Starting phenix.real_space_refine on Mon Dec 30 07:09:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fk0_29247/12_2024/8fk0_29247.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fk0_29247/12_2024/8fk0_29247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fk0_29247/12_2024/8fk0_29247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fk0_29247/12_2024/8fk0_29247.map" model { file = "/net/cci-nas-00/data/ceres_data/8fk0_29247/12_2024/8fk0_29247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fk0_29247/12_2024/8fk0_29247.cif" } resolution = 4.0 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= 0.003 sd= 0.035 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 14 5.16 5 C 8008 2.51 5 N 2016 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12628 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "B" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "D" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "J" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "K" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "F" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "L" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "M" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "N" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Time building chain proxies: 8.74, per 1000 atoms: 0.69 Number of scatterers: 12628 At special positions: 0 Unit cell: (90.72, 89.64, 164.16, 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 14 16.00 O 2590 8.00 N 2016 7.00 C 8008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.9 seconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 27 sheets defined 28.4% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 1 through 34 removed outlier: 3.684A pdb=" N GLY A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.741A pdb=" N ARG A 105 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 108 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 34 Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.695A pdb=" N ARG B 105 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 106 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 108 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 34 removed outlier: 3.758A pdb=" N THR C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 34 removed outlier: 3.607A pdb=" N GLY I 30 " --> pdb=" O PHE I 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 34 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.818A pdb=" N GLY D 106 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 34 removed outlier: 3.760A pdb=" N GLY J 30 " --> pdb=" O PHE J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 108 removed outlier: 3.657A pdb=" N GLY J 106 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 108 " --> pdb=" O ARG J 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 34 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.729A pdb=" N GLY E 106 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 108 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 34 Processing helix chain 'K' and resid 102 through 106 removed outlier: 3.579A pdb=" N ARG K 105 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY K 106 " --> pdb=" O THR K 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 102 through 106' Processing helix chain 'F' and resid 2 through 34 removed outlier: 3.535A pdb=" N PHE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY F 30 " --> pdb=" O PHE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.762A pdb=" N VAL F 108 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 34 Processing helix chain 'G' and resid 2 through 34 removed outlier: 3.545A pdb=" N PHE G 26 " --> pdb=" O VAL G 22 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY G 27 " --> pdb=" O GLY G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.839A pdb=" N VAL G 108 " --> pdb=" O ARG G 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 34 removed outlier: 3.831A pdb=" N GLY M 34 " --> pdb=" O GLY M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 108 removed outlier: 3.579A pdb=" N GLY M 106 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL M 108 " --> pdb=" O ARG M 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 34 removed outlier: 3.548A pdb=" N PHE H 29 