Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 19:43:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqc_23942/04_2023/7mqc_23942.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqc_23942/04_2023/7mqc_23942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqc_23942/04_2023/7mqc_23942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqc_23942/04_2023/7mqc_23942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqc_23942/04_2023/7mqc_23942.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqc_23942/04_2023/7mqc_23942.pdb" } resolution = 3.64 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= 0.002 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11279 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 45 5.16 5 C 7949 2.51 5 N 2316 2.21 5 O 2230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 27": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 120": "OE1" <-> "OE2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O GLU 124": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12556 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1512 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "C" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1530 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "E" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1528 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 76 Chain: "F" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "G" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1526 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 76 Chain: "H" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "I" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1527 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 88 Chain: "J" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "K" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1507 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 92 Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "M" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1520 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 86 Chain: "N" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "O" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1530 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 83 Chain: "P" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Time building chain proxies: 6.96, per 1000 atoms: 0.55 Number of scatterers: 12556 At special positions: 0 Unit cell: (111.6, 106.64, 91.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 16 15.00 O 2230 8.00 N 2316 7.00 C 7949 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: 5.39 Conformation dependent library (CDL) restraints added in 2.3 seconds 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 46.4% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.902A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 157 removed outlier: 3.907A pdb=" N VAL A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 175 through 196 Proline residue: A 187 - end of helix Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 80 through 93 removed outlier: 3.879A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.979A pdb=" N VAL C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 173 Processing helix chain 'C' and resid 175 through 196 Proline residue: C 187 - end of helix Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.904A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 145 through 157 removed outlier: 3.970A pdb=" N VAL E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 174 Processing helix chain 'E' and resid 175 through 196 Proline residue: E 187 - end of helix Processing helix chain 'G' and resid 62 through 71 Processing helix chain 'G' and resid 80 through 93 removed outlier: 3.758A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 117 through 127 Processing helix chain 'G' and resid 145 through 155 Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'G' and resid 175 through 196 Proline residue: G 187 - end of helix Processing helix chain 'I' and resid 62 through 70 Processing helix chain 'I' and resid 80 through 93 removed outlier: 3.943A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA I 86 " --> pdb=" O ARG I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 132 through 136 removed outlier: 4.172A pdb=" N SER I 136 " --> pdb=" O GLN I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 157 removed outlier: 3.771A pdb=" N VAL I 156 " --> pdb=" O ALA I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'I' and resid 175 through 196 Proline residue: I 187 - end of helix Processing helix chain 'K' and resid 62 through 71 Processing helix chain 'K' and resid 80 through 93 removed outlier: 3.829A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 117 through 127 Processing helix chain 'K' and resid 145 through 155 Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'K' and resid 175 through 196 Proline residue: K 187 - end of helix Processing helix chain 'M' and resid 62 through 71 Processing helix chain 'M' and resid 80 through 93 removed outlier: 3.860A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 117 through 127 Processing helix chain 'M' and resid 145 through 157 removed outlier: 3.907A pdb=" N VAL M 156 " --> pdb=" O ALA M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 173 Processing helix chain 'M' and resid 175 through 196 Proline residue: M 187 - end of helix Processing helix chain 'O' and resid 62 through 71 Processing helix chain 'O' and resid 80 through 93 removed outlier: 3.837A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA O 86 " --> pdb=" O ARG O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 110 Processing helix chain 'O' and resid 117 through 127 Processing helix chain 'O' and resid 145 through 157 removed outlier: 3.995A pdb=" N VAL O 156 " --> pdb=" O ALA O 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 173 Processing helix chain 'O' and resid 175 through 196 Proline residue: O 187 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.418A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.275A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 22 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.414A pdb=" N GLU E 3 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL E 52 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.362A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA G 23 " --> pdb=" O LEU G 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 3 through 8 removed outlier: 6.518A pdb=" N GLU I 3 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL I 52 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU I 27 " --> pdb=" O CYS I 39 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL I 41 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP I 25 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU I 43 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA I 23 " --> pdb=" O LEU I 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 8 removed outlier: 6.464A pdb=" N GLU K 3 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL K 52 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 4 through 8 removed outlier: 6.377A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 3 through 8 removed outlier: 6.475A pdb=" N GLU O 3 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL O 52 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1779 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: 3.24 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4133 1.34 - 1.46: 2484 1.46 - 1.58: 6121 1.58 - 1.69: 24 1.69 - 1.81: 58 Bond restraints: 12820 Sorted by residual: bond pdb=" N GLU C 173 " pdb=" CA GLU C 173 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.32e-02 5.74e+03 8.28e+00 bond pdb=" N VAL O 178 " pdb=" CA VAL O 178 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.71e+00 bond pdb=" N MET E 95 " pdb=" CA MET E 95 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.21e-02 6.83e+03 7.60e+00 bond pdb=" C MET E 95 " pdb=" N PRO E 96 " ideal model delta sigma weight residual 1.332 1.368 -0.036 1.34e-02 5.57e+03 7.41e+00 bond pdb=" C MET A 95 " pdb=" N PRO A 96 " ideal model delta sigma weight residual 1.332 1.368 -0.036 1.34e-02 5.57e+03 7.33e+00 ... (remaining 12815 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.75: 243 105.75 - 112.82: 7048 112.82 - 119.89: 4423 119.89 - 126.97: 5602 126.97 - 134.04: 195 Bond angle restraints: 17511 Sorted by residual: angle pdb=" CA VAL O 178 " pdb=" C VAL O 178 " pdb=" O VAL O 178 " ideal model delta sigma weight residual 120.85 117.11 3.74 1.06e+00 8.90e-01 1.24e+01 angle pdb=" CA MET C 95 " pdb=" C MET C 95 " pdb=" O MET C 95 " ideal model delta sigma weight residual 119.36 116.40 2.96 8.40e-01 1.42e+00 1.24e+01 angle pdb=" CA MET A 95 " pdb=" C MET A 95 " pdb=" O MET A 95 " ideal model delta sigma weight residual 119.36 116.48 2.88 8.40e-01 1.42e+00 1.17e+01 angle pdb=" C THR K 28 " pdb=" CA THR K 28 " pdb=" CB THR K 28 " ideal model delta sigma weight residual 111.65 103.62 8.03 2.40e+00 1.74e-01 1.12e+01 angle pdb=" CA MET E 95 " pdb=" C MET E 95 " pdb=" O MET E 95 " ideal model delta sigma