Starting phenix.real_space_refine on Wed Feb 12 09:52:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q64_13851/02_2025/7q64_13851.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q64_13851/02_2025/7q64_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_13851/02_2025/7q64_13851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q64_13851/02_2025/7q64_13851.map" model { file = "/net/cci-nas-00/data/ceres_data/7q64_13851/02_2025/7q64_13851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q64_13851/02_2025/7q64_13851.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.68, per 1000 atoms: 0.60 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: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.17 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: 2.44 Time building geometry restraints manager: 2.08 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: 0.03 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: 0.910 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.030 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.030 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:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.330 ------------------------------------------------------------------------------- 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= 0.943 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 : 0.817 Fit side-chains REVERT: Z 97 THR cc_start: 0.7690 (m) cc_final: 0.7486 (p) outliers start: 31 outliers final: 0 residues processed: 342 average time/residue: 0.5377 time to fit residues: 206.7834 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 : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 107 ASN b 105 GLN b 106 ASN c 105 GLN d 112 ASN D 107 ASN D 112 ASN G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 ASN M 107 ASN M 112 ASN ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 ASN P 107 ASN P 112 ASN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 107 ASN T 112 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 105 GLN W 112 ASN W 119 ASN ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 89 ASN Z 112 ASN Z 119 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.157454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.106364 restraints weight = 7807.462| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.24 r_work: 0.3265 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7960 Z= 0.344 Angle : 0.728 11.626 10760 Z= 0.370 Chirality : 0.043 0.274 1190 Planarity : 0.003 0.027 1460 Dihedral : 5.412 16.556 1070 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 8.15 % Allowed : 15.06 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 0.026 0.002 PHE K 120 *********************** 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 319 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 253 time to evaluate : 0.830 Fit side-chains REVERT: b 89 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8453 (p0) REVERT: d 113 LYS cc_start: 0.8782 (ttmt) cc_final: 0.7403 (tppt) REVERT: I 94 THR cc_start: 0.7793 (m) cc_final: 0.7552 (m) REVERT: Q 119 ASN cc_start: 0.6475 (m-40) cc_final: 0.6265 (m-40) REVERT: S 89 ASN cc_start: 0.8885 (p0) cc_final: 0.8637 (p0) REVERT: W 119 ASN cc_start: 0.6373 (m-40) cc_final: 0.5762 (m-40) REVERT: Y 100 SER cc_start: 0.8833 (p) cc_final: 0.8625 (t) outliers start: 66 outliers final: 26 residues processed: 290 average time/residue: 0.5988 time to fit residues: 196.6049 Evaluate side-chains 238 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain b residue 89 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 B residue 87 THR Chi-restraints excluded: chain D residue 90 THR 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 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 123 SER Chi-restraints excluded: chain N residue 87 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 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 122 THR Chi-restraints excluded: chain V residue 123 SER Chi-restraints excluded: chain W residue 87 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 48 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 57 optimal weight: 0.2980 chunk 23 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- 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 89 ASN c 105 GLN c 119 ASN D 107 ASN G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 ASN I 119 ASN K 112 ASN K 119 ASN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN R 119 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.156136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.104834 restraints weight = 7929.692| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.29 r_work: 0.3248 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3832 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= 0.330 Angle : 0.682 9.928 10760 Z= 0.345 Chirality : 0.042 0.305 1190 Planarity : 0.003 0.053 1460 Dihedral : 5.063 15.416 1070 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 10.00 % Allowed : 16.79 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.76 (0.12), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.002 PHE W 102 *********************** 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 310 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 229 time to evaluate : 0.856 Fit side-chains REVERT: A 106 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8155 (p0) REVERT: d 113 