Starting phenix.real_space_refine on Tue Mar 3 17:46:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q64_13851/03_2026/7q64_13851.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q64_13851/03_2026/7q64_13851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q64_13851/03_2026/7q64_13851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q64_13851/03_2026/7q64_13851.map" model { file = "/net/cci-nas-00/data/ceres_data/7q64_13851/03_2026/7q64_13851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q64_13851/03_2026/7q64_13851.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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: 3 Type Number sf(0) Gaussians C 4830 2.51 5 N 1340 2.21 5 O 1640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7810 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "a" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 244 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "b" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "c" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 255 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "d" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 244 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "B" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 255 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "C" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 244 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "D" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 255 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "F" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 244 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "G" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "H" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 255 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "I" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 244 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "J" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "K" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 255 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "L" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 244 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "M" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "N" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 255 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "O" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 244 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "P" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Q" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 255 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "R" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 244 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "S" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "T" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 255 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "U" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 244 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "V" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "W" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 255 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "X" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 244 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "Y" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Z" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 255 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Time building chain proxies: 1.88, per 1000 atoms: 0.24 Number of scatterers: 7810 At special positions: 0 Unit cell: (93.45, 80.85, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1640 8.00 N 1340 7.00 C 4830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 334.0 milliseconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.422A pdb=" N GLY b 93 " --> pdb=" O THR Y 94 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER Y 96 " --> pdb=" O GLY b 93 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA b 95 " --> pdb=" O SER Y 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 104 removed outlier: 6.721A pdb=" N LEU A 101 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE D 102 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU D 101 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE G 102 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU G 101 " --> pdb=" O SER J 100 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE J 102 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU J 101 " --> pdb=" O SER M 100 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE M 102 " --> pdb=" O LEU J 101 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU M 101 " --> pdb=" O SER P 100 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE P 102 " --> pdb=" O LEU M 101 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU P 101 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE S 102 " --> pdb=" O LEU P 101 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU S 101 " --> pdb=" O SER V 100 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE V 102 " --> pdb=" O LEU S 101 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU V 101 " --> pdb=" O SER Y 100 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE Y 102 " --> pdb=" O LEU V 101 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N SER b 100 " --> pdb=" O LEU Y 101 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N SER Y 103 " --> pdb=" O SER b 100 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE b 102 " --> pdb=" O SER Y 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 123 removed outlier: 6.527A pdb=" N PHE b 120 " --> pdb=" O GLY Y 121 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER Y 123 " --> pdb=" O PHE b 120 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR b 122 " --> pdb=" O SER Y 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 90 through 94 removed outlier: 6.506A pdb=" N THR a 90 " --> pdb=" O LEU X 91 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLY X 93 " --> pdb=" O THR a 90 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE a 92 " --> pdb=" O GLY X 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 97 through 101 removed outlier: 6.729A pdb=" N SER d 100 " --> pdb=" O THR a 99 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU a 101 " --> pdb=" O SER d 100 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLY a 98 " --> pdb=" O THR X 99 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU X 101 " --> pdb=" O GLY a 98 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N SER a 100 " --> pdb=" O LEU X 101 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER X 100 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU U 101 " --> pdb=" O SER X 100 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER U 100 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU R 101 " --> pdb=" O SER U 100 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER R 100 " --> pdb=" O THR O 99 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU O 101 " --> pdb=" O SER R 100 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER O 100 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU L 101 " --> pdb=" O SER O 100 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER L 100 " --> pdb=" O THR I 99 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU I 101 " --> pdb=" O SER L 100 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER I 100 " --> pdb=" O THR F 99 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU F 101 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER F 100 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU C 101 " --> pdb=" O SER F 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 104 through 111 removed outlier: 6.363A pdb=" N SER a 104 " --> pdb=" O GLN X 105 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASN X 107 " --> pdb=" O SER a 104 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASN a 106 " --> pdb=" O ASN X 107 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE X 109 " --> pdb=" O ASN a 106 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA a 108 " --> pdb=" O PHE X 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N GLN X 111 " --> pdb=" O ALA a 108 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA a 110 " --> pdb=" O GLN X 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'd' and resid 115 through 120 removed outlier: 8.881A pdb=" N THR a 115 " --> pdb=" O GLY d 116 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLY d 118 " --> pdb=" O THR a 115 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE a 117 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N PHE d 120 " --> pdb=" O PHE a 117 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN a 119 " --> pdb=" O PHE d 120 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY a 116 " --> pdb=" O THR X 115 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE X 117 " --> pdb=" O GLY a 116 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N THR U 115 " --> pdb=" O GLY X 116 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLY X 118 " --> pdb=" O THR U 115 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE U 117 " --> pdb=" O GLY X 118 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE X 120 " --> pdb=" O PHE U 117 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN U 119 " --> pdb=" O PHE X 120 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N THR R 115 " --> pdb=" O GLY U 116 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLY U 118 " --> pdb=" O THR R 115 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE R 117 " --> pdb=" O GLY U 118 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE U 120 " --> pdb=" O PHE R 117 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN R 119 " --> pdb=" O PHE U 120 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N THR O 115 " --> pdb=" O GLY R 116 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLY R 118 " --> pdb=" O THR O 115 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE O 117 " --> pdb=" O GLY R 118 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE R 120 " --> pdb=" O PHE O 117 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN O 119 " --> pdb=" O PHE R 120 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N THR L 115 " --> pdb=" O GLY O 116 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLY O 118 " --> pdb=" O THR L 115 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE L 117 " --> pdb=" O GLY O 118 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE O 120 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN L 119 " --> pdb=" O PHE O 120 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N THR I 115 " --> pdb=" O GLY L 116 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N GLY L 118 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE I 117 " --> pdb=" O GLY L 118 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE L 120 " --> pdb=" O PHE I 117 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN I 119 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N