weight residual 119.36 116.57 2.79 8.40e-01 1.42e+00 1.10e+01 ... (remaining 17506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7093 17.97 - 35.94: 352 35.94 - 53.91: 87 53.91 - 71.89: 21 71.89 - 89.86: 15 Dihedral angle restraints: 7568 sinusoidal: 2784 harmonic: 4784 Sorted by residual: dihedral pdb=" CA PHE I 78 " pdb=" C PHE I 78 " pdb=" N HIS I 79 " pdb=" CA HIS I 79 " ideal model delta harmonic sigma weight residual 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA PHE E 78 " pdb=" C PHE E 78 " pdb=" N HIS E 79 " pdb=" CA HIS E 79 " ideal model delta harmonic sigma weight residual 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA PHE K 78 " pdb=" C PHE K 78 " pdb=" N HIS K 79 " pdb=" CA HIS K 79 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 7565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1494 0.059 - 0.117: 531 0.117 - 0.176: 65 0.176 - 0.235: 11 0.235 - 0.293: 2 Chirality restraints: 2103 Sorted by residual: chirality pdb=" CA THR K 28 " pdb=" N THR K 28 " pdb=" C THR K 28 " pdb=" CB THR K 28 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA LEU K 38 " pdb=" N LEU K 38 " pdb=" C LEU K 38 " pdb=" CB LEU K 38 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU K 125 " pdb=" CB LEU K 125 " pdb=" CD1 LEU K 125 " pdb=" CD2 LEU K 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2100 not shown) Planarity restraints: 2164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 11 " -0.078 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO M 12 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO M 12 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO M 12 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 35 " 0.012 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" C ARG A 35 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG A 35 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP A 36 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 158 " 0.017 2.00e-02 2.50e+03 1.36e-02 3.70e+00 pdb=" CG TYR E 158 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR E 158 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR E 158 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 158 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 158 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 158 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 158 " 0.003 2.00e-02 2.50e+03 ... (remaining 2161 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1646 2.75 - 3.29: 11543 3.29 - 3.83: 20561 3.83 - 4.36: 24958 4.36 - 4.90: 43071 Nonbonded interactions: 101779 Sorted by model distance: nonbonded pdb=" OH TYR I 17 " pdb=" OD1 ASP I 51 " model vdw 2.215 2.440 nonbonded pdb=" NE2 GLN G 135 " pdb=" OP2 G H 604 " model vdw 2.254 2.520 nonbonded pdb=" NE2 GLN I 135 " pdb=" OP2 G J 604 " model vdw 2.296 2.520 nonbonded pdb=" NZ LYS G 119 " pdb=" O ILE G 130 " model vdw 2.321 2.520 nonbonded pdb=" O GLU E 3 " pdb=" OG1 THR E 49 " model vdw 2.333 2.440 ... (remaining 101774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 13 or (resid 14 through 16 and (name N or name C \ A or name C or name O or name CB )) or resid 17 through 27 or (resid 28 and (nam \ e N or name CA or name C or name O or name CB )) or resid 29 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 48 or (resid 49 through 51 and (name N or name CA or name C or name O or name \ CB )) or resid 52 through 60 or (resid 61 through 62 and (name N or name CA or n \ ame C or name O or name CB )) or resid 63 through 64 or (resid 65 through 67 and \ (name N or name CA or name C or name O or name CB )) or resid 68 through 112 or \ (resid 113 through 114 and (name N or name CA or name C or name O or name CB )) \ or resid 115 through 123 or (resid 124 and (name N or name CA or name C or name \ O or name CB )) or resid 125 through 126 or (resid 127 through 130 and (name N \ or name CA or name C or name O or name CB )) or resid 131 through 142 or (resid \ 143 and (name N or name CA or name C or name O or name CB )) or resid 144 throug \ h 145 or (resid 146 through 147 and (name N or name CA or name C or name O or na \ me CB )) or resid 148 or (resid 149 through 150 and (name N or name CA or name C \ or name O or name CB )) or resid 151 through 153 or (resid 154 and (name N or n \ ame CA or name C or name O or name CB )) or resid 155 through 156 or (resid 157 \ and (name N or name CA or name C or name O or name CB )) or resid 158 through 16 \ 3 or (resid 164 and (name N or name CA or name C or name O or name CB )) or resi \ d 165 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 