LYS cc_start: 0.8924 (ttmt) cc_final: 0.7596 (tptt) REVERT: d 115 THR cc_start: 0.8401 (t) cc_final: 0.7796 (p) REVERT: B 102 PHE cc_start: 0.5142 (m-80) cc_final: 0.4738 (p90) REVERT: G 113 LYS cc_start: 0.8971 (mmtp) cc_final: 0.8730 (mmtm) REVERT: H 115 THR cc_start: 0.8091 (p) cc_final: 0.7633 (t) REVERT: Q 101 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6681 (tm) REVERT: X 91 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6968 (tp) REVERT: Z 96 SER cc_start: 0.8876 (p) cc_final: 0.8337 (t) outliers start: 81 outliers final: 52 residues processed: 266 average time/residue: 0.5086 time to fit residues: 152.8786 Evaluate side-chains 264 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain b residue 89 ASN Chi-restraints excluded: chain b residue 97 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 d residue 90 THR Chi-restraints excluded: chain B 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 G residue 89 ASN Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 106 ASN 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 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 L residue 104 SER Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 115 THR 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 100 SER 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 96 SER 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 97 THR 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 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 72 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 10 optimal weight: 0.0970 chunk 94 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 89 optimal weight: 0.0470 overall best weight: 3.0282 ------------------------------------------------------------------------------- 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 107 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 = 0.4090 r_free = 0.4090 target = 0.155586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103144 restraints weight = 7849.803| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.39 r_work: 0.3210 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7960 Z= 0.370 Angle : 0.674 10.632 10760 Z= 0.343 Chirality : 0.042 0.296 1190 Planarity : 0.003 0.055 1460 Dihedral : 4.984 15.990 1070 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 10.25 % Allowed : 17.65 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.75 (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 0.023 0.002 PHE T 102 *********************** 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 295 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 212 time to evaluate : 0.894 Fit side-chains REVERT: A 106 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8585 (p0) REVERT: d 113 LYS cc_start: 0.8966 (ttmt) cc_final: 0.7515 (tptt) REVERT: B 102 PHE cc_start: 0.5209 (m-80) cc_final: 0.4777 (p90) REVERT: E 102 PHE cc_start: 0.6643 (m-10) cc_final: 0.6314 (m-10) REVERT: E 111 GLN cc_start: 0.9094 (mt0) cc_final: 0.8777 (mt0) REVERT: G 113 LYS cc_start: 0.9020 (mmtp) cc_final: 0.8776 (mmtm) REVERT: H 115 THR cc_start: 0.8081 (p) cc_final: 0.7696 (t) REVERT: Q 101 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6792 (tm) REVERT: R 91 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6303 (tm) REVERT: T 97 THR cc_start: 0.8288 (m) cc_final: 0.7988 (m) REVERT: V 99 THR cc_start: 0.8886 (p) cc_final: 0.8685 (t) outliers start: 83 outliers final: 64 residues processed: 252 average time/residue: 0.5833 time to fit residues: 164.8538 Evaluate side-chains 270 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 203 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 103 SER Chi-restraints excluded: chain A residue 106 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 97 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 B residue 87 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 122 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 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 K residue 96 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 115 THR 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 100 SER 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 123 SER Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain U residue 113 LYS Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 97 THR 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 94 THR Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 115 THR 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 9 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 70 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 99 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 overall best weight: 5.9188 ------------------------------------------------------------------------------- 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 ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.151606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.099831 restraints weight = 7818.044| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.16 r_work: 0.3159 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.072 7960 Z= 0.640 Angle : 0.802 11.993 10760 Z= 0.412 Chirality : 0.050 0.342 1190 Planarity : 0.004 0.056 1460 Dihedral : 5.384 17.453 1070 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 12.96 % Allowed : 16.