 100 ASP cc_start: 0.8277 (t70) cc_final: 0.7914 (OUTLIER) REVERT: I 200 LYS cc_start: 0.7252 (ptpt) cc_final: 0.6772 (ptpt) REVERT: L 1 MET cc_start: 0.5588 (tpt) cc_final: 0.5313 (tpp) REVERT: L 49 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7527 (mt-10) REVERT: L 100 ASP cc_start: 0.7711 (p0) cc_final: 0.7358 (p0) REVERT: L 132 ILE cc_start: 0.8143 (mt) cc_final: 0.7915 (mt) outliers start: 40 outliers final: 15 residues processed: 406 average time/residue: 1.2346 time to fit residues: 574.4230 Evaluate side-chains 336 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 320 time to evaluate : 2.456 ------------------------------------------------------------------------------- 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 221 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 157 optimal weight: 0.2980 chunk 216 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 ASN G 173 ASN G 193 GLN H 193 GLN I 193 GLN L 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.168779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137532 restraints weight = 23824.158| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.20 r_work: 0.3369 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 21432 Z= 0.202 Angle : 0.682 11.707 29064 Z= 0.353 Chirality : 0.051 0.186 3144 Planarity : 0.005 0.094 3684 Dihedral : 6.056 47.985 2749 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.22 % Favored : 93.66 % Rotamer: Outliers : 3.33 % Allowed : 15.86 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.16), residues: 2556 helix: 0.20 (0.17), residues: 848 sheet: -1.76 (0.28), residues: 345 loop : -1.21 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 208 HIS 0.007 0.001 HIS D 78 PHE 0.020 0.002 PHE D 33 TYR 0.023 0.002 TYR L 212 ARG 0.004 0.000 ARG H 144 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 797) hydrogen bonds : angle 5.83466 ( 2292) covalent geometry : bond 0.00489 (21420) covalent geometry : angle 0.68174 (29064) Misc. bond : bond 0.00047 ( 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 421 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 347 time to evaluate : 2.345 Fit side-chains REVERT: A 63 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7601 (tt) REVERT: A 154 LYS cc_start: 0.7737 (mtpp) cc_final: 0.7501 (mttt) REVERT: B 53 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7535 (tpp) REVERT: B 56 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8140 (ptm160) REVERT: B 73 ASP cc_start: 0.7373 (m-30) cc_final: 0.7137 (m-30) REVERT: C 24 ASP cc_start: 0.7730 (p0) cc_final: 0.6957 (m-30) REVERT: C 74 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: D 14 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7316 (pttp) REVERT: D 192 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7637 (mmpt) REVERT: E 14 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7664 (mtpt) REVERT: E 88 ASN cc_start: 0.8806 (m110) cc_final: 0.8576 (m-40) REVERT: F 87 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: G 49 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8084 (mt-10) REVERT: G 188 VAL cc_start: 0.8024 (t) cc_final: 0.7736 (m) REVERT: H 192 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7541 (tptp) REVERT: I 92 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: I 178 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8260 (p0) REVERT: I 200 LYS cc_start: 0.7278 (ptpt) cc_final: 0.6693 (ptpt) REVERT: J 104 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7175 (mt-10) REVERT: L 1 MET cc_start: 0.5689 (tpt) cc_final: 0.5415 (tpp) REVERT: L 49 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7719 (mt-10) REVERT: L 100 ASP cc_start: 0.7717 (p0) cc_final: 0.7375 (p0) REVERT: L 129 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7609 (tppt) outliers start: 74 outliers final: 33 residues processed: 392 average time/residue: 1.1627 time to fit residues: 526.4260 Evaluate side-chains 359 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 314 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 53 MET 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 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 14 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 F residue 136 VAL Chi-restraints excluded: chain G residue 42 CYS 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 136 VAL Chi-restraints excluded: chain H residue 192 LYS 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 118 ILE 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 43 THR Chi-restraints excluded: chain