or (resid 173 through 174 and (name N or name CA or name C \ or name O or name CB )) or resid 175 through 187 or (resid 188 and (name N or n \ ame CA or name C or name O or name CB )) or resid 189 through 192 or (resid 193 \ and (name N or name CA or name C or name O or name CB )) or resid 194 through 19 \ 9 or (resid 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 206)) selection = (chain 'C' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 through 16 and (nam \ e N or name CA or name C or name O or name CB )) or resid 17 through 27 or (resi \ d 28 and (name N or name CA or name C or name O or name CB )) or resid 29 throug \ h 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or re \ sid 37 through 48 or (resid 49 through 51 and (name N or name CA or name C or na \ me O or name CB )) or resid 52 through 60 or (resid 61 through 62 and (name N or \ name CA or name C or name O or name CB )) or resid 63 or (resid 64 through 67 a \ nd (name N or name CA or name C or name O or name CB )) or resid 68 through 93 o \ r (resid 94 and (name N or name CA or name C or name O or name CB )) or resid 95 \ through 123 or (resid 124 and (name N or name CA or name C or name O or name CB \ )) or resid 125 through 126 or (resid 127 through 130 and (name N or name CA or \ name C or name O or name CB )) or resid 131 through 137 or (resid 138 and (name \ N or name CA or name C or name O or name CB )) or resid 139 through 142 or (res \ id 143 and (name N or name CA or name C or name O or name CB )) or resid 144 thr \ ough 145 or (resid 146 through 147 and (name N or name CA or name C or name O or \ name CB )) or resid 148 or (resid 149 through 150 and (name N or name CA or nam \ e C or name O or name CB )) or resid 151 through 153 or (resid 154 and (name N o \ r name CA or name C or name O or name CB )) or resid 155 through 156 or (resid 1 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 158 through \ 163 or (resid 164 and (name N or name CA or name C or name O or name CB )) or r \ esid 165 through 170 or (resid 171 and (name N or name CA or name C or name O or \ name CB )) or resid 172 or (resid 173 through 174 and (name N or name CA or nam \ e C or name O or name CB )) or resid 175 or (resid 176 and (name N or name CA or \ name C or name O or name CB )) or resid 177 through 192 or (resid 193 and (name \ N or name CA or name C or name O or name CB )) or resid 194 through 199 or (res \ id 200 and (name N or name CA or name C or name O or name CB )) or resid 201 thr \ ough 205 or (resid 206 and (name N or name CA or name C or name O or name CB ))) \ ) selection = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 17 or (resid 18 through 21 and (name \ N or name CA or name C or name O or name CB )) or resid 22 through 27 or (resid \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 48 or (resid 49 through 51 and (name N or name CA or name C or name O or name C \ B )) or resid 52 through 63 or (resid 64 through 67 and (name N or name CA or na \ me C or name O or name CB )) or resid 68 through 93 or (resid 94 and (name N or \ name CA or name C or name O or name CB )) or resid 95 through 112 or (resid 113 \ through 114 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 5 through 119 or (resid 120 and (name N or name CA or name C or name O or name C \ B )) or resid 121 through 123 or (resid 124 and (name N or name CA or name C or \ name O or name CB )) or resid 125 through 126 or (resid 127 through 130 and (nam \ e N or name CA or name C or name O or name CB )) or resid 131 through 137 or (re \ sid 138 and (name N or name CA or name C or name O or name CB )) or resid 139 th \ rough 142 or (resid 143 and (name N or name CA or name C or name O or name CB )) \ or resid 144 through 153 or (resid 154 and (name N or name CA or name C or name \ O or name CB )) or resid 155 through 156 or (resid 157 and (name N or name CA o \ r name C or name O or name CB )) or resid 158 through 163 or (resid 164 and (nam \ e N or name CA or name C or name O or name CB )) or resid 165 through 170 or (re \ sid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 th \ rough 175 or (resid 176 and (name N or name CA or name C or name O or name CB )) \ or resid 177 through 187 or (resid 188 and (name N or name CA or name C or name \ O or name CB )) or resid 189 through 192 or (resid 193 and (name N or name CA o \ r name C or name O or name CB )) or resid 194 through 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 205 or (re \ sid 206 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 through 16 and (nam \ e N or name