Starting phenix.real_space_refine on Mon Jul 28 03:03:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ftt_50751/07_2025/9ftt_50751.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ftt_50751/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ftt_50751/07_2025/9ftt_50751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ftt_50751/07_2025/9ftt_50751.map" model { file = "/net/cci-nas-00/data/ceres_data/9ftt_50751/07_2025/9ftt_50751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ftt_50751/07_2025/9ftt_50751.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.03, per 1000 atoms: 0.60 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: 2.66 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.25 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: 2.52 Time building geometry restraints manager: 2.91 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.910 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), 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 HIS 0.002 0.001 HIS D 11 PHE 0.011 0.001 PHE E 54 TYR 0.007 0.001 TYR J 158 ARG 0.002 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.15593 ( 316) hydrogen bonds : angle 8.10151 ( 849) SS BOND : bond 0.00162 ( 9) SS BOND : angle 0.59090 ( 18) covalent geometry : bond 0.00232 (10171) covalent geometry : angle 0.46718 (13897) *********************** 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 : 1.013 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: 0.1678 time to fit residues: 80.4255 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 : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099885 restraints weight = 16389.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.102679 restraints weight = 7973.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104433 restraints weight = 4565.900| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1787 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= 0.234 Angle : 0.562 6.172 13915 Z= 0.311 Chirality : 0.043 0.154 1738 Planarity : 0.003 0.029 1861 Dihedral : 4.074 13.230 1472 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.83 % Allowed : 10.71 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.20), residues: 1417 helix: -2.59 (0.67), residues: 36 sheet: 0.60 (0.24), residues: 390 loop : -1.03 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 11 PHE 0.021 0.002 PHE F 118 TYR 0.012 0.002 TYR K 158 ARG 0.004 0.001 ARG K 38 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 316) hydrogen bonds : angle 6.59914 ( 849) SS BOND : bond 0.00477 ( 9) SS BOND : angle 1.25724 ( 18) covalent geometry : bond 0.00522 (10171) covalent geometry : angle 0.56055 (13897) *********************** 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 275 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.896 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: 0.8751 (mmtt) cc_final: 0.8381 (mmtp) REVERT: C 105 ASP cc_start: 0.8022 (p0) cc_final: 0.7684 (p0) REVERT: C 106 ARG cc_start: 0.7764 (tmm160) cc_final: 0.7313 (tmm-80) REVERT: D 13 LYS cc_start: 0.8696 (mmtp) cc_final: 0.8332 (mtpp) REVERT: D 33 GLN cc_start: 0.7643 (tp40) cc_final: 0.7401 (tp40) REVERT: D 59 ASN cc_start: 0.8407 (p0) cc_final: 0.8131 (p0) REVERT: D 60 ASP cc_start: 0.7320 (t70) cc_final: 0.7070 (t70) REVERT: D 120 SER cc_start: 0.8575 (p) cc_final: 0.8207 (p) REVERT: E 48 THR cc_start: 0.8917 (m) cc_final: 0.8572 (p) REVERT: F 38 ARG cc_start: 0.8379 (mtp180) cc_final: 0.7767 (mtm180) REVERT: F 78 ILE cc_start: 0.8805 (tt) cc_final: 0.8396 (tp) REVERT: H 4 THR cc_start: 0.8799 (m) cc_final: 0.8469 (t) REVERT: H 60 ASP cc_start: 0.8176 (t70) cc_final: 0.7828 (t0) REVERT: I 84 ASN cc_start: 0.8826 (p0) cc_final: 0.8555 (p0) REVERT: J 13 LYS cc_start: 0.8500 (mttm) cc_final: 0.8189 (mtpp) REVERT: J 157 GLN cc_start: 0.7510 (tt0) cc_final: 0.7301 (tt0) REVERT: K 38 ARG cc_start: 0.7772 (mtm180) cc_final: 0.7503 (mtm110) REVERT: K 84 ASN cc_start: 0.8677 (p0) cc_final: 0.8310 (p0) REVERT: K 113 LEU cc_start: 0.7952 (mt) cc_final: 0.7552 (mp) outliers start: 39 outliers final: 30 residues processed: 257 average time/residue: 0.1712 time to fit residues: 66.0751 Evaluate side-chains 251 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 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 72 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 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 64 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN K 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.095498 restraints weight = 16787.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.098202 restraints weight = 8160.