L residue 73 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 238 optimal weight: 5.9990 chunk 37 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 ASN D 193 GLN G 193 GLN H 193 GLN I 193 GLN L 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.171013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139596 restraints weight = 24019.017| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.13 r_work: 0.3366 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21432 Z= 0.156 Angle : 0.646 11.928 29064 Z= 0.331 Chirality : 0.049 0.187 3144 Planarity : 0.005 0.090 3684 Dihedral : 5.833 48.446 2749 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.59 % Favored : 94.29 % Rotamer: Outliers : 3.60 % Allowed : 17.70 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 2556 helix: 0.58 (0.18), residues: 853 sheet: -1.78 (0.28), residues: 340 loop : -1.14 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 208 HIS 0.004 0.001 HIS B 168 PHE 0.017 0.002 PHE D 33 TYR 0.025 0.002 TYR L 212 ARG 0.004 0.000 ARG G 151 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 797) hydrogen bonds : angle 5.60336 ( 2292) covalent geometry : bond 0.00375 (21420) covalent geometry : angle 0.64552 (29064) Misc. bond : bond 0.00031 ( 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 441 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 361 time to evaluate : 2.501 Fit side-chains REVERT: A 29 GLN cc_start: 0.7317 (pm20) cc_final: 0.6968 (mt0) REVERT: A 63 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7779 (tt) REVERT: A 154 LYS cc_start: 0.7669 (mtpp) cc_final: 0.7399 (mttt) REVERT: B 24 ASP cc_start: 0.3402 (OUTLIER) cc_final: 0.3083 (m-30) REVERT: B 56 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7988 (ptm160) REVERT: B 73 ASP cc_start: 0.7286 (m-30) cc_final: 0.6986 (m-30) REVERT: C 7 LYS cc_start: 0.7269 (ttmt) cc_final: 0.6515 (tptt) REVERT: C 24 ASP cc_start: 0.7651 (p0) cc_final: 0.6836 (m-30) REVERT: C 74 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7259 (mp10) REVERT: D 14 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7153 (pttp) REVERT: D 192 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7565 (mmpt) REVERT: E 14 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7632 (mtpt) REVERT: E 57 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8385 (t) REVERT: E 88 ASN cc_start: 0.8810 (m110) cc_final: 0.8550 (m-40) REVERT: F 7 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7573 (tptp) REVERT: F 63 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8034 (tt) REVERT: F 73 ASP cc_start: 0.8046 (m-30) cc_final: 0.7445 (m-30) REVERT: F 87 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: G 49 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8038 (mt-10) REVERT: G 188 VAL cc_start: 0.7919 (t) cc_final: 0.7606 (m) REVERT: H 76 PHE cc_start: 0.8589 (t80) cc_final: 0.8251 (t80) REVERT: I 92 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: I 111 MET cc_start: 0.9004 (mtm) cc_final: 0.8654 (mtp) REVERT: I 200 LYS cc_start: 0.7254 (ptpt) cc_final: 0.6918 (pttt) REVERT: J 73 ASP cc_start: 0.7790 (m-30) cc_final: 0.7444 (m-30) REVERT: J 104 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7055 (mt-10) REVERT: J 192 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7666 (tmmm) REVERT: L 49 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7696 (mt-10) REVERT: L 100 ASP cc_start: 0.7624 (p0) cc_final: 0.7264 (p0) outliers start: 80 outliers final: 44 residues processed: 407 average time/residue: 1.1437 time to fit residues: 541.1244 Evaluate side-chains 370 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 314 time to evaluate : 2.168 ------------------------------------------------------------------------------- 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 187 THR 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 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 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 F residue 136 VAL Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS 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 186 SER 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 118 ILE 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 47 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 158 optimal weight: 0.2980 chunk 92 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN G 173 ASN G 193 GLN H 193 GLN I 193 GLN L 74 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 = 0.3913 r_free = 0.3913 target = 0.175424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144290 