THR F 115 " --> pdb=" O GLY I 116 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N GLY I 118 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE F 117 " --> pdb=" O GLY I 118 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE I 120 " --> pdb=" O PHE F 117 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN F 119 " --> pdb=" O PHE I 120 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N THR C 115 " --> pdb=" O GLY F 116 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLY F 118 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE C 117 " --> pdb=" O GLY F 118 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE F 120 " --> pdb=" O PHE C 117 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN C 119 " --> pdb=" O PHE F 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 88 through 89 removed outlier: 6.511A pdb=" N ALA c 88 " --> pdb=" O ASN Z 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 94 through 96 removed outlier: 6.413A pdb=" N ALA c 95 " --> pdb=" O SER Z 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 100 through 101 removed outlier: 6.684A pdb=" N SER W 100 " --> pdb=" O LEU Z 101 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER T 100 " --> pdb=" O LEU W 101 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER Q 100 " --> pdb=" O LEU T 101 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER N 100 " --> pdb=" O LEU Q 101 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER K 100 " --> pdb=" O LEU N 101 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER H 100 " --> pdb=" O LEU K 101 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER E 100 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER B 100 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 104 through 107 removed outlier: 6.648A pdb=" N SER c 104 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASN Z 107 " --> pdb=" O SER c 104 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASN c 106 " --> pdb=" O ASN Z 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 111 through 112 removed outlier: 6.904A pdb=" N GLN c 111 " --> pdb=" O ASN Z 112 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.26: 1310 1.26 - 1.33: 1269 1.33 - 1.41: 961 1.41 - 1.48: 1590 1.48 - 1.55: 2830 Bond restraints: 7960 Sorted by residual: bond pdb=" CE1 PHE A 117 " pdb=" CZ PHE A 117 " ideal model delta sigma weight residual 1.382 1.303 0.079 3.00e-02 1.11e+03 6.85e+00 bond pdb=" CE1 PHE V 117 " pdb=" CZ PHE V 117 " ideal model delta sigma weight residual 1.382 1.304 0.078 3.00e-02 1.11e+03 6.84e+00 bond pdb=" CE1 PHE b 117 " pdb=" CZ PHE b 117 " ideal model delta sigma weight residual 1.382 1.304 0.078 3.00e-02 1.11e+03 6.82e+00 bond pdb=" CE1 PHE M 117 " pdb=" CZ PHE M 117 " ideal model delta sigma weight residual 1.382 1.304 0.078 3.00e-02 1.11e+03 6.78e+00 bond pdb=" CE1 PHE P 117 " pdb=" CZ PHE P 117 " ideal model delta sigma weight residual 1.382 1.304 0.078 3.00e-02 1.11e+03 6.78e+00 ... (remaining 7955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 10411 3.02 - 6.03: 279 6.03 - 9.05: 40 9.05 - 12.06: 10 12.06 - 15.08: 20 Bond angle restraints: 10760 Sorted by residual: angle pdb=" CA ASN G 107 " pdb=" CB ASN G 107 " pdb=" CG ASN G 107 " ideal model delta sigma weight residual 112.60 117.00 -4.40 1.00e+00 1.00e+00 1.94e+01 angle pdb=" CA ASN b 107 " pdb=" CB ASN b 107 " pdb=" CG ASN b 107 " ideal model delta sigma weight residual 112.60 117.00 -4.40 1.00e+00 1.00e+00 1.93e+01 angle pdb=" CA ASN J 107 " pdb=" CB ASN J 107 " pdb=" CG ASN J 107 " ideal model delta sigma weight residual 112.60 116.99 -4.39 1.00e+00 1.00e+00 1.93e+01 angle pdb=" CA ASN P 107 " pdb=" CB ASN P 107 " pdb=" CG ASN P 107 " ideal model delta sigma weight residual 112.60 116.99 -4.39 1.00e+00 1.00e+00 1.93e+01 angle pdb=" CA ASN A 107 " pdb=" CB ASN A 107 " pdb=" CG ASN A 107 " ideal model delta sigma weight residual 112.60 116.99 -4.39 1.00e+00 1.00e+00 1.93e+01 ... (remaining 10755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.54: 3721 10.54 - 21.07: 529 21.07 - 31.61: 119 31.61 - 42.15: 0 42.15 - 52.68: 1 Dihedral angle restraints: 4370 sinusoidal: 1440 harmonic: 2930 Sorted by residual: dihedral pdb=" CA ALA S 108 " pdb=" C ALA S 108 " pdb=" N PHE S 109 " pdb=" CA PHE S 109 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ALA Y 108 " pdb=" C ALA Y 108 " pdb=" N PHE Y 109 " pdb=" CA PHE Y 109 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ALA V 108 " pdb=" C ALA V 108 " pdb=" N PHE V 109 " pdb=" CA PHE V 109 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1018 0.100 - 0.200: 122 0.200 - 0.301: 30 0.301 - 0.401: 10 0.401 - 0.501: 10 Chirality restraints: 1190 Sorted by residual: chirality pdb=" CG LEU F 91 " pdb=" CB LEU F 91 " pdb=" CD1 LEU F 91 " pdb=" CD2 LEU F 91 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CG LEU I 91 " pdb=" CB LEU I 91 " pdb=" CD1 LEU I 91 " pdb=" CD2 LEU I 91 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" CG LEU X 91 " pdb=" CB LEU X 91 " pdb=" CD1 LEU X 91 " pdb=" CD2 LEU X 91 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.23e+00 ... (remaining 1187 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE b 117 " 0.021 2.00e-02 2.50e+03 1.81e-02 5.73e+00 pdb=" CG PHE b 117 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE b 117 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE b 117 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE b 117 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE b 117 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE b 117 