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY H 30 " --> pdb=" O PHE H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 108 removed outlier: 3.995A pdb=" N GLY H 106 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 108 " --> pdb=" O ARG H 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 4.118A pdb=" N SER A 77 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL A 78 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR A 67 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 44 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR A 131 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU A 46 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 52 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.207A pdb=" N ALA B 44 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B 131 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU B 46 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.650A pdb=" N ASN B 89 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 96 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER B 77 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL B 78 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N THR B 67 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 115 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.533A pdb=" N ALA C 39 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA C 44 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR C 131 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU C 46 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 110 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.533A pdb=" N ALA C 39 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 57 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 38 through 40 removed outlier: 6.452A pdb=" N ALA I 44 " --> pdb=" O ILE I 129 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR I 131 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU I 46 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR I 64 " --> pdb=" O ILE I 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 38 through 40 removed outlier: 3.573A pdb=" N ASN I 89 " --> pdb=" O LEU I 57 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER I 77 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL I 78 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR I 67 " --> pdb=" O VAL I 78 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR I 64 " --> pdb=" O ILE I 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 38 through 40 removed outlier: 3.699A pdb=" N THR D 52 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR D 115 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 64 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 38 through 40 removed outlier: 3.867A pdb=" N ASN D 89 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 77 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL D 78 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR D 67 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 64 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 38 through 40 removed outlier: 6.604A pdb=" N ALA J 44 " --> pdb=" O ILE J 129 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR J 131 " --> pdb=" O ALA J 44 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU J 46 " --> pdb=" O THR J 131 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU J 122 " --> pdb=" O LEU J 118 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR J 64 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 38 through 40 removed outlier: 3.825A pdb=" N ASN J 89 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER J 96 " --> pdb=" O SER J 77 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER J 77 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N THR J 67 " --> pdb=" O VAL J 78 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR J 64 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 38 through 40 Processing sheet with id=AB4, first strand: chain 'E' and resid 38 through 40 Processing sheet with id=AB5, first strand: chain 'K' and resid 38 through 40 removed outlier: 3.603A pdb=" N ASN K 89 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER K 77 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY K 68 " --> pdb=" O ILE K 117 