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099936 restraints weight = 4709.239| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 10180 Z= 0.299 Angle : 0.614 7.263 13915 Z= 0.339 Chirality : 0.045 0.146 1738 Planarity : 0.003 0.032 1861 Dihedral : 4.638 17.804 1472 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.52 % Allowed : 14.34 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.19), residues: 1417 helix: -3.24 (0.98), residues: 18 sheet: 0.46 (0.24), residues: 387 loop : -1.16 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 11 PHE 0.021 0.003 PHE G 154 TYR 0.012 0.002 TYR K 158 ARG 0.006 0.001 ARG J 106 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 316) hydrogen bonds : angle 6.76502 ( 849) SS BOND : bond 0.00599 ( 9) SS BOND : angle 1.35593 ( 18) covalent geometry : bond 0.00666 (10171) covalent geometry : angle 0.61245 (13897) *********************** 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 274 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.957 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: 0.8797 (mmtt) cc_final: 0.8106 (mttm) REVERT: C 105 ASP cc_start: 0.8189 (p0) cc_final: 0.7792 (p0) REVERT: C 106 ARG cc_start: 0.7833 (tmm160) cc_final: 0.7339 (tmm-80) REVERT: D 79 ASP cc_start: 0.8179 (t0) cc_final: 0.7966 (t0) REVERT: E 48 THR cc_start: 0.9000 (m) cc_final: 0.8692 (p) REVERT: F 33 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7876 (mm-40) REVERT: G 117 THR cc_start: 0.7710 (m) cc_final: 0.7416 (p) REVERT: G 155 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7665 (mtmm) REVERT: H 4 THR cc_start: 0.8820 (m) cc_final: 0.8553 (t) REVERT: H 44 GLN cc_start: 0.8427 (tp-100) cc_final: 0.8093 (tp40) REVERT: H 60 ASP cc_start: 0.8260 (t70) cc_final: 0.7848 (t0) REVERT: K 84 ASN cc_start: 0.8778 (p0) cc_final: 0.8412 (p0) REVERT: K 113 LEU cc_start: 0.7967 (mt) cc_final: 0.7564 (mp) outliers start: 46 outliers final: 42 residues processed: 258 average time/residue: 0.1646 time to fit residues: 64.1490 Evaluate side-chains 257 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL 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 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 D residue 155 LYS 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 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 9 THR 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 78 ILE 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 67 SER 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 3 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- 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** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN J 157 GLN K 18 ASN K 55 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.100770 restraints weight = 16339.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.103513 restraints weight = 7940.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105268 restraints weight = 4564.060| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2363 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= 0.132 Angle : 0.483 5.918 13915 Z= 0.267 Chirality : 0.041 0.135 1738 Planarity : 0.002 0.030 1861 Dihedral : 3.959 13.164 1472 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.44 % Allowed : 17.29 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1417 helix: -3.08 (1.00), residues: 18 sheet: 0.62 (0.24), residues: 375 loop : -1.08 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 11 PHE 0.017 0.002 PHE D 118 TYR 0.012 0.001 TYR K 158 ARG 0.004 0.000 ARG J 106 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 316) hydrogen bonds : angle 6.11710 ( 849) SS BOND : bond 0.00277 ( 9) SS BOND : angle 0.84887 ( 18) covalent geometry : bond 0.00288 (10171) covalent geometry : angle 0.48248 (13897) *********************** 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 266 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.979 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: 0.8811 (mmtt) cc_final: 0.8180 (mttm) REVERT: C 32 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.7947 (p) REVERT: C 36 GLN cc_start: 0.8433 (mp10) cc_final: 0.8188 (mt0) REVERT: C 105 ASP cc_start: 0.8015 (p0) cc_final: 0.7534 (p0) REVERT: C 106 ARG cc_start: 0.7719 (tmm160) cc_final: 0.7353 (tmm-80) REVERT: E 48 THR cc_start: 0.8860 (m) cc_final: 0.8502 (p) REVERT: F 33 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7814 (mm-40) REVERT: F 42 LEU cc_start: 0.7749 (mt) cc_final: 0.7492 (mt) REVERT: H 4 THR cc_start: 0.8792 (m) cc_final: 0.8494 (t) REVERT: H 60 ASP cc_start: 0.8078 (t70) cc_final: 0.7790 (t70) REVERT: K 84 ASN cc_start: 0.8747 (p0) cc_final: 0.8253 (p0) REVERT: K 113 LEU cc_start: 0.7953 (mt) cc_final: 0.7462 (mp) outliers start: 35 outliers final: 28 residues processed: 248 average