Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:09:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pes_20331/11_2022/6pes_20331.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pes_20331/11_2022/6pes_20331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pes_20331/11_2022/6pes_20331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pes_20331/11_2022/6pes_20331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pes_20331/11_2022/6pes_20331.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pes_20331/11_2022/6pes_20331.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4040 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 441 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "B" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 441 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "C" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 441 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "D" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 441 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "E" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 441 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "W" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 367 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "V" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 367 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "X" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 367 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "Y" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 367 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "Z" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 367 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Time building chain proxies: 2.49, per 1000 atoms: 0.62 Number of scatterers: 4040 At special positions: 0 Unit cell: (73.485, 117.15, 43.665, 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 825 8.00 N 700 7.00 C 2515 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: 1.57 Conformation dependent library (CDL) restraints added in 767.8 milliseconds 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1000 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 64.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.324A pdb=" N VAL B 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL D 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL B 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 57 removed outlier: 6.442A pdb=" N THR B 44 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY D 47 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N GLU B 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N VAL D 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N GLY D 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN B 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ALA D 53 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL D 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLU D 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR A 44 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLY B 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLU A 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL B 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA B 53 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN C 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL E 48 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN E 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.538A pdb=" N GLU B 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR D 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL D 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.543A pdb=" N VAL B 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 74 through 83 removed outlier: 6.361A pdb=" N VAL B 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL D 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA B 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLN D 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA B 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR D 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LYS B 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N GLU D 83 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N VAL B 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 74 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL B 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLN B 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA A 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N THR B 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LYS A 80 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N GLU B 83 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N VAL A 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A 81 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL C 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLU A 83 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR C 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL E 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLU C 83 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 88 through 96 removed outlier: 6.641A pdb=" N ILE B 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA D 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ALA B 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N GLY D 93 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N THR B 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N VAL D 95 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE B 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ALA A 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N GLY B 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N THR A 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N VAL B 95 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE A 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA A 91 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR C 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY A 93 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA C 91 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR E 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY C 93 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'W' and resid 45 through 56 removed outlier: 6.885A pdb=" N VAL V 48 " --> pdb=" O GLY W 47 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL W 49 " --> pdb=" O VAL V 48 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLN V 50 " --> pdb=" O VAL W 49 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL X 