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU K 122 " --> pdb=" O LEU K 118 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA K 44 " --> pdb=" O ILE K 129 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR K 131 " --> pdb=" O ALA K 44 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU K 46 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR K 52 " --> pdb=" O SER K 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 64 through 65 Processing sheet with id=AB7, first strand: chain 'F' and resid 38 through 40 removed outlier: 3.779A pdb=" N LEU F 57 " --> pdb=" O ASN F 89 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN F 89 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER F 77 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL F 78 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N THR F 67 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY F 68 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA F 44 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N THR F 131 " --> pdb=" O ALA F 44 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU F 46 " --> pdb=" O THR F 131 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR F 52 " --> pdb=" O SER F 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.558A pdb=" N ALA L 39 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA L 44 " --> pdb=" O ILE L 129 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N THR L 131 " --> pdb=" O ALA L 44 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU L 46 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY L 68 " --> pdb=" O ILE L 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.558A pdb=" N ALA L 39 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU L 57 " --> pdb=" O ASN L 89 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN L 89 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 64 through 65 removed outlier: 3.631A pdb=" N THR L 64 " --> pdb=" O ILE L 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 38 through 40 Processing sheet with id=AC3, first strand: chain 'G' and resid 75 through 77 removed outlier: 3.672A pdb=" N THR G 115 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA G 44 " --> pdb=" O ILE G 129 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR G 131 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU G 46 " --> pdb=" O THR G 131 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR G 45 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR G 54 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER G 47 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR G 52 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 38 through 40 removed outlier: 3.586A pdb=" N ALA M 39 " --> pdb=" O LYS M 58 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL M 55 " --> pdb=" O TYR M 91 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR M 91 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER M 96 " --> pdb=" O SER M 77 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER M 77 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL M 78 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR M 67 " --> pdb=" O VAL M 78 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY M 68 " --> pdb=" O ILE M 117 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE M 117 " --> pdb=" O GLY M 68 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA M 44 " --> pdb=" O ILE M 129 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR M 131 " --> pdb=" O ALA M 44 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU M 46 " --> pdb=" O THR M 131 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR M 52 " --> pdb=" O SER M 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 38 through 40 Processing sheet with id=AC6, first strand: chain 'H' and resid 75 through 76 removed outlier: 3.729A pdb=" N THR H 64 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 75 through 76 removed outlier: 6.640A pdb=" N ALA H 44 " --> pdb=" O ILE H 129 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR H 131 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU H 46 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR H 52 " --> pdb=" O SER H 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 38 through 40 removed outlier: 6.645A pdb=" N ALA N 44 " --> pdb=" O ILE N 129 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR N 131 " --> pdb=" O ALA N 44 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU N 46 " --> pdb=" O THR N 131 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU N 116 " --> pdb=" O VAL N 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 38 through 40 removed outlier: 3.935A pdb=" N LEU N 57 " --> pdb=" O ASN N 89 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN N 89 " --> pdb=" O LEU N 57 " (cutoff:3.500A) 751 hydrogen bonds defined for protein. 