Starting phenix.real_space_refine on Wed Sep 17 17:07:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ftt_50751/09_2025/9ftt_50751.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ftt_50751/09_2025/9ftt_50751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ftt_50751/09_2025/9ftt_50751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ftt_50751/09_2025/9ftt_50751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ftt_50751/09_2025/9ftt_50751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ftt_50751/09_2025/9ftt_50751.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 6156 2.51 5 N 1772 2.21 5 O 2116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10062 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 126 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "C" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1107 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain: "D" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1107 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain: "E" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1098 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "F" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1107 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain: "G" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1107 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain: "H" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1107 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain: "I" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1098 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "J" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1107 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain: "K" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1098 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Time building chain proxies: 2.51, per 1000 atoms: 0.25 Number of scatterers: 10062 At special positions: 0 Unit cell: (110.16, 92.016, 104.976, 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 18 16.00 O 2116 8.00 N 1772 7.00 C 6156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 61 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 61 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 61 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 61 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 61 " distance=2.03 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 61 " distance=2.03 Simple disulfide: pdb=" SG CYS K 21 " - pdb=" SG CYS K 61 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 369.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 21 sheets defined 2.8% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 40 through 43 removed outlier: 3.606A pdb=" N ALA C 43 " --> pdb=" O ALA C 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 43' Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.162A pdb=" N ASP D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'G' and resid 24 through 28 Processing helix chain 'I' and resid 24 through 28 Processing helix chain 'K' and resid 24 through 28 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 38 removed outlier: 7.642A pdb=" N ASP C 29 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR B 9 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR C 31 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N HIS B 11 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLN C 33 " --> pdb=" O HIS B 11 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS B 13 " --> pdb=" O GLN C 33 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C 35 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU B 15 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR B 4 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR C 158 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASN B 6 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL C 156 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLY B 8 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 154 " --> pdb=" O GLY B 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 31 through 38 removed outlier: 8.339A pdb=" N VAL D 32 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N HIS C 11 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU D 34 " --> pdb=" O HIS C 11 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LYS C 13 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN D 36 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU C 15 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARG D 38 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL C 17 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASN C 6 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL D 156 " --> pdb=" O ASN C 6 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 23 removed outlier: 5.646A pdb=" N GLY C 127 " --> pdb=" O ASP C 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 29 through 38 removed outlier: 6.128A pdb=" N ASP E 29 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR D 9 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR E 31 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N HIS D 11 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLN E 33 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS D 13 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY E 35 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU D 15 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ASN D 6 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL E 156 " --> pdb=" O ASN D 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 22 through 23 removed outlier: 5.928A pdb=" N GLY D 127 " --> pdb=" O ASP D 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 29 through 