CA or name C or name O or name CB )) or resid 17 through 27 or (resi \ d 28 and (name N or name CA or name C or name O or name CB )) or resid 29 throug \ h 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or re \ sid 37 through 46 or (resid 47 and (name N or name CA or name C or name O or nam \ e CB )) or resid 48 or (resid 49 through 51 and (name N or name CA or name C or \ name O or name CB )) or resid 52 through 60 or (resid 61 through 62 and (name N \ or name CA or name C or name O or name CB )) or resid 63 or (resid 64 through 67 \ and (name N or name CA or name C or name O or name CB )) or resid 68 through 71 \ or (resid 72 through 73 and (name N or name CA or name C or name O or name CB ) \ ) or resid 74 through 93 or (resid 94 and (name N or name CA or name C or name O \ or name CB )) or resid 95 through 112 or (resid 113 through 114 and (name N or \ name CA or name C or name O or name CB )) or resid 115 through 119 or (resid 120 \ and (name N or name CA or name C or name O or name CB )) or resid 121 through 1 \ 23 or (resid 124 and (name N or name CA or name C or name O or name CB )) or res \ id 125 through 137 or (resid 138 and (name N or name CA or name C or name O or n \ ame CB )) or resid 139 through 142 or (resid 143 and (name N or name CA or name \ C or name O or name CB )) or resid 144 through 148 or (resid 149 through 150 and \ (name N or name CA or name C or name O or name CB )) or resid 151 through 153 o \ r (resid 154 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 55 through 163 or (resid 164 and (name N or name CA or name C or name O or name \ CB )) or resid 165 through 175 or (resid 176 and (name N or name CA or name C or \ name O or name CB )) or resid 177 through 187 or (resid 188 and (name N or name \ CA or name C or name O or name CB )) or resid 189 through 192 or (resid 193 and \ (name N or name CA or name C or name O or name CB )) or resid 194 through 199 o \ r (resid 200 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 01 through 205 or (resid 206 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'I' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 through 16 and (name \ N or name CA or name C or name O or name CB )) or resid 17 through 35 or (resid \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 through \ 48 or (resid 49 through 51 and (name N or name CA or name C or name O or name C \ B )) or resid 52 through 60 or (resid 61 through 62 and (name N or name CA or na \ me C or name O or name CB )) or resid 63 or (resid 64 through 67 and (name N or \ name CA or name C or name O or name CB )) or resid 68 through 93 or (resid 94 an \ d (name N or name CA or name C or name O or name CB )) or resid 95 through 112 o \ r (resid 113 through 114 and (name N or name CA or name C or name O or name CB ) \ ) or resid 115 through 123 or (resid 124 and (name N or name CA or name C or nam \ e O or name CB )) or resid 125 through 127 or (resid 128 through 130 and (name N \ or name CA or name C or name O or name CB )) or resid 131 through 137 or (resid \ 138 and (name N or name CA or name C or name O or name CB )) or resid 139 throu \ gh 148 or (resid 149 through 150 and (name N or name CA or name C or name O or n \ ame CB )) or resid 151 through 153 or (resid 154 and (name N or name CA or name \ C or name O or name CB )) or resid 155 through 156 or (resid 157 and (name N or \ name CA or name C or name O or name CB )) or resid 158 through 170 or (resid 171 \ and (name N or name CA or name C or name O or name CB )) or resid 172 through 1 \ 75 or (resid 176 and (name N or name CA or name C or name O or name CB )) or res \ id 177 through 179 or (resid 180 through 181 and (name N or name CA or name C or \ name O or name CB )) or resid 182 through 187 or (resid 188 and (name N or name \ CA or name C or name O or name CB )) or resid 189 through 192 or (resid 193 and \ (name N or name CA or name C or name O or name CB )) or resid 194 through 199 o \ r (resid 200 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 01 through 205 or (resid 206 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'K' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 through 16 and (name \ N or name CA or name C or name O or name CB )) or resid 17 through 27 or (resid \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or res \ id 52 through 63 or (resid 64 through 67 and (name N or name CA or name C or nam \ e O or name CB )) or resid 68 through 112 or (resid 113 through 114 and (name N \ or name CA or name C or name O or name CB )) or resid 115 through 119 or (resid \ 120 