2157 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: 4.38 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3990 1.34 - 1.46: 2823 1.46 - 1.58: 5843 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 12684 Sorted by residual: bond pdb=" N VAL K 66 " pdb=" CA VAL K 66 " ideal model delta sigma weight residual 1.460 1.474 -0.014 1.23e-02 6.61e+03 1.38e+00 bond pdb=" N VAL N 66 " pdb=" CA VAL N 66 " ideal model delta sigma weight residual 1.460 1.474 -0.014 1.23e-02 6.61e+03 1.38e+00 bond pdb=" CG1 ILE N 16 " pdb=" CD1 ILE N 16 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.15e+00 bond pdb=" CA GLY G 76 " pdb=" C GLY G 76 " ideal model delta sigma weight residual 1.514 1.523 -0.008 8.20e-03 1.49e+04 1.06e+00 bond pdb=" CG ARG A 105 " pdb=" CD ARG A 105 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.75e-01 ... (remaining 12679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 17026 1.58 - 3.15: 305 3.15 - 4.73: 44 4.73 - 6.31: 6 6.31 - 7.88: 7 Bond angle restraints: 17388 Sorted by residual: angle pdb=" C SER C 101 " pdb=" N THR C 102 " pdb=" CA THR C 102 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" N ILE A 100 " pdb=" CA ILE A 100 " pdb=" C ILE A 100 " ideal model delta sigma weight residual 111.91 109.16 2.75 8.90e-01 1.26e+00 9.52e+00 angle pdb=" N VAL J 41 " pdb=" CA VAL J 41 " pdb=" C VAL J 41 " ideal model delta sigma weight residual 112.96 110.57 2.39 1.00e+00 1.00e+00 5.69e+00 angle pdb=" CB MET B 81 " pdb=" CG MET B 81 " pdb=" SD MET B 81 " ideal model delta sigma weight residual 112.70 119.59 -6.89 3.00e+00 1.11e-01 5.28e+00 angle pdb=" CA LEU N 8 " pdb=" CB LEU N 8 " pdb=" CG LEU N 8 " ideal model delta sigma weight residual 116.30 108.42 7.88 3.50e+00 8.16e-02 5.07e+00 ... (remaining 17383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 6827 16.45 - 32.90: 393 32.90 - 49.35: 55 49.35 - 65.81: 7 65.81 - 82.26: 12 Dihedral angle restraints: 7294 sinusoidal: 2226 harmonic: 5068 Sorted by residual: dihedral pdb=" CA ASN F 89 " pdb=" CB ASN F 89 " pdb=" CG ASN F 89 " pdb=" OD1 ASN F 89 " ideal model delta sinusoidal sigma weight residual 120.00 -173.49 -66.51 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CG ARG B 105 " pdb=" CD ARG B 105 " pdb=" NE ARG B 105 " pdb=" CZ ARG B 105 " ideal model delta sinusoidal sigma weight residual 90.00 50.99 39.01 2 1.50e+01 4.44e-03 8.45e+00 dihedral pdb=" CA PHE J 29 " pdb=" CB PHE J 29 " pdb=" CG PHE J 29 " pdb=" CD1 PHE J 29 " ideal model delta sinusoidal sigma weight residual 90.00 35.07 54.93 2 2.00e+01 2.50e-03 8.04e+00 ... (remaining 7291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1852 0.037 - 0.075: 428 0.075 - 0.112: 215 0.112 - 0.149: 71 0.149 - 0.187: 10 Chirality restraints: 2576 Sorted by residual: chirality pdb=" CG LEU G 57 " pdb=" CB LEU G 57 " pdb=" CD1 LEU G 57 " pdb=" CD2 LEU G 57 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CB VAL G 55 " pdb=" CA VAL G 55 " pdb=" CG1 VAL G 55 " pdb=" CG2 VAL G 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CB ILE N 17 " pdb=" CA ILE N 17 " pdb=" CG1 ILE N 17 " pdb=" CG2 ILE N 17 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 2573 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET N 81 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C MET N 81 " -0.020 2.00e-02 2.50e+03 pdb=" O MET N 81 " 0.008 2.00e-02 2.50e+03 pdb=" N THR N 82 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 72 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C ASN M 72 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN M 72 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY M 73 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 29 " 0.009 2.00e-02 2.50e+03 8.39e-03 