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 117 " -0.021 2.00e-02 2.50e+03 1.80e-02 5.70e+00 pdb=" CG PHE M 117 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 PHE M 117 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE M 117 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE M 117 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE M 117 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE M 117 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 117 " -0.021 2.00e-02 2.50e+03 1.80e-02 5.66e+00 pdb=" CG PHE D 117 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 PHE D 117 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE D 117 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE D 117 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE D 117 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 117 " -0.002 2.00e-02 2.50e+03 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2381 2.80 - 3.33: 7011 3.33 - 3.85: 14489 3.85 - 4.38: 17186 4.38 - 4.90: 31285 Nonbonded interactions: 72352 Sorted by model distance: nonbonded pdb=" OG1 THR K 99 " pdb=" O THR N 99 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR T 99 " pdb=" O THR W 99 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR B 99 " pdb=" O THR E 99 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR Q 99 " pdb=" O THR T 99 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR E 99 " pdb=" O THR H 99 " model vdw 2.276 3.040 ... (remaining 72347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 86 through 121) selection = chain 'B' selection = (chain 'D' and resid 86 through 121) selection = chain 'E' selection = (chain 'G' and resid 86 through 121) selection = chain 'H' selection = (chain 'J' and resid 86 through 121) selection = chain 'K' selection = (chain 'M' and resid 86 through 121) selection = chain 'N' selection = (chain 'P' and resid 86 through 121) selection = chain 'Q' selection = (chain 'S' and resid 86 through 121) selection = chain 'T' selection = (chain 'V' and resid 86 through 121) selection = chain 'W' selection = (chain 'Y' and resid 86 through 121) selection = chain 'Z' selection = (chain 'b' and resid 86 through 121) selection = chain 'c' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.100 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.330 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.014 0.079 7960 Z= 0.653 Angle : 1.344 15.079 10760 Z= 0.696 Chirality : 0.089 0.501 1190 Planarity : 0.006 0.028 1460 Dihedral : 10.199 52.683 2510 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.83 % Allowed : 2.47 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.01 (0.12), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.57 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.006 PHE M 117 Details of bonding type rmsd covalent geometry : bond 0.01413 ( 7960) covalent geometry : angle 1.34356 (10760) hydrogen bonds : bond 0.15786 ( 236) hydrogen bonds : angle 8.23608 ( 708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 321 time to evaluate : 0.274 Fit side-chains REVERT: Z 97 THR cc_start: 0.7691 (m) cc_final: 0.7486 (p) outliers start: 31 outliers final: 0 residues processed: 342 average time/residue: 0.2344 time to fit residues: 90.4720 Evaluate side-chains 206 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 107 ASN b 105 GLN b 106 ASN c 105 GLN ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 112 ASN G 105 GLN G 106 ASN G 107 ASN J 107 ASN L 119 ASN M 107 ASN M 112 ASN N 112 ASN P 106 ASN P 107 ASN P 112 ASN S 107 ASN T 112 ASN V 105 GLN W 112 ASN W 119 ASN Y 107 ASN Z 89 ASN Z 112 ASN Z 119 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.162061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.111555 restraints weight = 7884.569| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.27 r_work: 0.3349 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7960 Z= 0.153 Angle : 0.664 10.675 10760 Z= 0.338 Chirality : 0.041 0.284 1190 Planarity : 0.003 0.027 1460 Dihedral : 5.105 16.049 1070 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 7.16 % Allowed : 15.93 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.83 (0.12), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.44 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.002 PHE K 120 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7960) covalent geometry : angle 0.66399 (10760) hydrogen bonds : bond 0.05135 ( 236) hydrogen bonds : angle 5.84692 ( 708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 258 time to evaluate : 0.238 Fit side-chains REVERT: A 107 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.5367 (m-40) REVERT: A 123 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8651 (p) REVERT: b 89 ASN cc_start: 0.8581 (p0) cc_final: 0.8209 (p0) REVERT: d 113 LYS cc_start: 0.8691 (ttmt) cc_final: 0.7328 (tppt) REVERT: E 97 THR cc_start: 0.7282 (m) cc_final: 0.6924 (p) REVERT: G 112 ASN cc_start: 0.8281 (t0) cc_final: 0.8025 (t0) REVERT: G 113 LYS cc_start: 0.8475 (mttm) cc_final: 0.8216 (mttp) REVERT: I 94 THR cc_start: 0.7620 (m) cc_final: 0.7360 (m) REVERT: L 104 SER cc_start: 0.8994 (t) cc_final: 0.8752 (p) REVERT: Q 119 ASN cc_start: 0.6322 (m-40) cc_final: 0.5675 (m-40) REVERT: V 89 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8372 (p0) REVERT: W 94 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8603 (t) REVERT: W 119 ASN cc_start: 0.6031 (m-40) cc_final: 0.5495 (m-40) REVERT: Y 100 SER cc_start: 0.8822 (p) cc_final: 0.8555 (t) outliers start: 58 outliers final: 20 residues processed: 293 average time/residue: 0.2311 time to fit residues: 76.4419 Evaluate side-chains 239 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain b residue 122 THR Chi-restraints excluded: chain c residue 87 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 94 THR Chi-restraints excluded: chain Z residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 79 optimal weight: 0.0670 chunk 91 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 28 optimal weight: 30.0000 chunk 45 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 overall best weight: 2.