48 " --> pdb=" O GLY V 47 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL V 49 " --> pdb=" O VAL X 48 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN X 50 " --> pdb=" O VAL V 49 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL Y 48 " --> pdb=" O GLY X 47 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL X 49 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLN Y 50 " --> pdb=" O VAL X 49 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL Z 48 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL Y 49 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLN Z 50 " --> pdb=" O VAL Y 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'W' and resid 61 through 66 Processing sheet with id=AA9, first strand: chain 'W' and resid 69 through 71 Processing sheet with id=AB1, first strand: chain 'W' and resid 74 through 83 removed outlier: 8.950A pdb=" N VAL W 74 " --> pdb=" O THR V 75 " (cutoff:3.500A) removed outlier: 10.095A pdb=" N VAL V 77 " --> pdb=" O VAL W 74 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ALA W 76 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N GLN V 79 " --> pdb=" O ALA W 76 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ALA W 78 " --> pdb=" O GLN V 79 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N THR V 81 " --> pdb=" O ALA W 78 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LYS W 80 " --> pdb=" O THR V 81 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N GLU V 83 " --> pdb=" O LYS W 80 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL W 82 " --> pdb=" O GLU V 83 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N VAL V 74 " --> pdb=" O THR X 75 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N VAL X 77 " --> pdb=" O VAL V 74 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ALA V 76 " --> pdb=" O VAL X 77 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N GLN X 79 " --> pdb=" O ALA V 76 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N ALA V 78 " --> pdb=" O GLN X 79 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N THR X 81 " --> pdb=" O ALA V 78 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS V 80 " --> pdb=" O THR X 81 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLU X 83 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL V 82 " --> pdb=" O GLU X 83 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N VAL X 74 " --> pdb=" O THR Y 75 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N VAL Y 77 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ALA X 76 " --> pdb=" O VAL Y 77 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N GLN Y 79 " --> pdb=" O ALA X 76 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N ALA X 78 " --> pdb=" O GLN Y 79 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N THR Y 81 " --> pdb=" O ALA X 78 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS X 80 " --> pdb=" O THR Y 81 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU Y 83 " --> pdb=" O LYS X 80 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL X 82 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N VAL Y 74 " --> pdb=" O THR Z 75 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N VAL Z 77 " --> pdb=" O VAL Y 74 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N ALA Y 76 " --> pdb=" O VAL Z 77 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N GLN Z 79 " --> pdb=" O ALA Y 76 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ALA Y 78 " --> pdb=" O GLN Z 79 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N THR Z 81 " --> pdb=" O ALA Y 78 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS Y 80 " --> pdb=" O THR Z 81 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLU Z 83 " --> pdb=" O LYS Y 80 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL Y 82 " --> pdb=" O GLU Z 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'W' and resid 88 through 96 removed outlier: 8.432A pdb=" N ALA W 89 " --> pdb=" O ALA V 90 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR V 92 " --> pdb=" O ALA W 89 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N ALA W 91 " --> pdb=" O THR V 92 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N PHE V 94 " --> pdb=" O ALA W 91 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY W 93 " --> pdb=" O PHE V 94 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LYS V 96 " --> pdb=" O GLY W 93 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL W 95 " --> pdb=" O LYS V 96 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA V 89 " --> pdb=" O ALA X 90 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR X 92 " --> pdb=" O ALA V 89 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N ALA V 91 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N PHE X 94 " --> pdb=" O ALA V 91 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY V 93 " --> pdb=" O PHE X 94 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LYS X 96 " --> pdb=" O GLY V 93 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL V 95 " --> pdb=" O LYS X 96 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ALA X 89 " --> pdb=" O ALA Y 90 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR Y 92 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N ALA X 91 " --> pdb=" O THR Y 92 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N PHE Y 94 " --> pdb=" O ALA X 91 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY X 93 " --> pdb=" O PHE Y 94 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LYS Y 96 " --> pdb=" O GLY X 93 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL X 95 " --> pdb=" O LYS Y 96 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ALA Y 89 " --> pdb=" O ALA Z 90 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR Z 92 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N ALA Y 91 " --> pdb=" O THR Z 92 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N PHE Z 94 " --> pdb=" O ALA Y 91 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY Y 93 " --> pdb=" O PHE Z 94 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS Z 96 " --> pdb=" O GLY Y 93 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL Y 95 " --> pdb=" O LYS Z 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 124 hydrogen bonds defined for protein. 