38 removed outlier: 9.114A pdb=" N GLN F 30 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR E 9 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N VAL F 32 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N HIS E 11 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU F 34 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS E 13 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLN F 36 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU E 15 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG F 38 " --> pdb=" O GLU E 15 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL E 17 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE F 154 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR E 9 " --> pdb=" O ALA F 152 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA F 152 " --> pdb=" O THR E 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 29 through 38 removed outlier: 9.114A pdb=" N GLN F 30 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR E 9 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N VAL F 32 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N HIS E 11 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU F 34 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS E 13 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLN F 36 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU E 15 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG F 38 " --> pdb=" O GLU E 15 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL E 17 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 22 through 23 Processing sheet with id=AA9, first strand: chain 'G' and resid 29 through 38 removed outlier: 9.234A pdb=" N GLN G 30 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR F 9 " --> pdb=" O GLN G 30 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL G 32 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N HIS F 11 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU G 34 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LYS F 13 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN G 36 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU F 15 " --> pdb=" O GLN G 36 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG G 38 " --> pdb=" O GLU F 15 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL F 17 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR F 4 " --> pdb=" O TYR G 158 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR G 158 " --> pdb=" O THR F 4 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASN F 6 " --> pdb=" O VAL G 156 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL G 156 " --> pdb=" O ASN F 6 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY F 8 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR G 153 " --> pdb=" O LEU G 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 22 through 23 removed outlier: 4.310A pdb=" N ASP F 60 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY F 127 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 29 through 38 removed outlier: 8.948A pdb=" N GLN H 30 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR G 9 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N VAL H 32 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N HIS G 11 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU H 34 " --> pdb=" O HIS G 11 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LYS G 13 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN H 36 " --> pdb=" O LYS G 13 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU G 15 " --> pdb=" O GLN H 36 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG H 38 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL G 17 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N THR G 4 " --> pdb=" O TYR H 158 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR H 158 " --> pdb=" O THR G 4 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASN G 6 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL H 156 " --> pdb=" O ASN G 6 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS H 68 " --> pdb=" O GLN H 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 22 through 23 removed outlier: 6.483A pdb=" N THR G 48 " --> pdb=" O ALA G 139 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA G 139 " --> pdb=" O THR G 48 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER G 50 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR G 137 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP G 60 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLY G 127 " --> pdb=" O ASP G 60 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 29 through 33 removed outlier: 8.834A pdb=" N GLN I 30 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR H 9 " --> pdb=" O GLN I 30 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL I 32 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS H 11 " --> pdb=" O VAL I 32 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 29 through 33 removed outlier: 8.834A pdb=" N GLN I 30 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR H 9 " --> pdb=" O GLN I 30 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL I 32 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS H 11 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE I 154 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR H 9 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA I 152 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N HIS H 11 " --> pdb=" O ALA I 150 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA I 150 " --> pdb=" O HIS H 11 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS H 13 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA I 148 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU H 15 " --> pdb=" O GLY I 146 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY I 146 " --> pdb=" O GLU H 15 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 22 through 23 Processing sheet with id=AB7, first strand: chain 'J' and resid 29 through 38 removed outlier: 6.626A pdb=" N ASP J 29 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR I 9 " --> pdb=" O ASP J 29 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR J 31 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS I 11 " --> pdb=" O THR J 31 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLN J 33 " --> pdb=" O HIS I 11 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS I 13 " --> pdb=" O GLN J 33 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY J 35 " --> pdb=" O LYS I 13 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N THR I 4 " --> pdb=" O TYR J 158 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR J 158 " --> pdb=" O THR I 4 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASN I 6 " --> pdb=" O VAL J 156 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL J 156 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR J 122 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 22 through 23 removed outlier: 3.751A pdb=" N ALA I 47 " --> pdb=" O ALA I 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 22 through 23 Processing sheet with id=AC1, first strand: chain 'K' and resid 29 through 38 removed outlier: 3.710A pdb=" N GLN K 30 " --> pdb=" O THR J 9 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU J 15 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN K 36 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL J 17 " --> pdb=" O GLN K 36 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG K 38 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN J 6 " --> pdb=" O VAL K 156 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL K 156 " --> pdb=" O ASN J 6 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY J 8 " --> pdb=" O PHE K 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 22 through 23 removed outlier: 6.542A pdb=" N THR J 48 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ALA J 139 " --> pdb=" O THR J 48 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER J 50 " --> pdb=" O TYR J 137 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR J 137 " --> pdb=" O SER J 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 22 through 23 removed outlier: 5.860A pdb=" N GLY K 127 " --> pdb=" O ASP K 60 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN K 134 " --> pdb=" O LEU K 104 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 849 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: 1.36 Time building geometry restraints manager: 1.13 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: 3557 1.34 - 1.46: 1914 1.46 - 1.57: 4682 1.57 - 1.69: 0 1.69 - 1.80: 18 Bond restraints: 10171 Sorted by residual: bond pdb=" CA GLY K 127 " pdb=" C GLY K 127 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.67e+00 bond pdb=" N GLY K 127 " pdb=" CA GLY K 127 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.78e+00 bond pdb=" N GLY H 127 " pdb=" CA GLY H 127 " ideal model delta sigma weight residual 1.458 1.448 0.010 9.20e-03 1.18e+04 1.20e+00 bond pdb=" N GLY K 8 " pdb=" CA GLY K 8 " ideal model delta sigma weight residual 1.458 1.449 0.009 9.20e-03 1.18e+04 9.02e-01 bond pdb=" CA GLY D 53 " pdb=" C GLY D 53 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 7.82e-01 ... (remaining 10166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 13045 0.90 - 1.79: 733 1.79 - 2.69: 93 2.69 - 3.58: 20 3.58 - 4.48: 6 Bond angle restraints: 13897 Sorted by residual: angle pdb=" N GLY D 53 " pdb=" CA GLY D 53 " pdb=" C GLY D 53 " ideal model delta sigma weight residual 110.71 115.09 -4.38 1.53e+00 4.27e-01 8.21e+00 angle pdb=" CA GLY G 75 " pdb=" C GLY G 75 " pdb=" N THR G 76 " ideal model delta sigma weight residual 115.27 117.19 -1.92 7.60e-01 1.73e+00 6.38e+00 angle pdb=" N GLY K 53 " pdb=" CA GLY K 53 " pdb=" C GLY K 53 " ideal model delta sigma weight residual 110.95 115.09 -4.14 1.74e+00 3.30e-01 5.65e+00 angle pdb=" C VAL C 28 " pdb=" N ASP C 29 " pdb=" CA ASP C 29 " ideal model delta sigma weight residual 122.95 119.71 3.24 1.44e+00 4.82e-01 5.07e+00 angle pdb=" N GLY J 26 " pdb=" CA GLY J 26 " pdb=" C GLY J 26 " ideal model delta sigma weight residual 115.32 112.46 2.86 1.31e+00 5.83e-01 4.75e+00 ... (remaining 13892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.91: 5479 14.91 - 29.83: 337 29.83 - 44.74: 76 44.74 - 59.65: 24 59.65 - 74.57: 12 Dihedral angle restraints: 5928 sinusoidal: 1903 harmonic: 4025 Sorted by residual: dihedral pdb=" CB CYS D 21 " pdb=" SG CYS D 21 " pdb=" SG CYS D 61 " pdb=" CB CYS D 61 " ideal model delta sinusoidal sigma weight residual 93.00 136.79 -43.79 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS I 21 " pdb=" SG CYS I 21 " pdb=" SG CYS I 61 " pdb=" CB CYS I 61 " ideal model delta sinusoidal sigma weight residual 93.00 135.05 -42.05 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS E 21 " pdb=" SG CYS E 21 " pdb=" SG CYS E 61 " pdb=" CB CYS E 61 " ideal model delta sinusoidal sigma weight residual 93.00 132.39 -39.39 1 1.00e+01 1.00e-02 2.18e+01 ... (remaining 5925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1073 0.027 - 0.053: 401 0.053 - 0.080: 139 0.080 - 0.106: 78 0.106 - 0.133: 47 Chirality restraints: 1738 Sorted by residual: chirality pdb=" CA ILE J 131 " pdb=" N ILE J 131 " pdb=" C ILE J 131 " pdb=" CB ILE J 131 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE K 56 " pdb=" N ILE K 56 " pdb=" C ILE K 56 " pdb=" CB ILE K 56 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE H 131 " pdb=" N