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 106 ASN A 107 ASN b 107 ASN c 105 GLN c 119 ASN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN H 119 ASN K 112 ASN K 119 ASN L 107 ASN P 105 GLN V 105 GLN X 119 ASN ** Y 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 107 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.156444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.105433 restraints weight = 7806.758| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.17 r_work: 0.3260 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 7960 Z= 0.264 Angle : 0.710 9.933 10760 Z= 0.363 Chirality : 0.044 0.283 1190 Planarity : 0.004 0.060 1460 Dihedral : 5.153 15.791 1070 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 9.75 % Allowed : 16.91 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.74 (0.12), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.002 PHE N 120 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 7960) covalent geometry : angle 0.71001 (10760) hydrogen bonds : bond 0.04796 ( 236) hydrogen bonds : angle 5.64917 ( 708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 239 time to evaluate : 0.237 Fit side-chains REVERT: A 106 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8074 (p0) REVERT: d 113 LYS cc_start: 0.8894 (ttmt) cc_final: 0.7544 (tptt) REVERT: B 102 PHE cc_start: 0.5480 (m-80) cc_final: 0.4866 (p90) REVERT: H 94 THR cc_start: 0.8347 (p) cc_final: 0.8018 (m) REVERT: H 115 THR cc_start: 0.8168 (p) cc_final: 0.7715 (t) REVERT: L 104 SER cc_start: 0.9180 (t) cc_final: 0.8976 (p) REVERT: M 103 SER cc_start: 0.8967 (OUTLIER) cc_final: 0.8625 (p) REVERT: Q 101 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6698 (tm) REVERT: W 94 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8683 (t) REVERT: X 91 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7013 (tp) outliers start: 79 outliers final: 51 residues processed: 270 average time/residue: 0.2377 time to fit residues: 72.3854 Evaluate side-chains 265 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain b residue 99 THR Chi-restraints excluded: chain b residue 122 THR Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain c residue 87 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain P residue 89 ASN Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 123 SER Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 94 THR Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Z residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 30.0000 chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 106 ASN b 107 ASN c 119 ASN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 ASN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 107 ASN ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 ASN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 ASN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.151362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.099608 restraints weight = 7958.962| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.24 r_work: 0.3149 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 7960 Z= 0.436 Angle : 0.810 13.060 10760 Z= 0.415 Chirality : 0.051 0.291 1190 Planarity : 0.004 0.056 1460 Dihedral : 5.507 17.900 1070 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 12.59 % Allowed : 16.17 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.71 (0.12), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.003 PHE T 102 Details of bonding type rmsd covalent geometry : bond 0.00945 ( 7960) covalent geometry : angle 0.80990 (10760) hydrogen bonds : bond 0.05155 ( 236) hydrogen bonds : angle 5.76149 ( 708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 213 time to evaluate : 0.250 Fit side-chains REVERT: B 102 PHE cc_start: 0.5521 (m-80) cc_final: 0.4779 (p90) REVERT: B 105 GLN cc_start: 0.5550 (OUTLIER) cc_final: 0.4816 (tp-100) REVERT: E 111 GLN cc_start: 0.9153 (mt0) cc_final: 0.8849 (mt0) REVERT: H 94 THR cc_start: 0.8473 (p) cc_final: 0.8215 (m) REVERT: M 103 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8672 (p) REVERT: Q 101 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6673 (tm) REVERT: R 91 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6311 (tm) REVERT: U 89 ASN cc_start: 0.6257 (m-40) cc_final: 0.6034 (m-40) REVERT: W 94 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8472 (t) outliers start: 102 outliers final: 70 residues processed: 263 average time/residue: 0.2480 time to fit residues: 72.9711 Evaluate side-chains 270 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 195 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain b residue 96 SER Chi-restraints excluded: chain b residue 99 THR Chi-restraints excluded: chain b residue 103 SER Chi-restraints excluded: chain b residue 107 ASN Chi-restraints excluded: chain b residue 122 THR Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain c residue 87 THR Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain P residue 89 ASN Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 