372 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: 0.95 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 725 1.29 - 1.35: 625 1.35 - 1.42: 110 1.42 - 1.48: 689 1.48 - 1.54: 1896 Bond restraints: 4045 Sorted by residual: bond pdb=" CB VAL Z 66 " pdb=" CG2 VAL Z 66 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CB VAL Y 66 " pdb=" CG2 VAL Y 66 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CB VAL W 66 " pdb=" CG2 VAL W 66 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 9.95e+00 bond pdb=" CB VAL V 66 " pdb=" CG2 VAL V 66 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 9.87e+00 bond pdb=" CB VAL X 66 " pdb=" CG2 VAL X 66 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.82e+00 ... (remaining 4040 not shown) Histogram of bond angle deviations from ideal: 105.42 - 109.09: 402 109.09 - 112.77: 2068 112.77 - 116.45: 504 116.45 - 120.13: 722 120.13 - 123.81: 1769 Bond angle restraints: 5465 Sorted by residual: angle pdb=" C THR Z 59 " pdb=" N LYS Z 60 " pdb=" CA LYS Z 60 " ideal model delta sigma weight residual 122.93 119.54 3.39 1.51e+00 4.39e-01 5.05e+00 angle pdb=" C THR W 59 " pdb=" N LYS W 60 " pdb=" CA LYS W 60 " ideal model delta sigma weight residual 122.93 119.54 3.39 1.51e+00 4.39e-01 5.03e+00 angle pdb=" C THR V 59 " pdb=" N LYS V 60 " pdb=" CA LYS V 60 " ideal model delta sigma weight residual 122.93 119.55 3.38 1.51e+00 4.39e-01 5.00e+00 angle pdb=" C THR X 59 " pdb=" N LYS X 60 " pdb=" CA LYS X 60 " ideal model delta sigma weight residual 122.93 119.57 3.36 1.51e+00 4.39e-01 4.96e+00 angle pdb=" C THR Y 59 " pdb=" N LYS Y 60 " pdb=" CA LYS Y 60 " ideal model delta sigma weight residual 122.93 119.57 3.36 1.51e+00 4.39e-01 4.95e+00 ... (remaining 5460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.69: 2095 12.69 - 25.39: 220 25.39 - 38.08: 40 38.08 - 50.77: 15 50.77 - 63.46: 15 Dihedral angle restraints: 2385 sinusoidal: 800 harmonic: 1585 Sorted by residual: dihedral pdb=" CA VAL E 48 " pdb=" C VAL E 48 " pdb=" N VAL E 49 " pdb=" CA VAL E 49 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA VAL D 48 " pdb=" C VAL D 48 " pdb=" N VAL D 49 " pdb=" CA VAL D 49 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA VAL C 48 " pdb=" C VAL C 48 " pdb=" N VAL C 49 " pdb=" CA VAL C 49 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 2382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 517 0.052 - 0.103: 132 0.103 - 0.155: 71 0.155 - 0.206: 0 0.206 - 0.258: 5 Chirality restraints: 725 Sorted by residual: chirality pdb=" CB VAL Y 66 " pdb=" CA VAL Y 66 " pdb=" CG1 VAL Y 66 " pdb=" CG2 VAL Y 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL V 66 " pdb=" CA VAL V 66 " pdb=" CG1 VAL V 66 " pdb=" CG2 VAL V 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL X 66 " pdb=" CA VAL X 66 " pdb=" CG1 VAL X 66 " pdb=" CG2 VAL X 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 722 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS Y 60 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C LYS Y 60 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS Y 60 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU Y 61 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS W 60 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LYS W 60 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS W 60 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU W 61 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS X 60 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LYS X 60 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS X 60 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU X 61 " 0.023 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 1854 2.93 - 3.42: 3431 3.42 - 3.91: 6356 3.91 - 4.41: 6980 4.41 - 4.90: 13933 Nonbonded interactions: 32554 Sorted by model distance: nonbonded pdb=" NZ LYS X 58 " pdb=" OE2 GLU X 61 " model vdw 2.432 2.520 nonbonded pdb=" NZ LYS W 58 " pdb=" OE2 GLU W 61 " model vdw 2.432 2.520 nonbonded pdb=" NZ LYS V 58 " pdb=" OE2 GLU V 61 " model vdw 2.432 2.520 nonbonded pdb=" NZ LYS Y 58 " pdb=" OE2 GLU Y 61 " model vdw 2.432 2.520 nonbonded pdb=" NZ LYS Z 58 " pdb=" OE2 GLU Z 61 " model vdw 2.433 2.520 ... (remaining 32549 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2515 2.51 5 N 700 2.21 5 O 825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 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: 0.830 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 15.200 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.009 0.104 4045 Z= 0.595 Angle : 0.704 3.394 5465 Z= 0.422 Chirality : 0.060 0.258 725 Planarity : 0.007 0.040 685 Dihedral : 12.873 63.461 1385 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer Outliers : 0.00 % 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: -1.79 (0.32), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.24), residues: 570 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.456 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1812 time to fit residues: 17.5949 Evaluate side-chains 69 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 0.0070 chunk 43 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 49 optimal weight: 30.0000 overall best weight: 6.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN B 99 GLN C 99 GLN D 99 GLN W 50 GLN V 50 GLN X 50 GLN Y 50 GLN Z 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.019 4045 Z= 0.276 Angle : 0.499 3.200 5465 Z= 0.290 Chirality : 0.055 0.136 725 Planarity : 0.002 0.015 685 Dihedral : 4.903 15.791 585 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer Outliers : 5.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.24), residues: 570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.451 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 91 average time/residue: 0.1469 time to fit residues: 16.9837 Evaluate side-chains 93 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0425 time to fit residues: 1.8860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 34 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 40.0000 chunk 44 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 40 optimal weight: 0.3980 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN B 99 GLN D 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 4045 Z= 0.231 Angle : 0.481 3.605 5465 Z= 0.276 Chirality : 0.054 0.132 725 Planarity : 0.002 0.013 685 Dihedral : 4.681 16.284 585 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.24), residues: 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.488 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 79 average time/residue: 0.1393 time to fit residues: 14.1776 Evaluate side-chains 77 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0442 time to fit residues: 0.9275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 30.0000 chunk 37 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 4045 Z= 0.345 Angle : 0.530 3.932 5465 Z= 0.304 Chirality : 0.055 0.133 725 Planarity : 0.002 0.012 685 Dihedral : 4.974 17.539 585 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer Outliers : 4.