time/residue: 0.1769 time to fit residues: 66.6885 Evaluate side-chains 241 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 78 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 27 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 G residue 27 SER Chi-restraints excluded: chain G residue 28 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 52 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 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 41 SER Chi-restraints excluded: chain K residue 83 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 107 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 125 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.8362 ------------------------------------------------------------------------------- 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 ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN K 18 ASN K 36 GLN K 55 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.098372 restraints weight = 16633.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101118 restraints weight = 8030.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102858 restraints weight = 4603.918| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10180 Z= 0.207 Angle : 0.537 7.222 13915 Z= 0.295 Chirality : 0.042 0.143 1738 Planarity : 0.003 0.029 1861 Dihedral : 4.239 14.339 1472 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.52 % Allowed : 18.17 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1417 helix: -3.06 (0.97), residues: 18 sheet: 0.53 (0.24), residues: 375 loop : -1.11 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 11 PHE 0.019 0.002 PHE F 118 TYR 0.012 0.001 TYR D 158 ARG 0.003 0.000 ARG J 106 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 316) hydrogen bonds : angle 6.28095 ( 849) SS BOND : bond 0.00400 ( 9) SS BOND : angle 1.30906 ( 18) covalent geometry : bond 0.00460 (10171) covalent geometry : angle 0.53541 (13897) *********************** 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 271 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 1.136 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: symmetry clash REVERT: C 13 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8094 (mttm) REVERT: C 32 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.7996 (p) REVERT: C 36 GLN cc_start: 0.8429 (mp10) cc_final: 0.8166 (mt0) REVERT: C 105 ASP cc_start: 0.8134 (p0) cc_final: 0.7612 (p0) REVERT: C 106 ARG cc_start: 0.7728 (tmm160) cc_final: 0.7350 (tmm-80) REVERT: D 44 GLN cc_start: 0.7991 (pm20) cc_final: 0.7665 (pt0) REVERT: E 29 ASP cc_start: 0.8447 (p0) cc_final: 0.8213 (p0) REVERT: E 48 THR cc_start: 0.8912 (m) cc_final: 0.8596 (p) REVERT: F 33 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7811 (mm-40) REVERT: F 38 ARG cc_start: 0.8370 (mtp180) cc_final: 0.7842 (mtp-110) REVERT: F 42 LEU cc_start: 0.7919 (mt) cc_final: 0.7625 (mt) REVERT: H 4 THR cc_start: 0.8719 (m) cc_final: 0.8441 (t) REVERT: H 60 ASP cc_start: 0.8196 (t70) cc_final: 0.7901 (t70) REVERT: J 45 GLU cc_start: 0.7677 (tp30) cc_final: 0.6861 (tp30) REVERT: J 84 ASN cc_start: 0.8923 (p0) cc_final: 0.8702 (p0) REVERT: K 84 ASN cc_start: 0.8758 (p0) cc_final: 0.8263 (p0) REVERT: K 113 LEU cc_start: 0.7993 (mt) cc_final: 0.7411 (mp) outliers start: 46 outliers final: 42 residues processed: 251 average time/residue: 0.1690 time to fit residues: 64.3968 Evaluate side-chains 264 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 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 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 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 101 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 41 SER 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 6 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN K 18 ASN K 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099501 restraints weight = 16584.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.102273 restraints weight = 7996.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104032 restraints weight = 4601.003| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10180 Z= 0.153 Angle : 0.500 6.957 13915 Z= 0.273 Chirality : 0.042 0.140 1738 Planarity : 0.002 0.030 1861 Dihedral : 4.051 14.326 1472 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.72 % Allowed : 18.96 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1417 helix: -2.93 (0.98), residues: 18 sheet: 0.58 (0.24), residues: 375 loop : -1.09 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 11 PHE 0.018 0.002 PHE D 118 TYR 0.012 0.001 TYR D 158 ARG 0.003 0.000 ARG J 106 Details of bonding type rmsd hydrogen bonds : bond 0.03099 ( 316) hydrogen bonds : angle 6.07812 ( 849) SS BOND : bond 0.00319 ( 9) SS BOND : angle 1.12174 ( 18) covalent geometry : bond 0.00341 (10171) covalent geometry : angle 0.49853 (13897) *********************** 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 268 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 1.032 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: 0.8792 (mmtt) cc_final: 0.8120 (mttm) REVERT: C 32 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.7983 (p) REVERT: C 36 GLN cc_start: 0.8456 (mp10) cc_final: 0.8225 (mt0) REVERT: C 105 ASP cc_start: 0.8083 (p0) cc_final: 0.7484 (p0) REVERT: E 29 ASP cc_start: 0.8418 (p0) cc_final: 0.8215 (p0) REVERT: E 48 THR cc_start: 0.8861 (m) cc_final: 0.8568 (p) REVERT: F 33 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7770 (mm-40) REVERT: F 38 ARG cc_start: 0.8505 (mtp180) cc_final: 0.8026 (mtp-110) REVERT: H 4 THR cc_start: 0.8723 (m) cc_final: 0.8445 (t) REVERT: H 44 GLN cc_start: 0.8476 (tp40) cc_final: 0.8214 (tp40) REVERT: H 60 ASP cc_start: 0.8103 (t70) cc_final: 0.7903 (t70) REVERT: J 45 GLU cc_start: 0.7627 (tp30) cc_final: 0.6783 (tp30) REVERT: J 84 ASN cc_start: 0.8852 (p0) cc_final: 0.8596 (p0) REVERT: K 84 ASN cc_start: 0.8739 (p0) cc_final: 0.8309 (p0) REVERT: K 113 LEU cc_start: 0.8004 (mt) cc_final: 0.7479 (mp) outliers start: 48 outliers final: 40 residues processed: 245 average time/residue: 0.1649 time to fit residues: 61.4469 Evaluate side-chains 253 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 97 THR 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 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 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 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 18 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 117 optimal weight: 0.0980 chunk 50 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 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 134 GLN ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.095028 restraints weight = 17067.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.097709 restraints weight = 8236.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.099434 restraints weight = 4722.883| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 10180 Z= 0.323 Angle : 0.648 9.340 13915 Z= 0.354 Chirality : 0.045 0.164 1738 Planarity : 0.003 0.032 1861 Dihedral : 4.834 18.348 1472 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.40 % Allowed : 19.55 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 1417 helix: -3.44 (0.83), residues: 18 sheet: 0.22 (0.24), residues: 387 loop : -1.33 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 11 PHE 0.021 0.003 PHE I 12 TYR 0.013 0.002 TYR D 158 ARG 0.003 0.001 ARG J 38 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 316) hydrogen bonds : angle 6.72739 ( 849) SS BOND : bond 0.00667 ( 9) SS BOND : angle 1.81021 ( 18) covalent geometry : bond 0.00720 (10171) covalent geometry : angle 0.64520 (13897) *********************** 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 278 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 1.067 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: symmetry clash REVERT: C 13 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8142 (mttm) REVERT: C 36 GLN cc_start: 0.8477 (mp10) cc_final: 0.8268 (mt0) REVERT: C 105 ASP cc_start: 0.8249 (p0) cc_final: 0.7655 (p0) REVERT: D 44 GLN cc_start: 0.7883 (pm20) cc_final: 0.7640 (pt0) REVERT: E 48 THR cc_start: 0.8978 (m) cc_final: 0.8701 (p) REVERT: G 155 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8020 (ptpp) REVERT: H 44 GLN cc_start: 0.8406 (tp40) cc_final: 0.8187 (tp40) REVERT: H 60 ASP cc_start: 0.8331 (t70) cc_final: 0.7945 (t0) REVERT: H 159 GLN cc_start: 0.7405 (tt0) cc_final: 0.7147 (tm-30) REVERT: J 158 TYR cc_start: 0.8628 (m-80) cc_final: 0.7982 (m-80) REVERT: K 84 ASN cc_start: 0.8764 (p0) cc_final: 0.8396 (p0) REVERT: K 158 TYR cc_start: 0.8064 (m-80) cc_final: 0.7862 (m-10) outliers start: 55 outliers final: 49 residues processed: 255 average time/residue: 0.1639 time to fit residues: 63.4067 Evaluate side-chains 268 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 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 D residue 91 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 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 124 LEU 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 155 LYS 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 5 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 83 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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** G 134 GLN H 102 GLN ** 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 = 0.3249 r_free = 0.3249 target = 0.108298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097766 restraints weight = 16712.