123 SER Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 94 THR Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 123 SER Chi-restraints excluded: chain Z residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 78 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN c 119 ASN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.156999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106558 restraints weight = 7790.415| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.07 r_work: 0.3281 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7960 Z= 0.148 Angle : 0.620 11.034 10760 Z= 0.311 Chirality : 0.040 0.361 1190 Planarity : 0.003 0.035 1460 Dihedral : 4.779 15.197 1070 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 9.01 % Allowed : 20.12 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.76 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.39 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.001 PHE H 102 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7960) covalent geometry : angle 0.62011 (10760) hydrogen bonds : bond 0.03839 ( 236) hydrogen bonds : angle 5.46147 ( 708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 213 time to evaluate : 0.224 Fit side-chains REVERT: A 106 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8008 (p0) REVERT: d 113 LYS cc_start: 0.8962 (ttmt) cc_final: 0.7399 (tppt) REVERT: B 102 PHE cc_start: 0.5521 (m-80) cc_final: 0.4952 (p90) REVERT: E 102 PHE cc_start: 0.6668 (m-10) cc_final: 0.6381 (m-10) REVERT: E 111 GLN cc_start: 0.9053 (mt0) cc_final: 0.8809 (mt0) REVERT: H 94 THR cc_start: 0.8462 (p) cc_final: 0.8137 (m) REVERT: I 101 LEU cc_start: 0.8835 (mp) cc_final: 0.8596 (mp) REVERT: M 103 SER cc_start: 0.8916 (p) cc_final: 0.8557 (p) REVERT: P 100 SER cc_start: 0.8770 (m) cc_final: 0.8567 (t) REVERT: T 97 THR cc_start: 0.8410 (m) cc_final: 0.7955 (p) outliers start: 73 outliers final: 44 residues processed: 245 average time/residue: 0.2477 time to fit residues: 68.1580 Evaluate side-chains 248 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain b residue 96 SER Chi-restraints excluded: chain b residue 99 THR Chi-restraints excluded: chain b residue 103 SER Chi-restraints excluded: chain b residue 122 THR Chi-restraints excluded: chain c residue 87 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 123 SER Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Z residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 0.0270 chunk 72 optimal weight: 10.0000 chunk 79 optimal weight: 0.3980 chunk 48 optimal weight: 30.0000 chunk 22 optimal weight: 0.0170 chunk 15 optimal weight: 0.0770 chunk 61 optimal weight: 9.9990 chunk 80 optimal weight: 30.0000 overall best weight: 1.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.157536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106438 restraints weight = 7788.586| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.19 r_work: 0.3279 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7960 Z= 0.159 Angle : 0.616 11.023 10760 Z= 0.311 Chirality : 0.040 0.343 1190 Planarity : 0.003 0.047 1460 Dihedral : 4.563 14.854 1070 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 9.26 % Allowed : 19.88 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.72 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.001 PHE T 102 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7960) covalent geometry : angle 0.61600 (10760) hydrogen bonds : bond 0.03620 ( 236) hydrogen bonds : angle 5.36646 ( 708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 213 time to evaluate : 0.246 Fit side-chains REVERT: d 113 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.7416 (tppt) REVERT: B 102 PHE cc_start: 0.5367 (m-80) cc_final: 0.4892 (p90) REVERT: E 102 PHE cc_start: 0.6786 (m-10) cc_final: 0.6506 (m-10) REVERT: E 111 GLN cc_start: 0.9078 (mt0) cc_final: 0.8845 (mt0) REVERT: I 101 LEU cc_start: 0.8855 (mp) cc_final: 0.8616 (mp) REVERT: J 115 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8698 (m) REVERT: M 103 SER cc_start: 0.8925 (p) cc_final: 0.8575 (p) REVERT: Q 101 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6753 (tm) REVERT: T 97 THR cc_start: 0.8427 (m) cc_final: 0.7953 (p) outliers start: 75 outliers final: 55 residues processed: 247 average time/residue: 0.2488 time to fit residues: 68.8517 Evaluate side-chains 261 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain b residue 99 THR Chi-restraints excluded: chain b residue 103 SER Chi-restraints excluded: chain b residue 122 THR Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain c residue 87 THR Chi-restraints excluded: chain d residue 94 THR Chi-restraints excluded: chain d residue 113 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain P residue 89 ASN Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 123 SER Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Z residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 40.0000 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 25 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 106 ASN c 119 ASN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN I 111 GLN ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.153521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101828 restraints weight = 7863.716| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.23 r_work: 0.3179 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 7960 Z= 0.335 Angle : 0.732 10.978 10760 Z= 0.370 Chirality : 0.046 0.341 1190 Planarity : 0.004 0.049 1460 Dihedral : 4.883 16.798 1070 