restraints weight = 23607.490| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.12 r_work: 0.3451 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21432 Z= 0.133 Angle : 0.624 11.819 29064 Z= 0.318 Chirality : 0.048 0.191 3144 Planarity : 0.004 0.085 3684 Dihedral : 5.634 49.040 2749 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.40 % Favored : 94.48 % Rotamer: Outliers : 3.20 % Allowed : 20.14 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2556 helix: 0.82 (0.18), residues: 878 sheet: -1.74 (0.28), residues: 345 loop : -1.09 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 32 HIS 0.004 0.001 HIS B 168 PHE 0.016 0.001 PHE D 33 TYR 0.027 0.002 TYR L 212 ARG 0.003 0.000 ARG G 151 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 797) hydrogen bonds : angle 5.46975 ( 2292) covalent geometry : bond 0.00313 (21420) covalent geometry : angle 0.62371 (29064) Misc. bond : bond 0.00025 ( 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 417 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 346 time to evaluate : 2.343 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7242 (pm20) cc_final: 0.7017 (mt0) REVERT: A 63 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7925 (tt) REVERT: A 119 THR cc_start: 0.8169 (p) cc_final: 0.7869 (p) REVERT: A 154 LYS cc_start: 0.7732 (mtpp) cc_final: 0.7464 (mttt) REVERT: B 73 ASP cc_start: 0.7343 (m-30) cc_final: 0.6990 (m-30) REVERT: B 74 GLN cc_start: 0.6689 (mm-40) cc_final: 0.6074 (mt0) REVERT: C 7 LYS cc_start: 0.7177 (ttmt) cc_final: 0.6474 (tptt) REVERT: C 24 ASP cc_start: 0.7654 (p0) cc_final: 0.6830 (m-30) REVERT: D 4 ILE cc_start: 0.8092 (mm) cc_final: 0.7759 (mm) REVERT: D 14 LYS cc_start: 0.7602 (mtpt) cc_final: 0.7188 (pttp) REVERT: D 129 LYS cc_start: 0.7713 (mmpt) cc_final: 0.7472 (tptp) REVERT: D 187 THR cc_start: 0.8397 (m) cc_final: 0.8154 (p) REVERT: D 192 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7623 (mmpt) REVERT: E 57 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8442 (t) REVERT: E 88 ASN cc_start: 0.8715 (m110) cc_final: 0.8441 (m-40) REVERT: F 12 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7254 (mm-30) REVERT: F 73 ASP cc_start: 0.8132 (m-30) cc_final: 0.7870 (m-30) REVERT: F 87 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: G 49 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8065 (mt-10) REVERT: G 188 VAL cc_start: 0.7852 (t) cc_final: 0.7541 (m) REVERT: H 76 PHE cc_start: 0.8595 (t80) cc_final: 0.8263 (t80) REVERT: H 193 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7261 (pt0) REVERT: I 92 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: I 200 LYS cc_start: 0.7177 (ptpt) cc_final: 0.6860 (pttt) REVERT: J 73 ASP cc_start: 0.7793 (m-30) cc_final: 0.7398 (m-30) REVERT: J 104 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7185 (mt-10) REVERT: J 192 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7755 (tmmm) REVERT: K 86 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6618 (tptp) REVERT: L 49 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7553 (mt-10) REVERT: L 129 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7716 (mptp) outliers start: 71 outliers final: 42 residues processed: 386 average time/residue: 1.1235 time to fit residues: 503.4469 Evaluate side-chains 368 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 2.201 ------------------------------------------------------------------------------- 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 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 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 E residue 164 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 136 VAL Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS 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 207 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 128 ASP 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 86 LYS Chi-restraints excluded: chain K residue 112 ILE 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 129 LYS Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 118 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 187 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 79 optimal weight: 0.0170 chunk 139 optimal weight: 6.