1.23e+00 pdb=" CG PHE B 29 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 29 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 29 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 29 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 29 " 0.000 2.00e-02 2.50e+03 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 139 2.64 - 3.20: 12025 3.20 - 3.77: 18557 3.77 - 4.33: 24216 4.33 - 4.90: 42452 Nonbonded interactions: 97389 Sorted by model distance: nonbonded pdb=" O VAL E 108 " pdb=" OG SER K 119 " model vdw 2.069 3.040 nonbonded pdb=" O ILE G 100 " pdb=" OG1 THR G 103 " model vdw 2.168 3.040 nonbonded pdb=" OD1 ASN A 72 " pdb=" N GLY A 73 " model vdw 2.197 3.120 nonbonded pdb=" OD1 ASN H 74 " pdb=" OG SER H 99 " model vdw 2.220 3.040 nonbonded pdb=" NE2 GLN H 40 " pdb=" O GLY H 42 " model vdw 2.235 3.120 ... (remaining 97384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.580 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.003 0.042 12684 Z= 0.192 Angle : 0.555 7.883 17388 Z= 0.311 Chirality : 0.045 0.187 2576 Planarity : 0.002 0.030 2058 Dihedral : 11.080 82.258 4074 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.14 % Allowed : 0.35 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.90 (0.20), residues: 1820 helix: 2.72 (0.22), residues: 574 sheet: 0.03 (0.19), residues: 742 loop : -0.94 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE B 29 TYR 0.007 0.001 TYR L 91 ARG 0.007 0.001 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7435 (tpt170) REVERT: C 110 SER cc_start: 0.9240 (m) cc_final: 0.8748 (t) REVERT: F 125 THR cc_start: 0.9457 (t) cc_final: 0.9181 (m) REVERT: G 120 ASN cc_start: 0.6126 (t0) cc_final: 0.5478 (m-40) REVERT: M 89 ASN cc_start: 0.8807 (m110) cc_final: 0.7671 (m-40) REVERT: H 59 ASN cc_start: 0.6534 (OUTLIER) cc_final: 0.6328 (m-40) REVERT: N 17 ILE cc_start: 0.7996 (mm) cc_final: 0.7795 (mm) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.1950 time to fit residues: 64.0332 Evaluate side-chains 158 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 0.0000 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 89 ASN M 65 GLN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12684 Z= 0.263 Angle : 0.567 9.063 17388 Z= 0.305 Chirality : 0.047 0.198 2576 Planarity : 0.003 0.020 2058 Dihedral : 4.106 18.375 1878 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.36 % Allowed : 7.63 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.60 (0.19), residues: 1820 helix: 2.76 (0.22), residues: 574 sheet: -0.17 (0.20), residues: 616 loop : -1.25 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE G 32 TYR 0.018 0.002 TYR M 91 ARG 0.005 0.001 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: B 105 ARG cc_start: 0.7877 (tpp80) cc_final: 0.7514 (tpt170) REVERT: I 8 LEU cc_start: 0.9167 (tp) cc_final: 0.8925 (tp) REVERT: E 105 ARG cc_start: 0.8207 (mtm-85) cc_final: 0.7742 (mtm-85) REVERT: F 91 TYR cc_start: 0.7627 (m-10) cc_final: 0.7275 (m-10) REVERT: F 125 THR cc_start: 0.9612 (t) cc_final: 0.9333 (m) REVERT: H 32 PHE cc_start: 0.7689 (m-80) cc_final: 0.7454 (t80) REVERT: N 120 ASN cc_start: 0.8391 (p0) cc_final: 0.7958 (p0) outliers start: 34 outliers final: 22 residues processed: 190 average time/residue: 0.2031 time to fit residues: 59.1964 Evaluate side-chains 171 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 147 optimal weight: 0.0060 chunk 164 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12684 Z= 0.195 Angle : 0.516 8.982 17388 Z= 0.277 Chirality : 0.046 0.183 2576 Planarity : 0.002 0.016 2058 Dihedral : 3.951 16.750 1876 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.50 % Allowed : 11.44 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.55 (0.19), residues: 1820 helix: 2.82 (0.22), residues: 574 sheet: -0.32 (0.20), residues: 658 loop : -1.28 (0.21), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE C 29 TYR 0.007 0.001 TYR D 91 ARG 0.003 0.001 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9387 (m) cc_final: 0.9004 (t) REVERT: B 67 THR cc_start: 0.8636 (p) cc_final: 0.8429 (t) REVERT: B 105 ARG cc_start: 0.7880 (tpp80) cc_final: 0.7426 (tpt170) REVERT: J 105 ARG cc_start: 0.8331 (mtp85) cc_final: 0.8067 (tpp80) REVERT: E 105 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7762 (mtm-85) REVERT: F 125 THR cc_start: 0.9619 (t) cc_final: 0.9331 (m) REVERT: G 81 MET cc_start: 0.6378 (tpt) cc_final: 0.5702 (mpp) REVERT: M 28 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8603 (tt) REVERT: N 120 ASN cc_start: 0.8314 (p0) cc_final: 0.7923 (p0) outliers start: 36 outliers final: 26 residues processed: 182 average time/residue: 0.2052 time to fit residues: 57.3884 Evaluate side-chains 180 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 85 optimal weight: 0.0070 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 166 optimal weight: 0.5980 chunk 175 optimal weight: 9.9990 chunk 86 optimal weight: 0.0020 chunk 157 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN G 120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12684 Z= 0.132 Angle : 0.479 9.079 17388 Z= 0.257 Chirality : 0.045 0.181 2576 Planarity : 0.002 0.013 2058 Dihedral : 3.745 14.985 1876 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.57 % Allowed : 12.41 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.20), residues: 1820 helix: 2.93 (0.22), residues: 574 sheet: -0.25 (0.20), residues: 658 loop : -1.27 (0.21), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE G 29 TYR 0.009 0.001 TYR D 91 ARG 0.003 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 37 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7857 (p) REVERT: A 110 SER cc_start: 0.9310 (m) cc_final: 0.8888 (t) REVERT: B 105 ARG cc_start: 0.7879 (tpp80) cc_final: 0.7443 (tpt170) REVERT: J 105 ARG cc_start: 0.8327 (mtp85) cc_final: 0.8092 (tpp80) REVERT: E 105 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7875 (mtm-85) REVERT: F 91 TYR cc_start: 0.7485 (m-80) cc_final: 0.7280 (m-10) REVERT: F 125 THR cc_start: 0.9597 (t) cc_final: 0.9374 (m) REVERT: L 127 SER cc_start: 0.9127 (t) cc_final: 0.8634 (p) REVERT: N 65 GLN cc_start: 0.6865 (mm-40) cc_final: 0.6502 (tp-100) REVERT: N 120 ASN cc_start: 0.8246 (p0) cc_final: 0.7893 (p0) outliers start: 37 outliers final: 18 residues processed: 208 average time/residue: 0.2017 time to fit residues: 65.3347 Evaluate side-chains 184 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain H residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 130 optimal weight: 0.0030 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 30.0000 chunk 121 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN G 120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12684 Z= 0.219 Angle : 0.510 7.509 17388 Z= 0.275 Chirality : 0.046 0.205 2576 Planarity : 0.002 0.020 2058 Dihedral : 3.816 15.359 1876 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.84 % Allowed : 14.01 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.72 (0.19), residues: 1820 helix: 3.09 (0.22), residues: 532 sheet: -0.14 (0.20), residues: 658 loop : -1.13 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE G 29 TYR 0.008 0.001 TYR K 91 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9382 (m) cc_final: 0.8985 (t) REVERT: B 67 THR cc_start: 0.8621 (p) cc_final: 0.8419 (t) REVERT: B 105 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7434 (tpt170) REVERT: J 105 ARG cc_start: 0.8346 (mtp85) cc_final: 0.8133 (tpp80) REVERT: E 105 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.8004 (mtm-85) REVERT: F 10 LEU cc_start: 0.9366 (mm) cc_final: 0.9136 (mt) REVERT: F 125 THR cc_start: 0.9592 (t) cc_final: 0.9342 (m) REVERT: G 81 MET cc_start: 0.6760 (tpp) cc_final: 0.6226 (mmt) REVERT: N 65 GLN cc_start: 0.6941 (mm-40) cc_final: 0.6577 (tp-100) REVERT: N 120 ASN cc_start: 0.8333 (p0) cc_final: 0.8011 (p0) outliers start: 41 outliers final: 32 residues processed: 188 average time/residue: 0.2067 time to fit residues: 59.5641 Evaluate side-chains 188 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN G 120 ASN H 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12684 Z= 0.167 Angle : 0.487 7.666 17388 Z= 0.261 Chirality : 0.045 0.177 2576 Planarity : 0.002 0.019 2058 Dihedral : 3.718 14.174 1876 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.98 % Allowed : 15.12 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.20), residues: 1820 helix: 3.16 (0.23), residues: 532 sheet: -0.14 (0.20), residues: 658 loop : -1.11 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE G 29 TYR 0.008 