Starting phenix.real_space_refine on Fri Dec 8 08:41:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q64_13851/12_2023/7q64_13851.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q64_13851/12_2023/7q64_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q64_13851/12_2023/7q64_13851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q64_13851/12_2023/7q64_13851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q64_13851/12_2023/7q64_13851.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q64_13851/12_2023/7q64_13851.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.74, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.6 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: 1.31 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: 2.33 Time building geometry restraints manager: 3.56 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: 103.23 - 108.97: 875 108.97 - 114.70: 3570 114.70 - 120.44: 2868 120.44 - 126.17: 3387 126.17 - 131.91: 60 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 2.440 nonbonded pdb=" OG1 THR T 99 " pdb=" O THR W 99 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR B 99 " pdb=" O THR E 99 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR Q 99 " pdb=" O THR T 99 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR E 99 " pdb=" O THR H 99 " model vdw 2.276 2.440 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 86 through 121) selection = chain 'B' selection = (chain 'D' and resid 86 through 121) selection = chain 'E' selection = (chain 'G' and resid 86 through 121) selection = chain 'H' selection = (chain 'J' and resid 86 through 121) selection = chain 'K' selection = (chain 'M' and resid 86 through 121) selection = chain 'N' selection = (chain 'P' and resid 86 through 121) selection = chain 'Q' selection = (chain 'S' and resid 86 through 121) selection = chain 'T' selection = (chain 'V' and resid 86 through 121) selection = chain 'W' selection = (chain 'Y' and resid 86 through 121) selection = chain 'Z' selection = (chain 'b' and resid 86 through 121) selection = chain 'c' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.000 Extract box with map and model: 4.180 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 26.700 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.060 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.130 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 31 poor density : 321 time to evaluate : 0.857 Fit side-chains outliers start: 31 outliers final: 0 residues processed: 342 average time/residue: 0.5164 time to fit residues: 199.3086 Evaluate side-chains 206 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0983 ------------------------------------------------------------------------------- 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: 3.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 106 ASN A 107 ASN ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 GLN b 106 ASN b 107 ASN c 105 GLN ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 119 ASN ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 ASN P 107 ASN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 107 ASN T 112 ASN V 105 GLN W 112 ASN W 119 ASN ** Y 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 89 ASN Z 112 ASN Z 119 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 7960 Z= 0.406 Angle : 0.772 12.339 10760 Z= 0.390 Chirality : 0.044 0.293 1190 Planarity : 0.003 0.028 1460 Dihedral : 5.579 16.757 1070 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 8.02 % Allowed : 15.19 % 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: -5.81 (0.12), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.42 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 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 318 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 253 time to evaluate : 0.924 Fit side-chains outliers start: 65 outliers final: 29 residues processed: 288 average time/residue: 0.5470 time to fit residues: 176.7861 Evaluate side-chains 241 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 212 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 13 residues processed: 17 average time/residue: 0.0878 time to fit residues: 3.6326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- 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 ** 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 119 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN P 112 ASN ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 ASN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 112 ASN ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.075 7960 Z= 0.703 Angle : 0.872 11.950 10760 Z= 0.450 Chirality : 0.053 0.268 1190 Planarity : 0.004 0.058 1460 Dihedral : 5.909 18.105 1070 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 10.86 % Allowed : 15.31 % Favored : 73.83 % 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: -5.66 (0.12), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.003 PHE T 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 312 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 224 time to evaluate : 0.880 Fit side-chains outliers start: 88 outliers final: 66 residues processed: 269 average time/residue: 0.5365 time to fit residues: 161.8432 Evaluate side-chains 264 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 198 time to evaluate : 0.789 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 35 residues processed: 31 average time/residue: 0.0870 time to fit residues: 5.6326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 107 ASN c 105 GLN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN M 107 ASN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 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** Z 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7960 Z= 0.176 Angle : 0.605 9.599 10760 Z= 0.306 Chirality : 0.039 0.263 1190 Planarity : 0.003 0.061 1460 Dihedral : 4.850 15.378 1070 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 9.75 % Allowed : 18.02 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.72 (0.12), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.001 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 300 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 221 time to evaluate : 0.899 Fit side-chains outliers start: 79 outliers final: 53 residues processed: 270 average time/residue: 0.5184 time to fit residues: 158.2657 Evaluate side-chains 251 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 198 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 34 residues processed: 20 average time/residue: 0.1156 time to fit residues: 4.8916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.0870 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 overall best weight: 3.