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN G 193 GLN H 193 GLN ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 GLN 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 = 0.176487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.145642 restraints weight = 23386.736| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.01 r_work: 0.3457 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21432 Z= 0.128 Angle : 0.611 11.690 29064 Z= 0.311 Chirality : 0.048 0.191 3144 Planarity : 0.004 0.083 3684 Dihedral : 5.486 48.941 2749 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.20 % Favored : 94.68 % Rotamer: Outliers : 3.29 % Allowed : 20.77 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2556 helix: 0.98 (0.18), residues: 874 sheet: -1.73 (0.28), residues: 339 loop : -1.01 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 32 HIS 0.004 0.001 HIS B 168 PHE 0.016 0.001 PHE F 33 TYR 0.028 0.002 TYR L 212 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 797) hydrogen bonds : angle 5.38339 ( 2292) covalent geometry : bond 0.00301 (21420) covalent geometry : angle 0.61103 (29064) Misc. bond : bond 0.00024 ( 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 431 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 358 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7313 (pm20) cc_final: 0.7063 (mt0) REVERT: A 119 THR cc_start: 0.8146 (p) cc_final: 0.7890 (p) REVERT: A 154 LYS cc_start: 0.7740 (mtpp) cc_final: 0.7468 (mttt) REVERT: B 56 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7178 (ptm160) REVERT: B 73 ASP cc_start: 0.7420 (m-30) cc_final: 0.7056 (m-30) REVERT: B 192 LYS cc_start: 0.7970 (mmtp) cc_final: 0.7534 (mttp) REVERT: C 7 LYS cc_start: 0.7144 (ttmt) cc_final: 0.6472 (tptt) REVERT: C 10 GLU cc_start: 0.5649 (tp30) cc_final: 0.5428 (mm-30) REVERT: C 74 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: D 14 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7194 (pttp) REVERT: D 24 ASP cc_start: 0.7133 (p0) cc_final: 0.6114 (m-30) REVERT: D 192 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7598 (mmpt) REVERT: E 57 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8420 (t) REVERT: E 59 GLN cc_start: 0.8523 (mt0) cc_final: 0.8207 (mt0) REVERT: F 73 ASP cc_start: 0.8018 (m-30) cc_final: 0.7380 (m-30) REVERT: F 87 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: F 169 LYS cc_start: 0.8973 (tttp) cc_final: 0.8674 (tttp) REVERT: G 49 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8020 (mt-10) REVERT: G 188 VAL cc_start: 0.7758 (t) cc_final: 0.7412 (m) REVERT: H 76 PHE cc_start: 0.8513 (t80) cc_final: 0.8174 (t80) REVERT: H 108 LYS cc_start: 0.8188 (mttp) cc_final: 0.7167 (mmtm) REVERT: H 193 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7289 (pt0) REVERT: I 92 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: I 200 LYS cc_start: 0.7117 (ptpt) cc_final: 0.6833 (pttt) REVERT: J 73 ASP cc_start: 0.7715 (m-30) cc_final: 0.7314 (m-30) REVERT: J 86 LYS cc_start: 0.8332 (ttmt) cc_final: 0.7910 (tptt) REVERT: J 104 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7162 (mt-10) REVERT: J 192 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7688 (tmmm) REVERT: K 86 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6601 (tptp) REVERT: L 49 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7468 (mt-10) REVERT: L 129 LYS cc_start: 0.7973 (mppt) cc_final: 0.7697 (mptp) outliers start: 73 outliers final: 47 residues processed: 404 average time/residue: 1.1458 time to fit residues: 535.7722 Evaluate side-chains 372 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 315 time to evaluate : 2.332 ------------------------------------------------------------------------------- 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 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 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 164 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 136 VAL Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 78 HIS 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 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 118 ILE 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 J residue 207 ASP Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 196 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 18 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 220 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 0.0040 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 ASN G 193 GLN H 193 GLN ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 GLN L 193 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.177161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.146614 restraints weight = 23399.094| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.01 r_work: 0.3473 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2566 