0.001 TYR F 91 ARG 0.004 0.000 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9387 (m) cc_final: 0.8978 (t) REVERT: B 105 ARG cc_start: 0.7870 (tpp80) cc_final: 0.7423 (tpt170) REVERT: J 105 ARG cc_start: 0.8328 (mtp85) cc_final: 0.8110 (tpp80) REVERT: F 10 LEU cc_start: 0.9358 (mm) cc_final: 0.9105 (mt) REVERT: F 91 TYR cc_start: 0.7540 (m-10) cc_final: 0.7187 (m-10) REVERT: F 125 THR cc_start: 0.9572 (t) cc_final: 0.9329 (m) REVERT: G 81 MET cc_start: 0.6753 (tpp) cc_final: 0.6306 (mpp) REVERT: N 120 ASN cc_start: 0.8298 (p0) cc_final: 0.7904 (p0) outliers start: 43 outliers final: 27 residues processed: 202 average time/residue: 0.2078 time to fit residues: 64.9576 Evaluate side-chains 185 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain H residue 19 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN G 120 ASN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12684 Z= 0.210 Angle : 0.496 7.498 17388 Z= 0.268 Chirality : 0.045 0.166 2576 Planarity : 0.002 0.022 2058 Dihedral : 3.758 13.403 1876 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.47 % Allowed : 15.33 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.71 (0.20), residues: 1820 helix: 3.07 (0.22), residues: 532 sheet: -0.24 (0.19), residues: 700 loop : -1.02 (0.21), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE C 29 TYR 0.006 0.001 TYR F 91 ARG 0.004 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9421 (m) cc_final: 0.9003 (t) REVERT: B 105 ARG cc_start: 0.7885 (tpp80) cc_final: 0.7411 (tpt170) REVERT: I 72 ASN cc_start: 0.7966 (p0) cc_final: 0.7657 (p0) REVERT: J 105 ARG cc_start: 0.8324 (mtp85) cc_final: 0.8119 (tpp80) REVERT: F 10 LEU cc_start: 0.9410 (mm) cc_final: 0.9154 (mt) REVERT: F 91 TYR cc_start: 0.7722 (m-10) cc_final: 0.7380 (m-10) REVERT: F 125 THR cc_start: 0.9575 (t) cc_final: 0.9363 (m) REVERT: N 120 ASN cc_start: 0.8371 (p0) cc_final: 0.7999 (p0) outliers start: 50 outliers final: 37 residues processed: 194 average time/residue: 0.2013 time to fit residues: 60.6458 Evaluate side-chains 192 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.0870 chunk 70 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 33 optimal weight: 0.1980 chunk 111 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN G 120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12684 Z= 0.141 Angle : 0.493 11.011 17388 Z= 0.261 Chirality : 0.044 0.191 2576 Planarity : 0.002 0.020 2058 Dihedral : 3.632 13.537 1876 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.70 % Allowed : 16.44 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.79 (0.20), residues: 1820 helix: 3.17 (0.23), residues: 532 sheet: -0.22 (0.19), residues: 700 loop : -0.98 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE A 29 TYR 0.005 0.001 TYR G 91 ARG 0.006 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9374 (m) cc_final: 0.8947 (t) REVERT: B 105 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7410 (tpt170) REVERT: J 32 PHE cc_start: 0.9172 (m-80) cc_final: 0.8828 (m-80) REVERT: J 72 ASN cc_start: 0.6729 (p0) cc_final: 0.6062 (t0) REVERT: J 105 ARG cc_start: 0.8327 (mtp85) cc_final: 0.8100 (tpp80) REVERT: F 10 LEU cc_start: 0.9391 (mm) cc_final: 0.9104 (mt) REVERT: F 125 THR cc_start: 0.9526 (t) cc_final: 0.9300 (m) REVERT: L 81 MET cc_start: 0.7386 (ttm) cc_final: 0.6896 (mtp) REVERT: G 81 MET cc_start: 0.6712 (tpt) cc_final: 0.5884 (mpp) REVERT: H 91 TYR cc_start: 0.7957 (m-80) cc_final: 0.7717 (m-80) REVERT: N 120 ASN cc_start: 0.8341 (p0) cc_final: 0.7871 (p0) outliers start: 39 outliers final: 31 residues processed: 208 average time/residue: 0.1948 time to fit residues: 63.1039 Evaluate side-chains 193 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 37 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.2980 chunk 168 optimal weight: 5.9990 chunk 153 optimal weight: 0.3980 chunk 163 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 50 optimal weight: 0.2980 chunk 147 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN G 120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12684 Z= 0.138 Angle : 0.490 9.908 17388 Z= 0.261 Chirality : 0.044 0.183 2576 Planarity : 0.002 0.027 2058 Dihedral : 3.572 13.570 1876 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.50 % Allowed : 17.48 