ILE H 131 " pdb=" C ILE H 131 " pdb=" CB ILE H 131 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 1735 not shown) Planarity restraints: 1861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 131 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO K 132 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO K 132 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO K 132 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 144 " -0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO H 145 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO H 145 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO H 145 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 131 " 0.012 5.00e-02 4.00e+02 1.79e-02 5.10e-01 pdb=" N PRO C 132 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " 0.010 5.00e-02 4.00e+02 ... (remaining 1858 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 675 2.74 - 3.28: 9592 3.28 - 3.82: 16597 3.82 - 4.36: 19726 4.36 - 4.90: 35977 Nonbonded interactions: 82567 Sorted by model distance: nonbonded pdb=" O SER C 91 " pdb=" OG SER F 50 " model vdw 2.194 3.040 nonbonded pdb=" OD1 ASN C 98 " pdb=" OG1 THR C 140 " model vdw 2.202 3.040 nonbonded pdb=" O SER E 91 " pdb=" OG SER H 50 " model vdw 2.217 3.040 nonbonded pdb=" OD1 ASN I 98 " pdb=" OG1 THR I 140 " model vdw 2.225 3.040 nonbonded pdb=" NZ LYS D 68 " pdb=" OG1 THR D 123 " model vdw 2.302 3.120 ... (remaining 82562 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 'C' and resid 2 through 158) selection = (chain 'D' and resid 2 through 158) selection = chain 'E' selection = (chain 'F' and resid 2 through 158) selection = (chain 'G' and resid 2 through 158) selection = (chain 'H' and resid 2 through 158) selection = chain 'I' selection = (chain 'J' and resid 2 through 158) selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.370 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.002 0.017 10180 Z= 0.124 Angle : 0.467 4.479 13915 Z= 0.284 Chirality : 0.040 0.133 1738 Planarity : 0.002 0.027 1861 Dihedral : 11.322 74.568 3321 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.20), residues: 1417 helix: -2.79 (0.64), residues: 36 sheet: 0.76 (0.24), residues: 390 loop : -0.96 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 106 TYR 0.007 0.001 TYR J 158 PHE 0.011 0.001 PHE E 54 HIS 0.002 0.001 HIS D 11 Details of bonding type rmsd covalent geometry : bond 0.00232 (10171) covalent geometry : angle 0.46718 (13897) SS BOND : bond 0.00162 ( 9) SS BOND : angle 0.59090 ( 18) hydrogen bonds : bond 0.15593 ( 316) hydrogen bonds : angle 8.10151 ( 849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8361 (mmtp) REVERT: C 36 GLN cc_start: 0.8612 (mp10) cc_final: 0.8160 (mt0) REVERT: C 60 ASP cc_start: 0.8761 (m-30) cc_final: 0.8445 (m-30) REVERT: C 105 ASP cc_start: 0.7908 (p0) cc_final: 0.7544 (p0) REVERT: C 106 ARG cc_start: 0.7494 (tmm160) cc_final: 0.7106 (tmm-80) REVERT: D 13 LYS cc_start: 0.8563 (mmtp) cc_final: 0.8348 (mtpp) REVERT: D 29 ASP cc_start: 0.7835 (t70) cc_final: 0.7395 (t0) REVERT: D 33 GLN cc_start: 0.7604 (tp40) cc_final: 0.7388 (tp40) REVERT: D 59 ASN cc_start: 0.8567 (p0) cc_final: 0.8165 (p0) REVERT: D 120 SER cc_start: 0.8672 (p) cc_final: 0.8401 (p) REVERT: E 48 THR cc_start: 0.8693 (m) cc_final: 0.8363 (p) REVERT: E 64 ASN cc_start: 0.7995 (p0) cc_final: 0.7779 (p0) REVERT: E 68 LYS cc_start: 0.8494 (mttp) cc_final: 0.8267 (mtmm) REVERT: F 15 GLU cc_start: 0.7917 (tt0) cc_final: 0.7541 (tt0) REVERT: G 31 THR cc_start: 0.8506 (m) cc_final: 0.8266 (t) REVERT: G 62 ASP cc_start: 0.8131 (t0) cc_final: 0.7786 (t0) REVERT: G 144 THR cc_start: 0.8944 (m) cc_final: 0.8623 (p) REVERT: H 4 THR cc_start: 0.8719 (m) cc_final: 0.8404 (t) REVERT: H 60 ASP cc_start: 0.7990 (t70) cc_final: 0.7666 (t0) REVERT: I 84 ASN cc_start: 0.8826 (p0) cc_final: 0.8580 (p0) REVERT: I 95 SER cc_start: 0.8796 (p) cc_final: 0.8593 (t) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.0683 time to fit residues: 33.3429 Evaluate side-chains 236 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN C 159 GLN D 57 GLN D 64 ASN D 82 HIS D 89 GLN D 159 GLN E 59 ASN F 59 ASN F 102 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN H 98 ASN H 134 GLN ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN J 134 GLN J 157 GLN K 18 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098826 restraints weight = 16637.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101612 restraints weight = 8065.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103400 restraints weight = 4617.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104572 restraints weight = 2956.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105351 restraints weight = 2063.612| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10180 Z= 0.238 Angle : 0.569 6.202 13915 Z= 0.315 Chirality : 0.043 0.151 1738 Planarity : 0.003 0.030 1861 Dihedral : 4.143 13.329 1472 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.63 % Allowed : 11.00 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.20), residues: 1417 helix: -2.72 (0.56), residues: 54 sheet: 0.67 (0.24), residues: 387 loop : -1.03 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 38 TYR 0.013 0.002 TYR K 158 PHE 0.021 0.002 PHE F 118 HIS 0.004 0.001 HIS G 11 Details of bonding type rmsd covalent geometry : bond 0.00530 (10171) covalent geometry : angle 0.56790 (13897) SS BOND : bond 0.00504 ( 9) SS BOND : angle 1.26294 ( 18) hydrogen bonds : bond 0.04065 ( 316) hydrogen bonds : angle 6.62972 ( 849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8396 (mmtp) REVERT: C 105 ASP cc_start: 0.8076 (p0) cc_final: 0.7752 (p0) REVERT: C 106 ARG cc_start: 0.7735 (tmm160) cc_final: 0.7307 (tmm-80) REVERT: D 13 