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= 0.128 Angle : 0.624 11.584 29064 Z= 0.315 Chirality : 0.048 0.193 3144 Planarity : 0.004 0.082 3684 Dihedral : 5.426 49.198 2749 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.28 % Favored : 94.60 % Rotamer: Outliers : 3.60 % Allowed : 21.40 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2556 helix: 1.08 (0.18), residues: 876 sheet: -1.72 (0.28), residues: 334 loop : -0.95 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 32 HIS 0.004 0.001 HIS B 168 PHE 0.016 0.001 PHE J 33 TYR 0.025 0.001 TYR L 212 ARG 0.003 0.000 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 797) hydrogen bonds : angle 5.35427 ( 2292) covalent geometry : bond 0.00302 (21420) covalent geometry : angle 0.62405 (29064) Misc. bond : bond 0.00023 ( 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 409 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 329 time to evaluate : 2.475 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7311 (pm20) cc_final: 0.7048 (mt0) REVERT: A 119 THR cc_start: 0.8070 (p) cc_final: 0.7843 (p) REVERT: A 154 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7351 (mttt) REVERT: B 24 ASP cc_start: 0.3163 (OUTLIER) cc_final: 0.2963 (m-30) REVERT: B 73 ASP cc_start: 0.7332 (m-30) cc_final: 0.7021 (m-30) REVERT: B 144 ARG cc_start: 0.8576 (mtm180) cc_final: 0.7810 (mtm180) REVERT: B 192 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7559 (mttp) REVERT: C 7 LYS cc_start: 0.7143 (ttmt) cc_final: 0.6483 (tptt) REVERT: C 74 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: C 215 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6610 (mt) REVERT: D 14 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7166 (pttp) REVERT: D 24 ASP cc_start: 0.7147 (p0) cc_final: 0.6137 (m-30) REVERT: D 111 MET cc_start: 0.6708 (ptp) cc_final: 0.6328 (ptp) REVERT: D 192 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7583 (mmpt) REVERT: E 57 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8411 (t) REVERT: E 59 GLN cc_start: 0.8506 (mt0) cc_final: 0.8206 (mt0) REVERT: F 87 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: F 169 LYS cc_start: 0.8959 (tttp) cc_final: 0.8667 (tttp) REVERT: G 49 GLU cc_start: 0.8815 (mt-10) cc_final: 0.7953 (mt-10) REVERT: G 188 VAL cc_start: 0.7709 (t) cc_final: 0.7429 (m) REVERT: H 76 PHE cc_start: 0.8485 (t80) cc_final: 0.8196 (t80) REVERT: I 92 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: I 111 MET cc_start: 0.8867 (mtm) cc_final: 0.8587 (mtp) REVERT: I 178 ASP cc_start: 0.8097 (p0) cc_final: 0.7880 (p0) REVERT: J 1 MET cc_start: 0.6336 (tpp) cc_final: 0.5637 (tpt) REVERT: J 73 ASP cc_start: 0.7705 (m-30) cc_final: 0.7284 (m-30) REVERT: J 86 LYS cc_start: 0.8311 (ttmt) cc_final: 0.7884 (tptt) REVERT: J 104 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7160 (mt-10) REVERT: J 192 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7694 (tmmm) REVERT: K 86 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6886 (tptp) REVERT: L 49 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7442 (mt-10) REVERT: L 56 ARG cc_start: 0.8195 (ptp-170) cc_final: 0.7994 (ptp-170) REVERT: L 129 LYS cc_start: 0.7951 (mppt) cc_final: 0.7671 (mptp) outliers start: 80 outliers final: 48 residues processed: 381 average time/residue: 1.1460 time to fit residues: 509.3116 Evaluate side-chains 373 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 314 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 20 ILE Chi-restraints excluded: chain B residue 24 ASP 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 B residue 192 LYS 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 215 LEU 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 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 34 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS 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 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 118 ILE Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain J residue 207 ASP Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 196 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 141 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 152 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN H 193 GLN ** I 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 GLN K 54 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 = 0.3866 r_free = 0.3866 target = 0.170854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138498 restraints weight = 23637.697| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.21 