and (name N or name CA or name C or name O or name CB )) or resid 121 throug \ h 127 or (resid 128 through 130 and (name N or name CA or name C or name O or na \ me CB )) or resid 131 through 137 or (resid 138 and (name N or name CA or name C \ or name O or name CB )) or resid 139 through 142 or (resid 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 through 145 or (resid 146 \ through 147 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 8 or (resid 149 through 150 and (name N or name CA or name C or name O or name C \ B )) or resid 151 through 153 or (resid 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 through 156 or (resid 157 and (name N or name \ CA or name C or name O or name CB )) or resid 158 through 163 or (resid 164 and \ (name N or name CA or name C or name O or name CB )) or resid 165 through 166 or \ (resid 167 through 168 and (name N or name CA or name C or name O or name CB )) \ or resid 169 through 205 or (resid 206 and (name N or name CA or name C or name \ O or name CB )))) selection = (chain 'M' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 through 16 and (name \ N or name CA or name C or name O or name CB )) or resid 17 through 27 or (resid \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 48 or (resid 49 through 51 and (name N or name CA or name C or name O or name C \ B )) or resid 52 through 60 or (resid 61 through 62 and (name N or name CA or na \ me C or name O or name CB )) or resid 63 or (resid 64 through 67 and (name N or \ name CA or name C or name O or name CB )) or resid 68 through 123 or (resid 124 \ and (name N or name CA or name C or name O or name CB )) or resid 125 through 12 \ 9 or (resid 130 and (name N or name CA or name C or name O or name CB )) or resi \ d 131 through 137 or (resid 138 and (name N or name CA or name C or name O or na \ me CB )) or resid 139 through 142 or (resid 143 and (name N or name CA or name C \ or name O or name CB )) or resid 144 through 145 or (resid 146 through 147 and \ (name N or name CA or name C or name O or name CB )) or resid 148 or (resid 149 \ through 150 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 1 through 156 or (resid 157 and (name N or name CA or name C or name O or name C \ B )) or resid 158 through 163 or (resid 164 and (name N or name CA or name C or \ name O or name CB )) or resid 165 through 170 or (resid 171 and (name N or name \ CA or name C or name O or name CB )) or resid 172 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 192 or \ (resid 193 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 4 through 199 or (resid 200 and (name N or name CA or name C or name O or name C \ B )) or resid 201 through 205 or (resid 206 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'O' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 through 16 and (nam \ e N or name CA or name C or name O or name CB )) or resid 17 through 27 or (resi \ d 28 and (name N or name CA or name C or name O or name CB )) or resid 29 throug \ h 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or re \ sid 37 through 48 or (resid 49 through 51 and (name N or name CA or name C or na \ me O or name CB )) or resid 52 through 60 or (resid 61 through 62 and (name N or \ name CA or name C or name O or name CB )) or resid 63 or (resid 64 through 67 a \ nd (name N or name CA or name C or name O or name CB )) or resid 68 through 70 o \ r (resid 71 through 73 and (name N or name CA or name C or name O or name CB )) \ or resid 74 through 93 or (resid 94 and (name N or name CA or name C or name O o \ r name CB )) or resid 95 through 112 or (resid 113 through 114 and (name N or na \ me CA or name C or name O or name CB )) or resid 115 through 123 or (resid 124 a \ nd (name N or name CA or name C or name O or name CB )) or resid 125 through 126 \ or (resid 127 through 130 and (name N or name CA or name C or name O or name CB \ )) or resid 131 through 142 or (resid 143 and (name N or name CA or name C or n \ ame O or name CB )) or resid 144 through 145 or (resid 146 through 147 and (name \ N or name CA or name C or name O or name CB )) or resid 148 or (resid 149 throu \ gh 150 and (name N or name CA or name C or name O or name CB )) or resid 151 thr \ ough 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) \ or resid 155 through 156 or (resid 157 and (name N or name CA or name C or name \ O or name CB )) or resid 158 through 163 or (resid 164 and (name N or name CA or \ name C or name O or name CB )) or resid 165 through 166 or (resid 167 through 1 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 