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.70 (0.11), 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 0.033 0.003 PHE W 102 *********************** 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 314 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 209 time to evaluate : 0.830 Fit side-chains REVERT: A 106 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8713 (p0) REVERT: B 102 PHE cc_start: 0.5587 (m-80) cc_final: 0.4810 (p90) REVERT: E 102 PHE cc_start: 0.7021 (m-10) cc_final: 0.6724 (m-10) REVERT: E 111 GLN cc_start: 0.9193 (mt0) cc_final: 0.8924 (mt0) REVERT: H 115 THR cc_start: 0.8119 (p) cc_final: 0.7851 (t) REVERT: Q 101 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6647 (tm) REVERT: R 111 GLN cc_start: 0.8488 (tt0) cc_final: 0.8168 (tt0) REVERT: T 97 THR cc_start: 0.8492 (m) cc_final: 0.8111 (p) REVERT: V 99 THR cc_start: 0.8959 (p) cc_final: 0.8694 (t) outliers start: 105 outliers final: 79 residues processed: 265 average time/residue: 0.5440 time to fit residues: 161.8473 Evaluate side-chains 276 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 195 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 103 SER Chi-restraints excluded: chain A residue 106 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 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 c residue 115 THR Chi-restraints excluded: chain B residue 87 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 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 122 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 87 THR 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 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 L residue 104 SER Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 115 THR 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 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 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 U residue 96 SER Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 103 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 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 Y residue 123 SER Chi-restraints excluded: chain Z residue 87 THR Chi-restraints excluded: chain Z residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 106 ASN ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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** S 89 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.155395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.103600 restraints weight = 7806.753| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.23 r_work: 0.3209 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7960 Z= 0.299 Angle : 0.662 10.172 10760 Z= 0.330 Chirality : 0.040 0.329 1190 Planarity : 0.003 0.056 1460 Dihedral : 4.873 15.760 1070 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 10.00 % Allowed : 18.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.73 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.36 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHE W 102 *********************** 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 293 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 212 time to evaluate : 0.752 Fit side-chains REVERT: A 106 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8166 (p0) REVERT: d 115 THR cc_start: 0.8459 (t) cc_final: 0.7894 (p) REVERT: B 102 PHE cc_start: 0.5648 (m-80) cc_final: 0.4874 (p90) REVERT: B 113 LYS cc_start: 0.8914 (mttp) cc_final: 0.8693 (mptt) REVERT: E 90 THR cc_start: 0.8518 (p) cc_final: 0.8267 (p) REVERT: E 102 PHE cc_start: 0.6857 (m-10) cc_final: 0.6530 (m-10) REVERT: E 111 GLN cc_start: 0.9114 (mt0) cc_final: 0.8878 (mt0) REVERT: H 115 THR cc_start: 0.8089 (p) cc_final: 0.7881 (t) REVERT: P 100 SER cc_start: 0.8810 (m) cc_final: 0.8598 (t) REVERT: Q 101 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6653 (tm) REVERT: T 97 THR cc_start: 0.8492 (m) cc_final: 0.8136 (p) REVERT: V 99 THR cc_start: 0.8922 (p) cc_final: 0.8692 (t) REVERT: Z 97 THR cc_start: 0.8832 (m) cc_final: 0.8557 (p) outliers start: 81 outliers final: 60 residues processed: 255 average time/residue: 0.5696 time to fit residues: 162.7045 Evaluate side-chains 265 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 203 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 106 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 100 SER 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 B residue 87 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain D residue 106 ASN 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 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 104 SER 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 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 L residue 99 THR Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 115 THR 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 S residue 96 SER 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 97 THR 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 Y residue 123 SER 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 58 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 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 = 0.4055 r_free = 0.4055 target = 0.152804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.100906 restraints weight = 7785.572| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.25 r_work: 0.3193 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 7960 Z= 0.474 Angle : 0.724 10.621 10760 Z= 0.363 Chirality : 0.045 