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.20), residues: 1820 helix: 4.86 (0.20), residues: 434 sheet: -0.22 (0.19), residues: 700 loop : -0.87 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE G 32 TYR 0.006 0.001 TYR F 91 ARG 0.005 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9372 (m) cc_final: 0.8931 (t) REVERT: B 105 ARG cc_start: 0.7862 (tpp80) cc_final: 0.7404 (tpt170) REVERT: J 32 PHE cc_start: 0.9154 (m-80) cc_final: 0.8830 (m-80) REVERT: J 72 ASN cc_start: 0.6777 (p0) cc_final: 0.6126 (t0) REVERT: J 105 ARG cc_start: 0.8322 (mtp85) cc_final: 0.8036 (tpp80) REVERT: F 10 LEU cc_start: 0.9393 (mm) cc_final: 0.9098 (mt) REVERT: F 91 TYR cc_start: 0.7809 (m-10) cc_final: 0.7443 (m-10) REVERT: F 125 THR cc_start: 0.9519 (t) cc_final: 0.9282 (p) REVERT: L 81 MET cc_start: 0.7414 (ttm) cc_final: 0.6910 (mtp) REVERT: L 127 SER cc_start: 0.9164 (t) cc_final: 0.8739 (p) REVERT: G 81 MET cc_start: 0.6710 (tpt) cc_final: 0.5951 (mpp) REVERT: G 120 ASN cc_start: 0.4941 (OUTLIER) cc_final: 0.4548 (m-40) REVERT: M 84 ILE cc_start: 0.6737 (tt) cc_final: 0.6537 (pt) REVERT: H 19 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8058 (tp) REVERT: H 91 TYR cc_start: 0.7950 (m-80) cc_final: 0.7722 (m-80) REVERT: N 29 PHE cc_start: 0.7529 (t80) cc_final: 0.7305 (t80) REVERT: N 120 ASN cc_start: 0.8333 (p0) cc_final: 0.7875 (p0) outliers start: 36 outliers final: 31 residues processed: 197 average time/residue: 0.2031 time to fit residues: 61.7673 Evaluate side-chains 202 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 60 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 12684 Z= 0.206 Angle : 0.761 59.193 17388 Z= 0.443 Chirality : 0.045 0.265 2576 Planarity : 0.002 0.046 2058 Dihedral : 3.569 13.139 1876 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.57 % Allowed : 17.75 % Favored : 79.68 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.13 (0.20), residues: 1820 helix: 4.83 (0.20), residues: 434 sheet: -0.15 (0.20), residues: 658 loop : -0.97 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 29 TYR 0.006 0.001 TYR F 91 ARG 0.005 0.001 ARG A 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9367 (m) cc_final: 0.8935 (t) REVERT: B 105 ARG cc_start: 0.7863 (tpp80) cc_final: 0.7407 (tpt170) REVERT: J 32 PHE cc_start: 0.9151 (m-80) cc_final: 0.8825 (m-80) REVERT: J 72 ASN cc_start: 0.6779 (p0) cc_final: 0.6130 (t0) REVERT: J 105 ARG cc_start: 0.8324 (mtp85) cc_final: 0.8040 (tpp80) REVERT: F 10 LEU cc_start: 0.9396 (mm) cc_final: 0.9102 (mt) REVERT: F 125 THR cc_start: 0.9524 (t) cc_final: 0.9285 (p) REVERT: L 81 MET cc_start: 0.7409 (ttm) cc_final: 0.6911 (mtp) REVERT: L 127 SER cc_start: 0.9164 (t) cc_final: 0.8740 (p) REVERT: G 81 MET cc_start: 0.6740 (tpt) cc_final: 0.5996 (mpp) REVERT: H 19 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8060 (tp) REVERT: H 91 TYR cc_start: 0.7960 (m-80) cc_final: 0.7723 (m-80) REVERT: N 29 PHE cc_start: 0.7546 (t80) cc_final: 0.7304 (t80) REVERT: N 120 ASN cc_start: 0.8329 (p0) cc_final: 0.7875 (p0) outliers start: 37 outliers final: 31 residues processed: 193 average time/residue: 0.2033 time to fit residues: 60.8856 Evaluate side-chains 198 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.0060 chunk 153 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.0670 overall best weight: 0.5134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.113007 restraints weight = 21575.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113784 restraints weight = 15572.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.114421 restraints weight = 12145.273| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 12684 Z= 0.206 Angle : 0.761 59.193 17388 Z= 0.443 Chirality : 0.045 0.265 2576 Planarity : 0.002 0.046 2058 Dihedral : 3.569 13.139 1876 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.29 % Allowed : 17.89 % Favored : 79.82 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.13 (0.20), residues: 1820 helix: 4.83 (0.20), residues: 434 sheet: -0.15 (0.20), residues: 658 loop : -0.97 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 29 TYR 0.006 0.001 TYR F 91 ARG 0.005 0.001 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2335.28 seconds wall clock time: 44 minutes 9.30 seconds (2649.30 seconds total)