Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:35:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ufr_20759/11_2022/6ufr_20759.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ufr_20759/11_2022/6ufr_20759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ufr_20759/11_2022/6ufr_20759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ufr_20759/11_2022/6ufr_20759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ufr_20759/11_2022/6ufr_20759.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ufr_20759/11_2022/6ufr_20759.pdb" } resolution = 2.5 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 TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4420 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "I" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "F" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "J" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "H" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "B" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 2.63, per 1000 atoms: 0.60 Number of scatterers: 4420 At special positions: 0 Unit cell: (103.074, 96.37, 41.9, 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 940 8.00 N 760 7.00 C 2720 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: 1.48 Conformation dependent library (CDL) restraints added in 838.8 milliseconds 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1060 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 68.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 37 through 57 removed outlier: 9.090A pdb=" N VAL E 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N VAL D 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N TYR E 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N SER D 42 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N GLY E 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N THR D 44 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N LYS E 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N LYS D 46 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS E 45 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL D 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY E 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N HIS D 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL E 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL D 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N GLY E 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N THR D 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N ALA E 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N ALA D 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N VAL E 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU A 38 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR D 39 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 40 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY D 41 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER A 42 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS D 43 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR A 44 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS D 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA D 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR A 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL D 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA A 56 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU D 57 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU H 38 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR A 39 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL H 40 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY A 41 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER H 42 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS A 43 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR H 44 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS A 45 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL H 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA A 53 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR H 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 55 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA H 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU A 57 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N LEU I 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N GLY H 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N VAL I 40 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N LYS H 43 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N SER I 42 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N LYS H 45 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR I 44 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLY H 47 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS I 46 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL H 49 " --> pdb=" O LYS I 46 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL I 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N GLY H 51 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N HIS I 50 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ALA H 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N VAL I 52 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N VAL H 55 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N THR I 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N GLU H 57 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N ALA I 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 61 through 66 removed outlier: 6.751A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL D 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU I 61 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N THR H 64 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL I 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL H 66 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN I 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.395A pdb=" N VAL A 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 76 through 83 removed outlier: 6.616A pdb=" N ALA A 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLN D 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR D 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS A 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N GLU D 83 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA I 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLN H 79 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA I 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N THR H 81 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS I 80 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU H 83 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL I 82 " --> pdb=" O GLU H 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 88 through 97 removed outlier: 6.335A pdb=" N ILE E 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA D 91 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA E 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY D 93 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N THR E 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL D 95 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N PHE E 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N LYS D 97 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N LYS E 96 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE D 94 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 95 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LYS D 96 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LYS A 97 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA H 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N GLY H 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR A 92 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL H 95 