LYS cc_start: 0.8703 (mmtp) cc_final: 0.8341 (mtpp) REVERT: D 33 GLN cc_start: 0.7658 (tp40) cc_final: 0.7426 (tp40) REVERT: D 59 ASN cc_start: 0.8410 (p0) cc_final: 0.8145 (p0) REVERT: D 60 ASP cc_start: 0.7296 (t70) cc_final: 0.7049 (t70) REVERT: D 120 SER cc_start: 0.8576 (p) cc_final: 0.8210 (p) REVERT: E 48 THR cc_start: 0.8916 (m) cc_final: 0.8578 (p) REVERT: F 38 ARG cc_start: 0.8367 (mtp180) cc_final: 0.7736 (mtm180) REVERT: F 78 ILE cc_start: 0.8800 (tt) cc_final: 0.8393 (tp) REVERT: G 57 GLN cc_start: 0.7821 (tt0) cc_final: 0.7596 (tt0) REVERT: G 155 LYS cc_start: 0.7732 (ttmt) cc_final: 0.7454 (mtmm) REVERT: H 4 THR cc_start: 0.8776 (m) cc_final: 0.8448 (t) REVERT: H 60 ASP cc_start: 0.8189 (t70) cc_final: 0.7833 (t0) REVERT: I 68 LYS cc_start: 0.8415 (mttm) cc_final: 0.7975 (mttm) REVERT: I 84 ASN cc_start: 0.8828 (p0) cc_final: 0.8541 (p0) REVERT: J 13 LYS cc_start: 0.8458 (mttm) cc_final: 0.8149 (mtpp) REVERT: K 38 ARG cc_start: 0.7770 (mtm180) cc_final: 0.7501 (mtm110) REVERT: K 84 ASN cc_start: 0.8676 (p0) cc_final: 0.8327 (p0) REVERT: K 113 LEU cc_start: 0.7967 (mt) cc_final: 0.7559 (mp) outliers start: 37 outliers final: 29 residues processed: 261 average time/residue: 0.0803 time to fit residues: 31.7387 Evaluate side-chains 253 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 19 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN C 159 GLN D 64 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN K 18 ASN K 55 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.101884 restraints weight = 16376.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104714 restraints weight = 7826.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106481 restraints weight = 4441.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107638 restraints weight = 2831.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108438 restraints weight = 1977.537| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10180 Z= 0.129 Angle : 0.471 5.420 13915 Z= 0.261 Chirality : 0.041 0.145 1738 Planarity : 0.002 0.030 1861 Dihedral : 3.771 12.598 1472 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.75 % Allowed : 15.03 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.20), residues: 1417 helix: -2.50 (0.71), residues: 36 sheet: 0.73 (0.24), residues: 378 loop : -1.02 (0.17), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 106 TYR 0.012 0.001 TYR K 158 PHE 0.014 0.002 PHE D 118 HIS 0.003 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00283 (10171) covalent geometry : angle 0.46991 (13897) SS BOND : bond 0.00467 ( 9) SS BOND : angle 0.85271 ( 18) hydrogen bonds : bond 0.03304 ( 316) hydrogen bonds : angle 6.07986 ( 849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 LYS cc_start: 0.8401 (mmtt) cc_final: 0.7957 (mttm) REVERT: C 13 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8442 (mmtp) REVERT: C 36 GLN cc_start: 0.8529 (mp10) cc_final: 0.8201 (mt0) REVERT: C 105 ASP cc_start: 0.7999 (p0) cc_final: 0.7595 (p0) REVERT: D 13 LYS cc_start: 0.8615 (mmtp) cc_final: 0.8266 (mtpp) REVERT: D 33 GLN cc_start: 0.7693 (tp40) cc_final: 0.7401 (tp40) REVERT: D 59 ASN cc_start: 0.8136 (p0) cc_final: 0.7885 (p0) REVERT: D 60 ASP cc_start: 0.7203 (t70) cc_final: 0.6959 (t70) REVERT: E 48 THR cc_start: 0.8810 (m) cc_final: 0.8453 (p) REVERT: H 4 THR cc_start: 0.8769 (m) cc_final: 0.8428 (t) REVERT: H 60 ASP cc_start: 0.8090 (t70) cc_final: 0.7799 (t70) REVERT: J 13 LYS cc_start: 0.8512 (mttm) cc_final: 0.8236 (mtpp) REVERT: K 36 GLN cc_start: 0.8546 (mt0) cc_final: 0.8309 (mt0) REVERT: K 84 ASN cc_start: 0.8688 (p0) cc_final: 0.8230 (p0) REVERT: K 113 LEU cc_start: 0.7953 (mt) cc_final: 0.7554 (mp) outliers start: 28 outliers final: 24 residues processed: 243 average time/residue: 0.0799 time to fit residues: 29.4222 Evaluate side-chains 236 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 83 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 75 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN C 159 GLN D 64 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 134 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN K 18 ASN K 55 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.094799 restraints weight = 16959.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.097490 restraints weight = 8212.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099216 restraints weight = 4729.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.100369 restraints weight = 3053.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101136 restraints weight = 2146.372| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 10180 Z= 0.358 Angle : 0.673 7.971 13915 Z= 0.370 Chirality : 0.046 0.149 1738 Planarity : 0.003 0.037 1861 Dihedral : 4.884 19.789 1472 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.01 % Allowed : 15.32 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.19), residues: 1417 helix: -3.33 (0.92), residues: 18 sheet: 0.38 (0.24), residues: 387 loop : -1.25 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 106 TYR 0.012 0.002 TYR D 158 PHE 0.023 0.003 PHE G 154 HIS 0.010 0.002 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00800 (10171) covalent geometry : angle 0.67051 (13897) SS BOND : bond 0.00675 ( 9) SS BOND : angle 1.62125 ( 18) hydrogen bonds : bond 0.04167 ( 316) hydrogen bonds : angle 6.90990 ( 849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8086 (mttm) REVERT: C 32 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8227 (p) REVERT: C 105 ASP cc_start: 0.8213 (p0) cc_final: 0.7778 (p0) REVERT: D 13 LYS cc_start: 0.8757 (mmtp) cc_final: 0.8482 (mtpp) REVERT: D 44 GLN cc_start: 0.8065 (pm20) cc_final: 0.7741 (pt0) REVERT: D 79 ASP cc_start: 0.8217 (t0) cc_final: 0.7994 (t0) REVERT: D 120 SER cc_start: 0.8312 (p) cc_final: 0.8079 (p) REVERT: E 48 THR cc_start: 0.9033 (m) cc_final: 0.8756 (p) REVERT: F 38 ARG cc_start: 0.8496 (mtp180) cc_final: 0.8270 (mtp180) REVERT: G 155 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7723 (mtmm) REVERT: H 4 THR cc_start: 0.8797 (m) cc_final: 0.8531 (t) REVERT: H 60 ASP cc_start: 0.8290 (t70) cc_final: 0.7875 (t0) REVERT: J 45 GLU cc_start: 0.7861 (tp30) cc_final: 0.7114 (tp30) REVERT: K 84 ASN cc_start: 0.8736 (p0) cc_final: 0.8249 (p0) REVERT: K 113 LEU cc_start: 0.8007 (mt) cc_final: 0.7596 (mp) outliers start: 51 outliers final: 43 residues processed: 264 average time/residue: 0.0773 time to fit residues: 31.1900 Evaluate side-chains 254 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 157 GLN Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 91 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN C 159 GLN D 64 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN K 55 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.096607 restraints weight = 16770.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099295 restraints weight = 8104.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101028 restraints weight = 4643.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.102169 restraints weight = 2980.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102925 restraints weight = 2089.856| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10180 Z= 0.241 Angle : 0.584 7.376 13915 Z= 0.319 Chirality : 0.044 0.146 1738 Planarity : 0.003 0.032 1861 Dihedral : 4.576 16.271 1472 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.30 % Allowed : 18.07 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.19), residues: 1417 helix: -3.41 (0.90), residues: 18 sheet: 0.31 (0.24), residues: 387 loop : -1.28 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 106 TYR 0.012 0.002 TYR D 158 PHE 0.017 0.002 PHE D 118 HIS 0.005 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00535 (10171) covalent geometry : angle 0.58239 (13897) SS BOND : bond 0.00483 ( 9) SS BOND : angle 1.44978 ( 18) hydrogen bonds : bond 0.03588 ( 316) hydrogen bonds : angle 6.64776 ( 849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 221 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8090 (mttm) REVERT: C 32 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8241 (p) REVERT: C 36 GLN cc_start: 0.8521 (mp10) cc_final: 0.8241 (mt0) REVERT: C 105 ASP cc_start: 0.8096 (p0) cc_final: 0.7566 (p0) REVERT: C 151 ASP cc_start: 0.8129 (m-30) cc_final: 0.7894 (m-30) REVERT: D 44 GLN cc_start: 0.8009 (pm20) cc_final: 0.7676 (pt0) REVERT: E 48 THR cc_start: 0.8984 (m) cc_final: 0.8698 (p) REVERT: G 155 LYS cc_start: 0.8025 (ttmt) cc_final: 0.7693 (mtmm) REVERT: H 4 THR cc_start: 0.8692 (m) cc_final: 0.8451 (t) REVERT: H 44 GLN cc_start: 0.8490 (tp40) cc_final: 0.8225 (tp40) REVERT: H 60 ASP cc_start: 0.8278 (t70) cc_final: 0.8063 (t70) REVERT: J 158 TYR cc_start: 0.8604 (m-80) cc_final: 0.7979 (m-80) REVERT: K 84 ASN cc_start: 0.8713 (p0) cc_final: 0.8203 (p0) REVERT: K 113 LEU cc_start: 0.7955 (mt) cc_final: 0.7587 (mp) outliers start: 54 outliers final: 48 residues processed: 255 average time/residue: 0.0719 time to fit residues: 28.5120 Evaluate side-chains 265 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 159 GLN Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain J residue 55 ASN Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 125 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN C 159 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 GLN ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN K 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.095131 restraints weight = 17082.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.097803 restraints weight = 8260.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099523 restraints weight = 4739.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100662 restraints weight = 3050.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101432 restraints weight = 2144.400| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 10180 Z= 0.301 Angle : 0.638 8.651 13915 Z= 0.348 Chirality : 0.045 0.155 1738 Planarity : 0.003 0.032 1861 Dihedral : 4.847 18.286 1472 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 6.09 % Allowed : 17.68 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.19), residues: 1417 helix: -3.52 (0.86), residues: 18 sheet: 0.11 (0.24), residues: 387 loop : -1.44 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 38 TYR 0.011 0.002 TYR D 158 PHE 0.019 0.003 PHE I 12 HIS 0.006 0.002 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00672 (10171) covalent geometry : angle 0.63559 (13897) SS BOND : bond 0.00625 ( 9) SS BOND : angle 1.67484 ( 18) hydrogen bonds : bond 0.03752 ( 316) hydrogen bonds : angle 6.86019 ( 849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 226 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8074 (mttm) REVERT: C 105 ASP cc_start: 0.8215 (p0) cc_final: 0.7592 (p0) REVERT: D 44 GLN cc_start: 0.7994 (pm20) cc_final: 0.7669 (pt0) REVERT: E 48 THR cc_start: 0.9014 (m) cc_final: 0.8754 (p) REVERT: H 44 GLN cc_start: 0.8466 (tp40) cc_final: 0.8224 (tp40) REVERT: H 60 ASP cc_start: 0.8374 (t70) cc_final: 0.7981 (t0) REVERT: J 45 GLU cc_start: 0.7887 (tp30) cc_final: 0.7002 (tp30) REVERT: J 158 TYR cc_start: 0.8619 (m-80) cc_final: 0.7959 (m-80) REVERT: K 84 ASN cc_start: 0.8777 (p0) cc_final: 0.8405 (p0) outliers start: 62 outliers final: 58 residues processed: 265 average time/residue: 0.0793 time to fit residues: 31.9862 Evaluate side-chains 277 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 159 GLN Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain J residue 55 ASN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 156 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 113 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN C 159 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN K 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.098390 restraints weight = 16605.