r_work: 0.3354 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 21432 Z= 0.250 Angle : 0.701 11.226 29064 Z= 0.358 Chirality : 0.052 0.190 3144 Planarity : 0.005 0.089 3684 Dihedral : 5.811 52.500 2749 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.18 % Favored : 93.70 % Rotamer: Outliers : 3.60 % Allowed : 21.94 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2556 helix: 0.55 (0.17), residues: 892 sheet: -1.72 (0.28), residues: 342 loop : -1.10 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 32 HIS 0.006 0.002 HIS L 38 PHE 0.022 0.002 PHE F 33 TYR 0.025 0.002 TYR I 25 ARG 0.007 0.001 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 797) hydrogen bonds : angle 5.60249 ( 2292) covalent geometry : bond 0.00608 (21420) covalent geometry : angle 0.70064 (29064) Misc. bond : bond 0.00054 ( 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 405 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 325 time to evaluate : 2.139 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7297 (pm20) cc_final: 0.7081 (mt0) REVERT: A 154 LYS cc_start: 0.7788 (mtpp) cc_final: 0.7534 (mttt) REVERT: B 24 ASP cc_start: 0.3592 (OUTLIER) cc_final: 0.3279 (m-30) REVERT: B 73 ASP cc_start: 0.7499 (m-30) cc_final: 0.7114 (m-30) REVERT: C 154 LYS cc_start: 0.8383 (mtpt) cc_final: 0.8181 (mtmm) REVERT: D 24 ASP cc_start: 0.7324 (p0) cc_final: 0.6280 (m-30) REVERT: D 55 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8617 (mttm) REVERT: D 192 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7639 (mmpt) REVERT: E 57 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8341 (t) REVERT: E 59 GLN cc_start: 0.8746 (mt0) cc_final: 0.8470 (mt0) REVERT: F 87 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: G 49 GLU cc_start: 0.8867 (mt-10) cc_final: 0.7959 (mt-10) REVERT: G 188 VAL cc_start: 0.7917 (t) cc_final: 0.7607 (m) REVERT: H 65 VAL cc_start: 0.8643 (t) cc_final: 0.8430 (p) REVERT: H 76 PHE cc_start: 0.8635 (t80) cc_final: 0.8319 (t80) REVERT: I 92 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: I 104 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6870 (pt0) REVERT: I 178 ASP cc_start: 0.8310 (p0) cc_final: 0.8076 (p0) REVERT: I 200 LYS cc_start: 0.7103 (ptpt) cc_final: 0.6873 (pttt) REVERT: J 73 ASP cc_start: 0.7949 (m-30) cc_final: 0.7596 (m-30) REVERT: J 87 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: J 104 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7255 (mt-10) REVERT: J 192 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7713 (tmmm) REVERT: K 86 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.6953 (tptp) REVERT: L 49 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7540 (mt-10) REVERT: L 112 ILE cc_start: 0.2945 (OUTLIER) cc_final: 0.2693 (tp) outliers start: 80 outliers final: 50 residues processed: 378 average time/residue: 1.1383 time to fit residues: 497.4164 Evaluate side-chains 369 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 309 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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 24 ASP 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 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 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 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS 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 34 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 188 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 118 ILE 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 J residue 207 ASP Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 112 ILE 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 112 ILE 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 228 optimal weight: 5.9990 chunk 237 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 226 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 238 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN G 193 GLN H 193 GLN I 78 HIS ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3911 r_free = 0.3911 target = 0.175089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.143390 restraints weight = 23437.546| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.24 r_work: 0.3429 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2510 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= 0.140 Angle : 0.649 12.143 29064 Z= 0.327 Chirality : 0.049 0.245 3144 Planarity : 0.004 0.085 3684 Dihedral : 5.578 52.584 2749 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % Rotamer: Outliers : 3.15 % Allowed : 22.79 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2556 helix: 0.90 (0.18), residues: 870 sheet: -1.66 (0.29), residues: 334 loop : -0.98 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 81 HIS 0.004 0.001 HIS C 168 PHE 0.017 0.001 PHE J 33 TYR 0.025 0.002 TYR I 25 ARG 0.006 0.000 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 797) hydrogen bonds : angle 5.45413 ( 2292) covalent geometry : bond 0.00332 (21420) covalent geometry : angle 0.64860 (29064) Misc. bond : bond 0.00027 ( 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 392 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 322 time to evaluate : 2.305 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7411 (pm20) cc_final: 0.7050 (mt0) REVERT: A 119 THR cc_start: 0.8200 (p) cc_final: 0.7959 (p) REVERT: A 154 LYS cc_start: 0.7662 (mtpp) cc_final: 0.7420 (mttt) REVERT: A 176 ILE cc_start: 0.7750 (mm) cc_final: 0.7519 (mp) REVERT: B 73 ASP cc_start: 0.7301 (m-30) cc_final: 0.6886 (m-30) REVERT: B 192 LYS cc_start: 0.8107 (mmtp) cc_final: 0.7644 (mttp) REVERT: C 7 LYS cc_start: 0.7290 (ttmt) cc_final: 0.6514 (tptt) REVERT: C 74 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: D 14 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7253 (pttp) REVERT: D 24 ASP cc_start: 0.7247 (p0) cc_final: 0.6201 (m-30) REVERT: D 49 GLU cc_start: 0.8612 (mt-10) cc_final: 0.7975 (tt0) REVERT: D 192 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7616 (mmpt) REVERT: E 57 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8369 (t) REVERT: F 1 MET cc_start: 0.6424 (mmp) cc_final: 0.5974 (tpp) REVERT: F 87 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: F 133 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8283 (mmm-85) REVERT: F 169 LYS cc_start: 0.8975 (tttp) cc_final: 0.8694 (tttp) REVERT: G 49 GLU cc_start: 0.8802 (mt-10) cc_final: 0.7867 (mt-10) REVERT: G 188 VAL cc_start: 0.7858 (t) cc_final: 0.7594 (m) REVERT: H 76 PHE cc_start: 0.8573 (t80) cc_final: 0.8267 (t80) REVERT: I 92 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: I 178 ASP cc_start: 0.8211 (p0) cc_final: 0.7978 (p0) REVERT: J 73 ASP cc_start: 0.7602 (m-30) cc_final: 0.7136 (m-30) REVERT: J 87 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: J 104 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7216 (mt-10) REVERT: J 192 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7660 (tmmm) REVERT: K 86 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6960 (tptp) REVERT: L 49 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7422 (mt-10) REVERT: L 112 ILE cc_start: 0.2846 (OUTLIER) cc_final: 0.2579 (tp) outliers start: 70 outliers final: 47 residues processed: 368 average time/residue: 1.1039 time to fit residues: 472.3661 Evaluate side-chains 363 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 306 time to evaluate : 2.246 ------------------------------------------------------------------------------- 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 136 VAL 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 29 GLN Chi-restraints excluded: chain D residue 34 VAL 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 E residue 164 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 136 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS 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 186 SER Chi-restraints excluded: chain I residue 188 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 118 ILE Chi-restraints excluded: chain J residue 128 ASP 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 86 LYS 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 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 76 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN G 193 GLN H 193 GLN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.175397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143674 restraints weight = 23500.364| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.21 r_work: 0.3439 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21432 Z= 0.144 Angle : 0.643 11.904 29064 Z= 0.326 Chirality : 0.049 0.222 3144 Planarity : 0.004 0.085 3684 Dihedral : 5.521 52.608 2749 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 2.84 % Allowed : 23.11 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 2556 helix: 0.98 (0.18), residues: 870 sheet: -1.64 (0.29), residues: 334 loop : -0.93 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 81 HIS 0.005 0.001 HIS B 38 PHE 0.017 0.001 PHE J 33 TYR 0.026 0.002 TYR I 25 ARG 0.006 0.000 