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.100495 restraints weight = 8076.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.102229 restraints weight = 4624.018| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10180 Z= 0.201 Angle : 0.566 7.939 13915 Z= 0.306 Chirality : 0.043 0.172 1738 Planarity : 0.003 0.041 1861 Dihedral : 4.481 15.684 1472 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.40 % Allowed : 20.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.19), residues: 1417 helix: -3.48 (0.84), residues: 18 sheet: 0.23 (0.24), residues: 387 loop : -1.28 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 11 PHE 0.016 0.002 PHE D 118 TYR 0.015 0.001 TYR D 158 ARG 0.008 0.001 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 316) hydrogen bonds : angle 6.46534 ( 849) SS BOND : bond 0.00450 ( 9) SS BOND : angle 1.55889 ( 18) covalent geometry : bond 0.00449 (10171) covalent geometry : angle 0.56314 (13897) *********************** 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 278 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 0.976 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: symmetry clash REVERT: C 13 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8189 (mttm) REVERT: C 57 GLN cc_start: 0.8306 (tt0) cc_final: 0.8080 (tt0) REVERT: C 105 ASP cc_start: 0.8011 (p0) cc_final: 0.7472 (p0) REVERT: D 44 GLN cc_start: 0.7963 (pm20) cc_final: 0.7704 (pt0) REVERT: E 48 THR cc_start: 0.8893 (m) cc_final: 0.8589 (p) REVERT: F 38 ARG cc_start: 0.8316 (mtp180) cc_final: 0.8080 (mtp180) REVERT: G 155 LYS cc_start: 0.8422 (pttt) cc_final: 0.8030 (ptpp) REVERT: H 60 ASP cc_start: 0.8222 (t70) cc_final: 0.8020 (t70) REVERT: J 45 GLU cc_start: 0.7803 (tp30) cc_final: 0.7040 (tp30) REVERT: J 158 TYR cc_start: 0.8573 (m-80) cc_final: 0.7937 (m-80) REVERT: K 84 ASN cc_start: 0.8732 (p0) cc_final: 0.8345 (p0) outliers start: 55 outliers final: 52 residues processed: 258 average time/residue: 0.2116 time to fit residues: 82.9207 Evaluate side-chains 267 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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 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 62 ASP Chi-restraints excluded: chain E residue 65 VAL 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 124 LEU 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 H residue 157 GLN 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 76 THR Chi-restraints excluded: chain K residue 83 THR 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 126 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN K 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.098787 restraints weight = 16600.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101527 restraints weight = 7986.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103269 restraints weight = 4556.293| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10180 Z= 0.165 Angle : 0.537 7.840 13915 Z= 0.291 Chirality : 0.042 0.154 1738 Planarity : 0.003 0.030 1861 Dihedral : 4.230 15.752 1472 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.01 % Allowed : 21.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.20), residues: 1417 helix: -3.36 (0.88), residues: 18 sheet: 0.40 (0.25), residues: 375 loop : -1.23 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 11 PHE 0.017 0.002 PHE D 118 TYR 0.013 0.001 TYR D 158 ARG 0.006 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 316) hydrogen bonds : angle 6.20991 ( 849) SS BOND : bond 0.00347 ( 9) SS BOND : angle 1.32352 ( 18) covalent geometry : bond 0.00368 (10171) covalent geometry : angle 0.53508 (13897) *********************** 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 276 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 1.055 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: symmetry clash REVERT: C 13 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8139 (mttm) REVERT: C 105 ASP cc_start: 0.8093 (p0) cc_final: 0.7525 (p0) REVERT: D 44 GLN cc_start: 0.7961 (pm20) cc_final: 0.7670 (pt0) REVERT: E 48 THR cc_start: 0.8865 (m) cc_final: 0.8561 (p) REVERT: F 38 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7792 (mtp-110) REVERT: G 155 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8048 (ptpp) REVERT: H 60 ASP cc_start: 0.8184 (t70) cc_final: 0.7943 (t70) REVERT: J 158 TYR cc_start: 0.8592 (m-80) cc_final: 0.7964 (m-80) REVERT: K 84 ASN cc_start: 0.8674 (p0) cc_final: 0.8281 (p0) outliers start: 51 outliers final: 49 residues processed: 256 average time/residue: 0.1645 time to fit residues: 64.0786 Evaluate side-chains 270 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 65 VAL 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 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 104 LEU 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 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 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 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 130 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** ** G 159 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 = 0.3293 r_free = 0.3293 target = 0.111504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101053 restraints weight = 16600.