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101084 restraints weight = 8002.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102827 restraints weight = 4594.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.103971 restraints weight = 2948.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104741 restraints weight = 2065.915| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10180 Z= 0.184 Angle : 0.554 7.656 13915 Z= 0.302 Chirality : 0.043 0.150 1738 Planarity : 0.003 0.034 1861 Dihedral : 4.438 14.411 1472 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.21 % Allowed : 19.65 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.19), residues: 1417 helix: -3.47 (0.85), residues: 18 sheet: 0.28 (0.25), residues: 375 loop : -1.34 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 136 TYR 0.013 0.002 TYR D 158 PHE 0.019 0.002 PHE D 118 HIS 0.004 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00409 (10171) covalent geometry : angle 0.55233 (13897) SS BOND : bond 0.00415 ( 9) SS BOND : angle 1.33603 ( 18) hydrogen bonds : bond 0.03289 ( 316) hydrogen bonds : angle 6.50074 ( 849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8096 (mttm) REVERT: C 36 GLN cc_start: 0.8517 (mp10) cc_final: 0.8303 (mt0) REVERT: C 57 GLN cc_start: 0.8356 (tt0) cc_final: 0.8122 (tt0) REVERT: C 105 ASP cc_start: 0.8098 (p0) cc_final: 0.7507 (p0) REVERT: E 48 THR cc_start: 0.8930 (m) cc_final: 0.8655 (p) REVERT: F 38 ARG cc_start: 0.8342 (mtp180) cc_final: 0.8081 (mtp180) REVERT: F 42 LEU cc_start: 0.7821 (mt) cc_final: 0.7607 (mt) REVERT: H 44 GLN cc_start: 0.8373 (tp40) cc_final: 0.8112 (tp40) REVERT: H 60 ASP cc_start: 0.8272 (t70) cc_final: 0.7876 (t0) REVERT: J 45 GLU cc_start: 0.7914 (tp30) cc_final: 0.7394 (tp30) REVERT: J 158 TYR cc_start: 0.8602 (m-80) cc_final: 0.7995 (m-80) REVERT: K 84 ASN cc_start: 0.8733 (p0) cc_final: 0.8259 (p0) REVERT: K 113 LEU cc_start: 0.8031 (mt) cc_final: 0.7554 (mp) outliers start: 53 outliers final: 48 residues processed: 261 average time/residue: 0.0739 time to fit residues: 29.8790 Evaluate side-chains 266 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 55 ASN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 4 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 159 GLN ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN J 157 GLN K 36 GLN K 55 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.097175 restraints weight = 16683.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.099811 restraints weight = 8080.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.101533 restraints weight = 4659.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102680 restraints weight = 3004.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103449 restraints weight = 2109.526| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10180 Z= 0.225 Angle : 0.581 8.657 13915 Z= 0.316 Chirality : 0.044 0.163 1738 Planarity : 0.003 0.039 1861 Dihedral : 4.545 15.131 1472 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.21 % Allowed : 20.24 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.19), residues: 1417 helix: -3.57 (0.83), residues: 18 sheet: 0.21 (0.24), residues: 387 loop : -1.37 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 136 TYR 0.012 0.002 TYR D 158 PHE 0.017 0.002 PHE D 118 HIS 0.004 0.001 HIS G 11 Details of bonding type rmsd covalent geometry : bond 0.00504 (10171) covalent geometry : angle 0.57889 (13897) SS BOND : bond 0.00468 ( 9) SS BOND : angle 1.41532 ( 18) hydrogen bonds : bond 0.03397 ( 316) hydrogen bonds : angle 6.58355 ( 849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8134 (mttm) REVERT: C 32 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8431 (p) REVERT: C 36 GLN cc_start: 0.8484 (mp10) cc_final: 0.8262 (mt0) REVERT: C 105 ASP cc_start: 0.8023 (p0) cc_final: 0.7574 (p0) REVERT: D 44 GLN cc_start: 0.8022 (pm20) cc_final: 0.7750 (pt0) REVERT: E 48 THR cc_start: 0.8931 (m) cc_final: 0.8647 (p) REVERT: F 42 LEU cc_start: 0.7936 (mt) cc_final: 0.7718 (mt) REVERT: H 60 ASP cc_start: 0.8191 (t70) cc_final: 0.7879 (t0) REVERT: J 45 GLU cc_start: 0.7825 (tp30) cc_final: 0.7425 (tp30) REVERT: J 158 TYR cc_start: 0.8584 (m-80) cc_final: 0.7961 (m-80) REVERT: K 84 ASN cc_start: 0.8754 (p0) cc_final: 0.8353 (p0) REVERT: K 158 TYR cc_start: 0.7649 (m-10) cc_final: 0.7438 (m-80) outliers start: 53 outliers final: 52 residues processed: 261 average time/residue: 0.0734 time to fit residues: 29.3950 Evaluate side-chains 274 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 55 ASN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 117 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN J 157 GLN K 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100128 restraints weight = 16499.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102821 restraints weight = 7953.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104541 restraints weight = 4542.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105676 restraints weight = 2909.