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 797) hydrogen bonds : angle 5.41668 ( 2292) covalent geometry : bond 0.00343 (21420) covalent geometry : angle 0.64330 (29064) Misc. bond : bond 0.00028 ( 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 374 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 311 time to evaluate : 2.360 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7361 (pm20) cc_final: 0.7069 (mt0) REVERT: A 119 THR cc_start: 0.8185 (p) cc_final: 0.7960 (p) REVERT: A 154 LYS cc_start: 0.7687 (mtpp) cc_final: 0.7446 (mttt) REVERT: A 176 ILE cc_start: 0.7751 (mm) cc_final: 0.7513 (mp) REVERT: B 73 ASP cc_start: 0.7257 (m-30) cc_final: 0.6850 (m-30) REVERT: B 192 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7721 (mttp) REVERT: C 7 LYS cc_start: 0.7268 (ttmt) cc_final: 0.6497 (tptt) REVERT: C 74 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7431 (mp10) REVERT: D 14 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7345 (ttpm) REVERT: D 24 ASP cc_start: 0.7253 (p0) cc_final: 0.6210 (m-30) REVERT: D 49 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8069 (mt-10) REVERT: D 192 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7647 (mmpt) REVERT: E 57 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8400 (t) REVERT: F 1 MET cc_start: 0.6451 (mmp) cc_final: 0.5989 (tpp) REVERT: F 87 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: F 169 LYS cc_start: 0.8985 (tttp) cc_final: 0.8715 (tttp) REVERT: G 49 GLU cc_start: 0.8794 (mt-10) cc_final: 0.7861 (mt-10) REVERT: G 188 VAL cc_start: 0.7843 (t) cc_final: 0.7530 (m) REVERT: H 76 PHE cc_start: 0.8543 (t80) cc_final: 0.8257 (t80) REVERT: I 92 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: J 73 ASP cc_start: 0.7645 (m-30) cc_final: 0.7184 (m-30) REVERT: J 87 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: J 104 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7217 (mt-10) REVERT: J 192 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7658 (tmmm) REVERT: K 86 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6953 (tptp) REVERT: L 49 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7473 (mt-10) REVERT: L 112 ILE cc_start: 0.2849 (OUTLIER) cc_final: 0.2609 (tp) outliers start: 63 outliers final: 46 residues processed: 355 average time/residue: 1.1243 time to fit residues: 469.2666 Evaluate side-chains 355 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 299 time to evaluate : 2.313 ------------------------------------------------------------------------------- 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 136 VAL 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 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 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS 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 I residue 34 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 188 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 118 ILE Chi-restraints excluded: chain J residue 128 ASP 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 86 LYS 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 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.4980 chunk 168 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 200 optimal weight: 0.5980 chunk 235 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS 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** L 193 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.176639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144933 restraints weight = 23563.033| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.17 r_work: 0.3447 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21432 Z= 0.134 Angle : 0.638 11.628 29064 Z= 0.322 Chirality : 0.049 0.216 3144 Planarity : 0.004 0.084 3684 Dihedral : 5.436 52.411 2749 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.44 % Favored : 94.44 % Rotamer: Outliers : 2.79 % Allowed : 23.60 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2556 helix: 1.07 (0.18), residues: 874 sheet: -1.72 (0.28), residues: 346 loop : -0.95 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 81 HIS 0.006 0.001 HIS B 38 PHE 0.017 0.001 PHE J 33 TYR 0.025 0.002 TYR L 212 ARG 0.007 0.000 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 797) hydrogen bonds : angle 5.37937 ( 2292) covalent geometry : bond 0.00319 (21420) covalent geometry : angle 0.63771 (29064) Misc. bond : bond 0.00027 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16742.83 seconds wall clock time: 285 minutes 37.23 seconds (17137.23 seconds total)