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N PHE A 94 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N LYS H 97 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N LYS A 96 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N ILE I 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N ALA H 91 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ALA I 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N GLY H 93 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR I 92 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL H 95 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE I 94 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LYS H 97 " --> pdb=" O PHE I 94 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS I 96 " --> pdb=" O LYS H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 37 through 57 removed outlier: 9.128A pdb=" N LEU C 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N GLY F 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N VAL C 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 10.409A pdb=" N LYS F 43 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N SER C 42 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N LYS F 45 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR C 44 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY F 47 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS C 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL F 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLY F 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N HIS C 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA F 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N VAL C 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N VAL F 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N THR C 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N GLU F 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ALA C 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N VAL C 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N VAL B 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N TYR C 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N SER B 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N GLY C 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N THR B 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N LYS C 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N LYS B 46 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS C 45 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL B 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY C 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N HIS B 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL B 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLY C 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 10.363A pdb=" N THR B 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ALA C 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N ALA B 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N VAL C 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N LEU G 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N GLY B 41 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N VAL G 40 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N LYS B 43 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N SER G 42 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N LYS B 45 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR G 44 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N GLY B 47 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS G 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL B 49 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL G 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY B 51 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N HIS G 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA B 53 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL G 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N VAL B 55 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N THR G 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N GLU B 57 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N ALA G 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU J 38 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR G 39 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL J 40 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY G 41 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER J 42 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS G 43 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR J 44 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS G 45 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL J 52 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA G 53 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR J 54 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL G 55 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA J 56 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU G 57 " --> pdb=" O ALA J 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 61 through 66 removed outlier: 6.717A pdb=" N GLU C 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR F 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL C 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL F 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN C 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU G 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR B 64 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL G 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL B 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN G 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 70 through 72 removed outlier: 6.433A pdb=" N VAL C 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL G 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 76 through 83 removed outlier: 6.620A pdb=" N ALA C 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLN F 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA C 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR F 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS C 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLU F 83 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA G 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLN B 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA G 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N THR B 81 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS G 80 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLU B 83 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL G 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 88 through 97 removed outlier: 6.755A pdb=" N PHE F 94 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL C 95 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS F 96 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS C 97 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA B 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLY B 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N THR C 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL B 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N PHE C 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N LYS B 97 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N LYS C 96 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE B 94 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL G 95 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS B 96 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS G 97 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA G 89 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA J 90 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA G 91 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR J 92 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY G 93 " --> pdb=" O THR J 92 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 740 1.28 - 1.35: 670 1.35 - 1.41: 170 1.41 - 1.48: 769 1.48 - 1.54: 2001 Bond restraints: 4350 Sorted by residual: bond pdb=" N GLU J 83 " pdb=" CA GLU J 83 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.20e-02 6.94e+03 5.52e+00 bond pdb=" N GLU F 83 " pdb=" CA GLU F 83 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.20e-02 6.94e+03 5.30e+00 bond pdb=" N GLU G 83 " pdb=" CA GLU G 83 " ideal model delta sigma weight residual 1.460 1.487 -0.028 1.20e-02 6.94e+03 5.28e+00 bond pdb=" N GLU A 83 " pdb=" CA GLU A 83 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.20e-02 6.94e+03 5.19e+00 bond pdb=" N GLU H 83 " pdb=" CA GLU H 83 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.20e-02 6.94e+03 5.18e+00 ... (remaining 4345 not shown) Histogram of bond angle deviations from ideal: 106.20 - 111.22: 2078 111.22 - 116.23: 912 116.23 - 121.25: 1672 121.25 - 126.27: 1198 126.27 - 131.28: 10 Bond angle restraints: 5870 Sorted by residual: angle pdb=" C THR H 59 " pdb=" N LYS H 60 " pdb=" CA LYS H 60 " ideal model delta sigma weight residual 122.42 118.11 4.31 1.55e+00 4.16e-01 7.74e+00 angle pdb=" C THR F 59 " pdb=" N LYS F 60 " pdb=" CA LYS F 60 " ideal model delta sigma weight residual 122.42 118.12 4.30 1.55e+00 4.16e-01 7.69e+00 angle pdb=" C THR J 59 " pdb=" N LYS J 60 " pdb=" CA LYS J 60 " ideal model delta sigma weight residual 122.42 118.13 4.29 1.55e+00 4.16e-01 7.64e+00 angle pdb=" C THR E 59 " pdb=" N LYS E 60 " pdb=" CA LYS E 60 " ideal model delta sigma weight residual 122.42 118.14 4.28 1.55e+00 4.16e-01 7.62e+00 angle pdb=" C THR B 59 " pdb=" N LYS B 60 " pdb=" CA LYS B 60 " ideal model delta sigma weight residual 122.42 118.15 4.27 1.55e+00 4.16e-01 7.59e+00 ... (remaining 5865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 2330 14.90 - 29.80: 150 29.80 - 44.70: 20 44.70 - 59.60: 30 59.60 - 74.50: 10 Dihedral angle restraints: 2540 sinusoidal: 850 harmonic: 1690 Sorted by residual: dihedral pdb=" CA GLY E 73 " pdb=" C GLY E 73 " pdb=" N VAL E 74 " pdb=" CA VAL E 74 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY C 73 " pdb=" C GLY C 73 " pdb=" N VAL C 74 " pdb=" CA VAL C 74 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY A 73 " pdb=" C GLY A 73 " pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 2537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 289 0.040 - 0.079: 232 0.079 - 0.118: 199 0.118 - 0.157: 35 0.157 - 0.197: 15 Chirality restraints: 770 Sorted by residual: chirality pdb=" CB THR E 44 " pdb=" CA THR E 44 " pdb=" OG1 THR E 44 " pdb=" CG2 THR E 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CB THR B 44 " pdb=" CA THR B 44 " pdb=" OG1 THR B 44 " pdb=" CG2 THR B 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CB THR H 44 " pdb=" CA THR H 44 " pdb=" OG1 THR H 44 " pdb=" CG2 THR H 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 767 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 75 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C THR C 75 " 0.064 2.00e-02 2.50e+03 pdb=" O THR C 75 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA C 76 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 75 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C THR D 75 " -0.064 2.00e-02 2.50e+03 pdb=" O THR D 75 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA D 76 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 75 " -0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C THR B 75 " 0.064 2.00e-02 2.50e+03 pdb=" O THR B 75 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 76 " -0.022 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 351 2.75 - 3.29: 3533 3.29 - 3.82: 7636 3.82 - 4.36: 8344 4.36 - 4.90: 16105 Nonbonded interactions: 35969 Sorted by model distance: nonbonded pdb=" O GLY D 67 " pdb=" O HOH D 201 " model vdw 2.209 2.440 nonbonded pdb=" O GLY J 67 " pdb=" O HOH J 201 " model vdw 2.209 2.440 nonbonded pdb=" O GLY C 67 " pdb=" O HOH C 201 " model vdw 2.209 2.440 nonbonded pdb=" O GLY H 67 " pdb=" O HOH H 201 " model vdw 2.209 2.440 nonbonded pdb=" O GLY I 67 " pdb=" O HOH I 201 " model vdw 2.209 2.440 ... (remaining 35964 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' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 2720 2.51 5 N 760 2.21 5 O 940 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 0.910 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 15.580 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 : 0.012 0.061 4350 Z= 0.847 Angle : 0.960 5.959 5870 Z= 0.568 Chirality : 0.071 0.197 770 Planarity : 0.009 0.037 720 Dihedral : 13.714 74.498 1480 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % 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: -1.99 (0.27), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.21), residues: 610 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.502 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.9850 time to fit residues: 142.3062 Evaluate side-chains 126 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.545 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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: 0.8700 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 4350 Z= 0.153 Angle : 0.516 5.810 5870 Z= 0.289 Chirality : 0.054 0.124 770 Planarity : 0.002 0.008 720 Dihedral : 5.499 16.634 630 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 5.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.26), residues: 610 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 0.626 Fit side-chains outliers start: 24 outliers final: 2 residues processed: 134 average time/residue: 0.9533 time to fit residues: 133.0811 Evaluate side-chains 123 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0423 time to fit residues: 0.7864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 43 optimal weight: 40.0000 chunk 53 optimal weight: 20.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- 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: 0.8774 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 4350 Z= 0.302 Angle : 0.613 6.407 5870 Z= 0.344 Chirality : 0.056 0.141 770 Planarity : 0.002 0.010 720 Dihedral : 6.069 19.391 630 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 5.00 % 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: -0.87 (0.34), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.26), residues: 610 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.566 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 122 average time/residue: 1.0064 time to fit residues: 127.6753 Evaluate side-chains 125 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 5 residues processed: 6 average time/residue: 0.0439 time to fit residues: 1.1530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 40.0000 chunk 28 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 57 optimal weight: 40.0000 chunk 51 optimal weight: 40.0000 chunk 15 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 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: 0.8761 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 4350 Z= 0.252 Angle : 0.579 6.246 5870 Z= 0.323 Chirality : 0.055 0.134 770 Planarity : 0.002 0.011 720 Dihedral : 5.806 18.525 630 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 7.73 % 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: -0.83 (0.34), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.63 (0.26), residues: 610 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 0.548 Fit side-chains outliers start: 34 outliers final: 18 residues processed: 126 average time/residue: 0.9622 time to fit residues: 126.2428 Evaluate side-chains 132 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.529 