0.361 1190 Planarity : 0.003 0.033 1460 Dihedral : 4.964 17.310 1070 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 10.49 % Allowed : 18.77 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.70 (0.11), 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 0.024 0.002 PHE W 102 *********************** 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 296 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 211 time to evaluate : 0.861 Fit side-chains REVERT: A 106 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8419 (p0) REVERT: d 115 THR cc_start: 0.8539 (t) cc_final: 0.7968 (p) REVERT: B 102 PHE cc_start: 0.5591 (m-80) cc_final: 0.4834 (p90) REVERT: B 113 LYS cc_start: 0.8933 (mttp) cc_final: 0.8706 (mptt) REVERT: E 102 PHE cc_start: 0.6783 (m-10) cc_final: 0.6475 (m-10) REVERT: P 100 SER cc_start: 0.8825 (m) cc_final: 0.8581 (t) REVERT: Q 101 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6802 (tm) REVERT: T 97 THR cc_start: 0.8440 (m) cc_final: 0.8124 (p) REVERT: V 99 THR cc_start: 0.8966 (p) cc_final: 0.8698 (m) REVERT: W 101 LEU cc_start: 0.7494 (tp) cc_final: 0.7033 (mt) REVERT: Y 107 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8654 (p0) REVERT: Z 97 THR cc_start: 0.8831 (m) cc_final: 0.8574 (p) outliers start: 85 outliers final: 74 residues processed: 260 average time/residue: 0.5386 time to fit residues: 157.4376 Evaluate side-chains 279 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 202 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 103 SER Chi-restraints excluded: chain A residue 106 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 100 SER 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 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 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 E residue 104 SER 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 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 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 L residue 99 THR Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 115 THR 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 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 96 SER Chi-restraints excluded: chain V residue 103 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 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 107 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.0070 chunk 47 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 97 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** J 105 GLN J 107 ASN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.158690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108593 restraints weight = 7841.116| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.24 r_work: 0.3299 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7960 Z= 0.199 Angle : 0.616 11.784 10760 Z= 0.301 Chirality : 0.040 0.406 1190 Planarity : 0.003 0.033 1460 Dihedral : 4.458 15.386 1070 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 6.54 % Allowed : 23.09 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.74 (0.11), 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 0.021 0.001 PHE K 102 *********************** 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 276 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.863 Fit side-chains REVERT: d 113 LYS cc_start: 0.9016 (ttmt) cc_final: 0.7407 (tppt) REVERT: d 115 THR cc_start: 0.8456 (t) cc_final: 0.7894 (p) REVERT: B 102 PHE cc_start: 0.5642 (m-80) cc_final: 0.5081 (p90) REVERT: B 113 LYS cc_start: 0.8891 (mttp) cc_final: 0.8655 (mptt) REVERT: E 102 PHE cc_start: 0.6350 (m-10) cc_final: 0.5897 (m-10) REVERT: J 115 THR cc_start: 0.9000 (p) cc_final: 0.8703 (m) REVERT: Q 101 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6809 (tm) REVERT: T 97 THR cc_start: 0.8457 (m) cc_final: 0.8164 (p) REVERT: V 99 THR cc_start: 0.8893 (p) cc_final: 0.8603 (m) REVERT: W 101 LEU cc_start: 0.7414 (tp) cc_final: 0.7114 (mt) REVERT: Z 97 THR cc_start: 0.8799 (m) cc_final: 0.8586 (p) outliers start: 53 outliers final: 36 residues processed: 250 average time/residue: 0.6179 time to fit residues: 171.6932 Evaluate side-chains 252 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain b residue 96 SER Chi-restraints excluded: chain b residue 97 THR 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 c residue 87 THR Chi-restraints excluded: chain d residue 94 THR Chi-restraints excluded: chain B residue 87 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 J residue 97 THR Chi-restraints excluded: chain J residue 100 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 L residue 104 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 Q residue 96 SER Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 103 SER 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 Y residue 123 SER 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 42 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 51 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** H 119 ASN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN M 106 ASN N 105 GLN P 105 GLN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.158579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108325 restraints weight = 7873.088| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.26 r_work: 0.3302 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7960 Z= 0.230 Angle : 0.618 10.608 10760 Z= 0.306 Chirality : 0.040 