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.23 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.23), residues: 570 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.575 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 84 average time/residue: 0.1449 time to fit residues: 15.4894 Evaluate side-chains 87 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0408 time to fit residues: 1.4851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 9.9990 chunk 30 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.029 4045 Z= 0.389 Angle : 0.565 8.893 5465 Z= 0.319 Chirality : 0.056 0.139 725 Planarity : 0.002 0.014 685 Dihedral : 5.042 17.797 585 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer Outliers : 2.44 % 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: -2.51 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.23), residues: 570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.462 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 81 average time/residue: 0.1442 time to fit residues: 14.8255 Evaluate side-chains 80 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.459 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0461 time to fit residues: 0.9239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 53 optimal weight: 0.0010 chunk 44 optimal weight: 50.0000 chunk 24 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 0.2980 chunk 51 optimal weight: 8.9990 overall best weight: 2.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 4045 Z= 0.132 Angle : 0.450 7.693 5465 Z= 0.250 Chirality : 0.053 0.132 725 Planarity : 0.002 0.010 685 Dihedral : 4.244 13.977 585 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer Outliers : 1.71 % 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: -2.30 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.24), residues: 570 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.441 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 81 average time/residue: 0.1393 time to fit residues: 14.5252 Evaluate side-chains 73 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0475 time to fit residues: 0.8438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 44 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 0.0980 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.017 4045 Z= 0.201 Angle : 0.471 7.019 5465 Z= 0.262 Chirality : 0.053 0.128 725 Planarity : 0.002 0.010 685 Dihedral : 4.347 15.723 585 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer Outliers : 1.71 % 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: -2.31 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.24), residues: 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.482 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 74 average time/residue: 0.1439 time to fit residues: 13.7920 Evaluate side-chains 78 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0443 time to fit residues: 1.0974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 30.0000 chunk 46 optimal weight: 8.9990 chunk 49 optimal weight: 50.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.025 4045 Z= 0.344 Angle : 0.543 6.399 5465 Z= 0.303 Chirality : 0.055 0.134 725 Planarity : 0.002 0.014 685 Dihedral : 4.812 17.606 585 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer Outliers : 1.95 % 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: -2.47 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.23), residues: 570 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.436 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.1266 time to fit residues: 13.1967 Evaluate side-chains 76 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0390 time to fit residues: 0.9622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 46 optimal weight: 30.0000 chunk 49 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 4045 Z= 0.368 Angle : 0.562 6.157 5465 Z= 0.315 Chirality : 0.055 0.135 725 Planarity : 0.002 0.014 685 Dihedral : 4.961 18.986 585 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer Outliers : 0.73 % 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: -2.61 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.23), residues: 570 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.495 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 0.1419 time to fit residues: 14.9563 Evaluate side-chains 74 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0404 time to fit residues: 0.7015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.0270 chunk 36 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 overall best weight: 6.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 4045 Z= 0.267 Angle : 0.526 6.382 5465 Z= 0.291 Chirality : 0.055 0.143 725 Planarity : 0.002 0.012 685 Dihedral : 4.737 17.911 585 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 0.73 % 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: -2.55 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.23), residues: 570 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.445 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 73 average time/residue: 0.1313 time to fit residues: 12.4679 Evaluate side-chains 74 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0372 time to fit residues: 0.8012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 43 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 2 optimal weight: 0.0070 chunk 31 optimal weight: 0.0770 overall best weight: 3.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.191291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.166767 restraints weight = 4269.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.170103 restraints weight = 1826.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.172342 restraints weight = 1084.822| |-----------------------------------------------------------------------------| r_work (final): 0.4790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4045 Z= 0.187 Angle : 0.493 6.768 5465 Z= 0.269 Chirality : 0.054 0.139 725 Planarity : 0.002 0.010 685 Dihedral : 4.479 17.213 585 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 0.00 % 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: -2.43 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.24), residues: 570 =============================================================================== Job complete usr+sys time: 974.87 seconds wall clock time: 18 minutes 46.73 seconds (1126.73 seconds total)