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN b 89 ASN c 105 GLN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN H 119 ASN ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 ASN ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 7960 Z= 0.368 Angle : 0.658 9.269 10760 Z= 0.334 Chirality : 0.041 0.212 1190 Planarity : 0.003 0.035 1460 Dihedral : 4.881 17.126 1070 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 10.86 % Allowed : 17.78 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.65 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHE T 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 294 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 206 time to evaluate : 0.914 Fit side-chains outliers start: 88 outliers final: 68 residues processed: 263 average time/residue: 0.5187 time to fit residues: 154.5729 Evaluate side-chains 264 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 196 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 44 residues processed: 25 average time/residue: 0.0820 time to fit residues: 4.6528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.0170 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 106 ASN c 105 GLN c 119 ASN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 ASN ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7960 Z= 0.173 Angle : 0.567 8.912 10760 Z= 0.285 Chirality : 0.038 0.261 1190 Planarity : 0.003 0.038 1460 Dihedral : 4.389 15.699 1070 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 9.26 % Allowed : 19.63 % Favored : 71.11 % 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: -5.66 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.31 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.001 PHE B 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 278 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 203 time to evaluate : 0.907 Fit side-chains outliers start: 75 outliers final: 58 residues processed: 251 average time/residue: 0.5219 time to fit residues: 148.1441 Evaluate side-chains 255 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 197 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 39 residues processed: 19 average time/residue: 0.0884 time to fit residues: 3.8470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 30.0000 chunk 57 optimal weight: 9.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN c 105 GLN c 119 ASN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 ASN ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.068 7960 Z= 0.655 Angle : 0.776 9.926 10760 Z= 0.399 Chirality : 0.049 0.235 1190 Planarity : 0.004 0.027 1460 Dihedral : 5.035 17.898 1070 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 10.86 % Allowed : 17.90 % 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: -5.64 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.29 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE K 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 285 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 197 time to evaluate : 0.914 Fit side-chains outliers start: 88 outliers final: 76 residues processed: 247 average time/residue: 0.5507 time to fit residues: 153.1130 Evaluate side-chains 264 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 188 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 46 residues processed: 30 average time/residue: 0.0866 time to fit residues: 5.6301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 106 ASN c 119 ASN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7960 Z= 0.193 Angle : 0.588 10.230 10760 Z= 0.293 Chirality : 0.038 0.224 1190 Planarity : 0.003 0.036 1460 Dihedral : 4.407 16.615 1070 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 7.90 % Allowed : 21.60 % Favored : 70.49 % 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: -5.65 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE B 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 267 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 203 time to evaluate : 0.893 Fit side-chains outliers start: 64 outliers final: 56 residues processed: 248 average time/residue: 0.5601 time to fit residues: 157.8170 Evaluate side-chains 256 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 200 time to evaluate : 0.789 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 41 residues processed: 15 average time/residue: 0.0962 time to fit residues: 3.4398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 58 optimal weight: 30.0000 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 119 ASN G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.071 7960 Z= 0.701 Angle : 0.798 9.966 10760 Z= 0.413 Chirality : 0.051 0.215 1190 Planarity : 0.004 0.035 1460 Dihedral : 5.031 18.337 1070 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 8.40 % Allowed : 20.37 % 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: -5.65 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.003 PHE N 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 261 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 193 time to evaluate : 0.889 Fit side-chains outliers start: 68 outliers final: 61 residues processed: 241 average time/residue: 0.5644 time to fit residues: 152.8111 Evaluate side-chains 247 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 186 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 46 residues processed: 15 average time/residue: 0.0805 time to fit residues: 3.2500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 106 ASN c 119 ASN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7960 Z= 0.194 Angle : 0.586 7.626 10760 Z= 0.294 Chirality : 0.039 0.236 1190 Planarity : 0.003 0.045 1460 Dihedral : 4.389 16.845 1070 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 6.30 % Allowed : 23.21 % Favored : 70.49 % 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 (0.08), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE K 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 258 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 207 time to evaluate : 0.837 Fit side-chains outliers start: 51 outliers final: 43 residues processed: 251 average time/residue: 0.5718 time to fit residues: 161.3002 Evaluate side-chains 241 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 198 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 38 residues processed: 5 average time/residue: 0.1171 time to fit residues: 1.8691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN N 105 GLN ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 ASN ** 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 = 0.4075 r_free = 0.4075 target = 0.152636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.102294 restraints weight = 7686.953| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.07 r_work: 0.3215 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7960 Z= 0.434 Angle : 0.678 9.082 10760 Z= 0.344 Chirality : 0.042 0.229 1190 Planarity : 0.003 0.038 1460 Dihedral : 4.617 17.748 1070 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 7.04 % Allowed : 22.96 % Favored : 70.00 % 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: -5.64 (0.11), residues: 1040 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.29 (0.09), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHE Q 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3173.97 seconds wall clock time: 57 minutes 28.62 seconds (3448.62 seconds total)