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 10.12 % Allowed : 20.00 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.67 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.31 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.002 PHE T 102 Details of bonding type rmsd covalent geometry : bond 0.00729 ( 7960) covalent geometry : angle 0.73151 (10760) hydrogen bonds : bond 0.04313 ( 236) hydrogen bonds : angle 5.57337 ( 708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 211 time to evaluate : 0.267 Fit side-chains REVERT: A 106 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8495 (m-40) REVERT: a 113 LYS cc_start: 0.8860 (ptpt) cc_final: 0.8367 (ptmt) REVERT: b 107 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8814 (p0) REVERT: d 113 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.7419 (tppt) REVERT: B 102 PHE cc_start: 0.5658 (m-80) cc_final: 0.4833 (p90) REVERT: C 99 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8203 (m) REVERT: E 102 PHE cc_start: 0.6851 (m-10) cc_final: 0.6516 (m-10) REVERT: E 111 GLN cc_start: 0.9137 (mt0) cc_final: 0.8931 (mt0) REVERT: M 103 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8632 (p) REVERT: T 97 THR cc_start: 0.8502 (m) cc_final: 0.8143 (p) outliers start: 82 outliers final: 66 residues processed: 252 average time/residue: 0.2493 time to fit residues: 70.4946 Evaluate side-chains 273 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 202 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain b residue 96 SER Chi-restraints excluded: chain b residue 99 THR Chi-restraints excluded: chain b residue 100 SER Chi-restraints excluded: chain b residue 103 SER Chi-restraints excluded: chain b residue 107 ASN Chi-restraints excluded: chain b residue 122 THR Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain c residue 87 THR Chi-restraints excluded: chain c residue 96 SER Chi-restraints excluded: chain d residue 94 THR Chi-restraints excluded: chain d residue 113 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain P residue 89 ASN Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 123 SER Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Z residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 106 ASN c 105 GLN c 119 ASN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.157478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106557 restraints weight = 7821.112| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.18 r_work: 0.3261 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7960 Z= 0.143 Angle : 0.631 11.833 10760 Z= 0.311 Chirality : 0.040 0.335 1190 Planarity : 0.003 0.051 1460 Dihedral : 4.524 15.334 1070 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 8.02 % Allowed : 22.59 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.69 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.33 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.001 PHE T 102 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7960) covalent geometry : angle 0.63137 (10760) hydrogen bonds : bond 0.03467 ( 236) hydrogen bonds : angle 5.37520 ( 708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 214 time to evaluate : 0.268 Fit side-chains REVERT: a 113 LYS cc_start: 0.8925 (ptpt) cc_final: 0.8498 (ptmt) REVERT: b 107 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8653 (p0) REVERT: c 96 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8188 (t) REVERT: d 113 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.7425 (tppt) REVERT: B 102 PHE cc_start: 0.5471 (m-80) cc_final: 0.4909 (p90) REVERT: E 102 PHE cc_start: 0.6592 (m-10) cc_final: 0.6303 (m-10) REVERT: M 103 SER cc_start: 0.8951 (p) cc_final: 0.8600 (p) REVERT: Q 101 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6647 (tm) REVERT: T 97 THR cc_start: 0.8422 (m) cc_final: 0.8103 (p) REVERT: T 101 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6676 (tp) REVERT: Z 97 THR cc_start: 0.8791 (m) cc_final: 0.8340 (p) outliers start: 65 outliers final: 50 residues processed: 247 average time/residue: 0.2578 time to fit residues: 71.2052 Evaluate side-chains 256 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain b residue 96 SER Chi-restraints excluded: chain b residue 99 THR Chi-restraints excluded: chain b residue 103 SER Chi-restraints excluded: chain b residue 107 ASN Chi-restraints excluded: chain b residue 122 THR Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain c residue 87 THR Chi-restraints excluded: chain c residue 96 SER Chi-restraints excluded: chain d residue 94 THR Chi-restraints excluded: chain d residue 113 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 123 SER Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Z residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 47 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN c 105 GLN c 119 ASN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN P 105 GLN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.151199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099389 restraints weight = 7872.153| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.33 r_work: 0.3137 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.069 7960 Z= 0.447 Angle : 0.810 12.477 10760 Z= 0.414 Chirality : 0.051 0.323 1190 Planarity : 0.004 0.045 1460 Dihedral : 5.011 17.667 1070 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 10.00 % Allowed : 21.23 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.67 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.037 0.003 PHE T 102 Details of bonding type rmsd covalent geometry : bond 0.00977 ( 7960) covalent geometry : angle 0.81023 (10760) hydrogen bonds : bond 0.04694 ( 236) hydrogen bonds : angle 5.71673 ( 708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 202 time to evaluate : 0.279 Fit side-chains REVERT: a 113 LYS cc_start: 0.8909 (ptpt) cc_final: 0.8471 (ptmt) REVERT: b 107 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8842 (p0) REVERT: B 102 PHE cc_start: 0.5648 (m-80) cc_final: 0.4883 (p90) REVERT: C 99 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8274 (m) REVERT: E 102 PHE cc_start: 0.6699 (m-10) cc_final: 0.6376 (m-10) REVERT: M 103 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8603 (p) REVERT: Q 101 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6757 (tm) REVERT: T 97 THR cc_start: 0.8576 (m) cc_final: 0.8264 (p) REVERT: Z 97 THR cc_start: 0.8797 (m) cc_final: 0.8525 (p) outliers start: 81 outliers final: 69 residues processed: 244 average time/residue: 0.2436 time to fit residues: 66.8829 Evaluate side-chains 268 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 195 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain b residue 96 SER Chi-restraints excluded: chain b residue 99 THR Chi-restraints excluded: chain b residue 103 SER Chi-restraints excluded: chain b residue 107 ASN Chi-restraints excluded: chain b residue 122 THR Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain c residue 87 THR Chi-restraints excluded: chain c residue 96 SER Chi-restraints excluded: chain d residue 94 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain P residue 89 ASN Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 123 SER Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Z residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN c 119 ASN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.155036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.103301 restraints weight = 7805.367| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.28 r_work: 0.3197 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7960 Z= 0.217 Angle : 0.686 11.602 10760 Z= 0.340 Chirality : 0.043 0.306 1190 Planarity : 0.004 0.053 1460 Dihedral : 4.678 16.441 1070 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 9.01 % Allowed : 22.10 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.72 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.08), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.036 0.002 PHE K 102 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 7960) covalent geometry : angle 0.68644 (10760) hydrogen bonds : bond 0.03780 ( 236) hydrogen bonds : angle 5.53024 ( 708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 205 time to evaluate : 0.283 Fit side-chains REVERT: A 106 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8551 (m-40) REVERT: a 113 LYS cc_start: 0.8902 (ptpt) cc_final: 0.8447 (ptmt) REVERT: b 107 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8718 (p0) REVERT: c 96 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8202 (t) REVERT: d 96 SER cc_start: 0.8560 (p) cc_final: 0.8280 (m) REVERT: B 102 PHE cc_start: 0.5675 (m-80) cc_final: 0.5069 (p90) REVERT: C 99 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8072 (m) REVERT: E 102 PHE cc_start: 0.6464 (m-10) cc_final: 0.6023 (m-10) REVERT: M 103 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8609 (p) REVERT: Q 101 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6643 (tm) REVERT: T 97 THR cc_start: 0.8511 (m) cc_final: 0.8199 (p) REVERT: Z 97 THR cc_start: 0.8758 (m) cc_final: 0.8504 (p) outliers start: 73 outliers final: 61 residues processed: 244 average time/residue: 0.2568 time to fit residues: 70.1041 Evaluate side-chains 264 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 197 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain b residue 96 SER Chi-restraints excluded: chain b residue 99 THR Chi-restraints excluded: chain b residue 103 SER Chi-restraints excluded: chain b residue 107 ASN Chi-restraints excluded: chain b residue 122 THR Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain c residue 87 THR Chi-restraints excluded: chain c residue 96 SER Chi-restraints excluded: chain d residue 94 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain P residue 89 ASN Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 123 SER Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 123 SER Chi-restraints excluded: chain Z residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN c 119 ASN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 ASN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 ASN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.153690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101974 restraints weight = 7792.240| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.32 r_work: 0.3181 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7960 Z= 0.275 Angle : 0.713 11.492 10760 Z= 0.354 Chirality : 0.044 0.294 1190 Planarity : 0.004 0.048 1460 Dihedral : 4.680 16.926 1070 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 9.63 % Allowed : 21.11 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.72 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.08), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.002 PHE T 102 Details of bonding type rmsd covalent geometry : bond 0.00600 ( 7960) covalent geometry : angle 0.71299 (10760) hydrogen bonds : bond 0.03988 ( 236) hydrogen bonds : angle 5.55870 ( 708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2758.10 seconds wall clock time: 47 minutes 50.62 seconds (2870.62 seconds total)