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 7 residues processed: 11 average time/residue: 0.0416 time to fit residues: 1.4975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 30.0000 chunk 43 optimal weight: 50.0000 chunk 23 optimal weight: 50.0000 chunk 49 optimal weight: 0.0670 chunk 40 optimal weight: 20.0000 chunk 29 optimal weight: 40.0000 chunk 52 optimal weight: 40.0000 chunk 14 optimal weight: 30.0000 chunk 19 optimal weight: 40.0000 chunk 11 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 overall best weight: 20.0134 ------------------------------------------------------------------------------- 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: 0.8809 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.061 4350 Z= 0.534 Angle : 0.794 7.612 5870 Z= 0.444 Chirality : 0.061 0.162 770 Planarity : 0.003 0.015 720 Dihedral : 6.685 21.193 630 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 7.73 % 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: -1.01 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.25), residues: 610 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 0.552 Fit side-chains outliers start: 34 outliers final: 18 residues processed: 124 average time/residue: 1.0490 time to fit residues: 134.9604 Evaluate side-chains 127 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 6 residues processed: 12 average time/residue: 0.0418 time to fit residues: 1.5313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 20.0000 chunk 58 optimal weight: 40.0000 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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: 0.8760 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4350 Z= 0.225 Angle : 0.560 6.081 5870 Z= 0.313 Chirality : 0.055 0.133 770 Planarity : 0.002 0.008 720 Dihedral : 5.736 18.223 630 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 6.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.34), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.26), residues: 610 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 0.553 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 125 average time/residue: 1.0048 time to fit residues: 130.6777 Evaluate side-chains 131 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 7 average time/residue: 0.0420 time to fit residues: 1.2155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 chunk 57 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 23 optimal weight: 50.0000 chunk 34 optimal weight: 20.0000 chunk 17 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 30.0000 overall best weight: 14.3996 ------------------------------------------------------------------------------- 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: 0.8795 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 4350 Z= 0.391 Angle : 0.682 6.748 5870 Z= 0.382 Chirality : 0.058 0.149 770 Planarity : 0.003 0.012 720 Dihedral : 6.294 19.915 630 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 7.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.25), residues: 610 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 0.563 Fit side-chains outliers start: 32 outliers final: 17 residues processed: 126 average time/residue: 1.0406 time to fit residues: 136.2343 Evaluate side-chains 133 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 6 residues processed: 11 average time/residue: 0.0436 time to fit residues: 1.5285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 40.0000 chunk 45 optimal weight: 30.0000 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 23 optimal weight: 50.0000 chunk 42 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- 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: 0.8782 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 4350 Z= 0.313 Angle : 0.625 6.464 5870 Z= 0.349 Chirality : 0.056 0.142 770 Planarity : 0.002 0.011 720 Dihedral : 6.032 19.032 630 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.25), residues: 610 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.471 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 123 average time/residue: 1.0741 time to fit residues: 137.0668 Evaluate side-chains 128 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.503 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 5 residues processed: 6 average time/residue: 0.0416 time to fit residues: 1.2526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 35 optimal weight: 30.0000 chunk 56 optimal weight: 40.0000 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 59 optimal weight: 50.0000 chunk 55 optimal weight: 20.0000 chunk 47 optimal weight: 50.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- 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: 0.8800 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 4350 Z= 0.413 Angle : 0.705 6.985 5870 Z= 0.394 Chirality : 0.059 0.154 770 Planarity : 0.003 0.013 720 Dihedral : 6.399 20.273 630 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 5.23 % 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: -0.95 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.25), residues: 610 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.544 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 123 average time/residue: 1.0873 time to fit residues: 138.9284 Evaluate side-chains 129 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.0436 time to fit residues: 1.1576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 43 optimal weight: 30.0000 chunk 7 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 47 optimal weight: 40.0000 chunk 19 optimal weight: 10.0000 overall best weight: 11.3994 ------------------------------------------------------------------------------- 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: 0.8783 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 4350 Z= 0.319 Angle : 0.634 6.529 5870 Z= 0.354 Chirality : 0.056 0.144 770 Planarity : 0.002 0.011 720 Dihedral : 6.089 19.213 630 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 2.95 % 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: -0.92 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.69 (0.25), residues: 610 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.619 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 1.0841 time to fit residues: 140.6817 Evaluate side-chains 128 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.0422 time to fit residues: 0.9519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 41 optimal weight: 40.0000 chunk 2 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.132686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.117478 restraints weight = 4002.163| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.52 r_work: 0.3636 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 1.29 restraints_weight: 0.2500 r_work: 0.3611 rms_B_bonded: 1.36 restraints_weight: 0.1250 r_work: 0.3597 rms_B_bonded: 1.50 restraints_weight: 0.0625 r_work: 0.3580 rms_B_bonded: 1.71 restraints_weight: 0.0312 r_work: 0.3559 rms_B_bonded: 1.99 restraints_weight: 0.0156 r_work: 0.3535 rms_B_bonded: 2.36 restraints_weight: 0.0078 r_work: 0.3506 rms_B_bonded: 2.84 restraints_weight: 0.0039 r_work: 0.3471 rms_B_bonded: 3.46 restraints_weight: 0.0020 r_work: 0.3429 rms_B_bonded: 4.25 restraints_weight: 0.0010 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 4350 Z= 0.248 Angle : 0.575 6.021 5870 Z= 0.322 Chirality : 0.055 0.135 770 Planarity : 0.002 0.009 720 Dihedral : 5.789 18.282 630 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.34), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.26), residues: 610 =============================================================================== Job complete usr+sys time: 2063.76 seconds wall clock time: 37 minutes 20.12 seconds (2240.12 seconds total)