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103822 restraints weight = 7930.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105584 restraints weight = 4502.185| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2907 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= 0.132 Angle : 0.516 7.866 13915 Z= 0.279 Chirality : 0.042 0.143 1738 Planarity : 0.002 0.030 1861 Dihedral : 4.001 13.987 1472 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.91 % Allowed : 21.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.20), residues: 1417 helix: -2.96 (0.95), residues: 18 sheet: 0.51 (0.25), residues: 375 loop : -1.15 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 11 PHE 0.016 0.002 PHE D 118 TYR 0.013 0.001 TYR D 158 ARG 0.005 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.02939 ( 316) hydrogen bonds : angle 5.99039 ( 849) SS BOND : bond 0.00282 ( 9) SS BOND : angle 1.14033 ( 18) covalent geometry : bond 0.00294 (10171) covalent geometry : angle 0.51474 (13897) ********************** 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 273 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 1.204 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: 0.8855 (mmtt) cc_final: 0.8252 (mttm) REVERT: C 105 ASP cc_start: 0.7952 (p0) cc_final: 0.7468 (p0) REVERT: D 44 GLN cc_start: 0.7917 (pm20) cc_final: 0.7652 (pt0) REVERT: E 48 THR cc_start: 0.8731 (m) cc_final: 0.8445 (p) REVERT: F 38 ARG cc_start: 0.8260 (mtp180) cc_final: 0.7758 (mtp-110) REVERT: G 155 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7965 (ptpp) REVERT: H 60 ASP cc_start: 0.8082 (t70) cc_final: 0.7836 (t70) REVERT: J 33 GLN cc_start: 0.8699 (tt0) cc_final: 0.8450 (tp40) REVERT: J 158 TYR cc_start: 0.8572 (m-80) cc_final: 0.7973 (m-80) REVERT: K 84 ASN cc_start: 0.8625 (p0) cc_final: 0.8240 (p0) outliers start: 50 outliers final: 46 residues processed: 252 average time/residue: 0.1796 time to fit residues: 69.0487 Evaluate side-chains 266 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 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 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 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 131 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 155 LYS 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 H residue 157 GLN 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 117 THR Chi-restraints excluded: chain J residue 123 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 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 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.0170 chunk 84 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.9022 ------------------------------------------------------------------------------- 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 59 ASN ** I 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 = 0.3300 r_free = 0.3300 target = 0.111992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.101577 restraints weight = 16293.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104332 restraints weight = 7860.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106079 restraints weight = 4481.714| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10180 Z= 0.128 Angle : 0.511 7.228 13915 Z= 0.278 Chirality : 0.042 0.139 1738 Planarity : 0.002 0.030 1861 Dihedral : 3.879 14.223 1472 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.13 % Allowed : 23.08 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1417 helix: -2.61 (1.09), residues: 18 sheet: 0.61 (0.25), residues: 375 loop : -1.08 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 11 PHE 0.017 0.002 PHE D 118 TYR 0.013 0.001 TYR D 158 ARG 0.005 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.02853 ( 316) hydrogen bonds : angle 5.82479 ( 849) SS BOND : bond 0.00278 ( 9) SS BOND : angle 1.06398 ( 18) covalent geometry : bond 0.00286 (10171) covalent geometry : angle 0.51034 (13897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3506.55 seconds wall clock time: 63 minutes 30.69 seconds (3810.69 seconds total)