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106467 restraints weight = 2027.546| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10180 Z= 0.136 Angle : 0.521 7.459 13915 Z= 0.283 Chirality : 0.042 0.150 1738 Planarity : 0.002 0.029 1861 Dihedral : 4.143 15.339 1472 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.62 % Allowed : 21.61 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.20), residues: 1417 helix: -3.45 (0.86), residues: 18 sheet: 0.34 (0.25), residues: 375 loop : -1.25 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 136 TYR 0.013 0.001 TYR D 158 PHE 0.017 0.002 PHE D 118 HIS 0.002 0.001 HIS G 11 Details of bonding type rmsd covalent geometry : bond 0.00301 (10171) covalent geometry : angle 0.51990 (13897) SS BOND : bond 0.00296 ( 9) SS BOND : angle 1.06830 ( 18) hydrogen bonds : bond 0.02993 ( 316) hydrogen bonds : angle 6.18443 ( 849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8109 (mttm) REVERT: C 32 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8262 (p) REVERT: C 36 GLN cc_start: 0.8471 (mp10) cc_final: 0.8244 (mt0) REVERT: C 105 ASP cc_start: 0.8018 (p0) cc_final: 0.7570 (p0) REVERT: D 44 GLN cc_start: 0.7944 (pm20) cc_final: 0.7662 (pt0) REVERT: E 48 THR cc_start: 0.8819 (m) cc_final: 0.8575 (p) REVERT: F 38 ARG cc_start: 0.8301 (mtp180) cc_final: 0.8057 (mtp180) REVERT: F 42 LEU cc_start: 0.7693 (mt) cc_final: 0.7452 (mt) REVERT: G 155 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7980 (ptpp) REVERT: H 60 ASP cc_start: 0.8168 (t70) cc_final: 0.7927 (t70) REVERT: J 45 GLU cc_start: 0.7861 (tp30) cc_final: 0.7395 (tp30) REVERT: J 158 TYR cc_start: 0.8560 (m-80) cc_final: 0.8001 (m-80) REVERT: K 84 ASN cc_start: 0.8649 (p0) cc_final: 0.8217 (p0) REVERT: K 158 TYR cc_start: 0.7501 (m-10) cc_final: 0.7291 (m-80) outliers start: 47 outliers final: 37 residues processed: 257 average time/residue: 0.0742 time to fit residues: 29.4845 Evaluate side-chains 264 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 55 ASN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 10 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 120 optimal weight: 0.0970 chunk 60 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN J 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.098077 restraints weight = 16538.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.100786 restraints weight = 8010.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102485 restraints weight = 4593.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103619 restraints weight = 2957.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104247 restraints weight = 2076.016| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10180 Z= 0.188 Angle : 0.560 8.069 13915 Z= 0.304 Chirality : 0.043 0.153 1738 Planarity : 0.003 0.034 1861 Dihedral : 4.298 14.629 1472 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.13 % Allowed : 22.20 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.20), residues: 1417 helix: -3.44 (0.85), residues: 18 sheet: 0.27 (0.24), residues: 387 loop : -1.22 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 136 TYR 0.013 0.002 TYR D 158 PHE 0.016 0.002 PHE D 118 HIS 0.003 0.001 HIS H 11 Details of bonding type rmsd covalent geometry : bond 0.00422 (10171) covalent geometry : angle 0.55850 (13897) SS BOND : bond 0.00390 ( 9) SS BOND : angle 1.39361 ( 18) hydrogen bonds : bond 0.03194 ( 316) hydrogen bonds : angle 6.27168 ( 849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8241 (mttm) REVERT: C 32 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8335 (p) REVERT: C 105 ASP cc_start: 0.8018 (p0) cc_final: 0.7566 (p0) REVERT: D 44 GLN cc_start: 0.7927 (pm20) cc_final: 0.7701 (pt0) REVERT: E 48 THR cc_start: 0.8847 (m) cc_final: 0.8567 (p) REVERT: F 38 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7944 (mtp180) REVERT: F 42 LEU cc_start: 0.7799 (mt) cc_final: 0.7570 (mt) REVERT: G 155 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8013 (ptpp) REVERT: H 60 ASP cc_start: 0.8164 (t70) cc_final: 0.7800 (t0) REVERT: J 45 GLU cc_start: 0.7886 (tp30) cc_final: 0.7429 (tp30) REVERT: J 158 TYR cc_start: 0.8592 (m-80) cc_final: 0.8026 (m-80) REVERT: K 62 ASP cc_start: 0.6404 (t70) cc_final: 0.5591 (t70) REVERT: K 84 ASN cc_start: 0.8672 (p0) cc_final: 0.8265 (p0) REVERT: K 158 TYR cc_start: 0.7490 (m-10) cc_final: 0.7280 (m-80) outliers start: 42 outliers final: 39 residues processed: 246 average time/residue: 0.0743 time to fit residues: 28.0692 Evaluate side-chains 267 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 55 ASN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 8 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 120 optimal weight: 0.0050 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.099915 restraints weight = 16569.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102686 restraints weight = 8055.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104449 restraints weight = 4632.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105596 restraints weight = 2984.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106395 restraints weight = 2098.261| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10180 Z= 0.145 Angle : 0.529 7.713 13915 Z= 0.287 Chirality : 0.042 0.143 1738 Planarity : 0.002 0.029 1861 Dihedral : 4.085 14.061 1472 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.72 % Allowed : 22.00 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.20), residues: 1417 helix: -3.27 (0.91), residues: 18 sheet: 0.38 (0.25), residues: 375 loop : -1.16 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 136 TYR 0.013 0.001 TYR D 158 PHE 0.015 0.002 PHE D 118 HIS 0.002 0.001 HIS H 11 Details of bonding type rmsd covalent geometry : bond 0.00323 (10171) covalent geometry : angle 0.52740 (13897) SS BOND : bond 0.00304 ( 9) SS BOND : angle 1.21238 ( 18) hydrogen bonds : bond 0.02986 ( 316) hydrogen bonds : angle 6.08924 ( 849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1456.55 seconds wall clock time: 26 minutes 2.95 seconds (1562.95 seconds total)