0.400 1190 Planarity : 0.003 0.030 1460 Dihedral : 4.326 16.894 1070 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.54 % Allowed : 23.21 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.74 (0.11), 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 0.020 0.001 PHE T 102 *********************** 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 273 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 0.809 Fit side-chains REVERT: c 96 SER cc_start: 0.8639 (OUTLIER) cc_final: 0.8185 (t) REVERT: d 113 LYS cc_start: 0.9024 (ttmt) cc_final: 0.7380 (tppt) REVERT: d 115 THR cc_start: 0.8436 (t) cc_final: 0.7857 (p) REVERT: B 113 LYS cc_start: 0.8864 (mttp) cc_final: 0.8625 (mptt) REVERT: E 102 PHE cc_start: 0.6305 (m-10) cc_final: 0.5971 (m-10) REVERT: J 115 THR cc_start: 0.8996 (p) cc_final: 0.8704 (m) REVERT: T 97 THR cc_start: 0.8465 (m) cc_final: 0.8158 (p) REVERT: V 99 THR cc_start: 0.8921 (p) cc_final: 0.8650 (m) REVERT: V 100 SER cc_start: 0.8681 (m) cc_final: 0.8479 (t) REVERT: Z 97 THR cc_start: 0.8779 (m) cc_final: 0.8557 (p) outliers start: 53 outliers final: 45 residues processed: 248 average time/residue: 0.6052 time to fit residues: 166.8648 Evaluate side-chains 258 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain b residue 97 THR 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 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 115 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 123 SER 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 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 100 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 99 THR Chi-restraints excluded: chain L residue 104 SER 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 Q residue 96 SER Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 96 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 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 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 94 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN c 119 ASN B 105 GLN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN E 119 ASN G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN H 119 ASN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 ASN N 105 GLN P 105 GLN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.149976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.098752 restraints weight = 7882.608| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.14 r_work: 0.3141 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.073 7960 Z= 0.704 Angle : 0.835 12.991 10760 Z= 0.428 Chirality : 0.053 0.404 1190 Planarity : 0.004 0.029 1460 Dihedral : 5.050 17.839 1070 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 7.41 % Allowed : 23.58 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.70 (0.11), 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 0.045 0.003 PHE T 102 ********************** 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 273 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 0.825 Fit side-chains REVERT: A 106 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8538 (m-40) REVERT: b 107 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8866 (p0) REVERT: B 113 LYS cc_start: 0.8975 (mttp) cc_final: 0.8669 (mttt) REVERT: L 89 ASN cc_start: 0.6235 (m-40) cc_final: 0.5994 (m-40) REVERT: Q 101 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6711 (tm) REVERT: T 97 THR cc_start: 0.8600 (m) cc_final: 0.8308 (p) REVERT: Z 97 THR cc_start: 0.8790 (m) cc_final: 0.8560 (p) outliers start: 60 outliers final: 53 residues processed: 247 average time/residue: 0.5603 time to fit residues: 154.5401 Evaluate side-chains 255 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 199 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 115 THR 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 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 115 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 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 115 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 J residue 100 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 99 THR Chi-restraints excluded: chain L residue 104 SER 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 91 LEU Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 91 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 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 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 62 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 38 optimal weight: 30.0000 chunk 80 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 H 119 ASN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.155268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.105388 restraints weight = 7877.902| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.17 r_work: 0.3245 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7960 Z= 0.294 Angle : 0.670 11.472 10760 Z= 0.328 Chirality : 0.042 0.407 1190 Planarity : 0.003 0.033 1460 Dihedral : 4.611 16.734 1070 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.93 % Allowed : 24.94 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.73 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.36 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.002 PHE N 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5765.12 seconds wall clock time: 102 minutes 58.97 seconds (6178.97 seconds total)