169 through \ 170 or (resid 171 and (name N or name CA or name C or name O or name CB )) or r \ esid 172 through 179 or (resid 180 through 181 and (name N or name CA or name C \ or name O or name CB )) or resid 182 through 187 or (resid 188 and (name N or na \ me CA or name C or name O or name CB )) or resid 189 through 192 or (resid 193 a \ nd (name N or name CA or name C or name O or name CB )) or resid 194 through 199 \ or (resid 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 through 205 or (resid 206 and (name N or name CA or name C or name O or nam \ e CB )))) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 1.880 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 34.590 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.007 0.050 12820 Z= 0.447 Angle : 0.806 8.034 17511 Z= 0.486 Chirality : 0.057 0.293 2103 Planarity : 0.005 0.120 2164 Dihedral : 13.146 89.857 4448 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer Outliers : 0.61 % 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: 1.03 (0.20), residues: 1624 helix: 0.57 (0.18), residues: 704 sheet: 0.44 (0.24), residues: 248 loop : 1.22 (0.26), residues: 672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 192 time to evaluate : 1.688 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 195 average time/residue: 0.2352 time to fit residues: 67.4967 Evaluate side-chains 140 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.476 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1077 time to fit residues: 2.3303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 32 GLN A 54 GLN E 54 GLN G 64 ASN O 54 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 12820 Z= 0.306 Angle : 0.543 5.624 17511 Z= 0.292 Chirality : 0.048 0.141 2103 Planarity : 0.004 0.032 2164 Dihedral : 6.843 62.977 1941 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer Outliers : 1.57 % 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: 1.67 (0.21), residues: 1624 helix: 1.77 (0.20), residues: 696 sheet: 0.66 (0.26), residues: 240 loop : 0.75 (0.26), residues: 688 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.569 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 177 average time/residue: 0.2229 time to fit residues: 59.8853 Evaluate side-chains 158 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1130 time to fit residues: 4.6270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 32 GLN A 54 GLN G 64 ASN G 184 GLN O 54 GLN O 134 GLN O 184 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 12820 Z= 0.253 Angle : 0.486 6.292 17511 Z= 0.261 Chirality : 0.046 0.281 2103 Planarity : 0.004 0.034 2164 Dihedral : 6.661 58.996 1941 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 0.78 % 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: 1.41 (0.21), residues: 1624 helix: 1.39 (0.19), residues: 752 sheet: 0.82 (0.27), residues: 240 loop : 0.62 (0.28), residues: 632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 1.533 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 167 average time/residue: 0.2209 time to fit residues: 55.9544 Evaluate side-chains 159 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1256 time to fit residues: 3.1614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 32 GLN G 32 GLN G 54 GLN G 64 ASN K 184 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 184 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 12820 Z= 0.314 Angle : 0.510 5.016 17511 Z= 0.274 Chirality : 0.047 0.155 2103 Planarity : 0.004 0.036 2164 Dihedral : 6.842 59.822 1941 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.78 % 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: 0.96 (0.21), residues: 1624 helix: 1.03 (0.19), residues: 768 sheet: 0.68 (0.29), residues: 240 loop : 0.31 (0.28), residues: 616 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 163 time to evaluate : 1.493 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 165 average time/residue: 0.2180 time to fit residues: 55.2107 Evaluate side-chains 164 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1175 time to fit residues: 3.9327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 32 GLN G 64 ASN G 184 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 12820 Z= 0.264 Angle : 0.470 5.048 17511 Z= 0.254 Chirality : 0.046 0.132 2103 Planarity : 0.003 0.036 2164 Dihedral : 6.668 59.077 1941 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.78 % 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: 0.96 (0.21), residues: 1624 helix: 1.03 (0.19), residues: 776 sheet: 0.69 (0.30), residues: 240 loop : 0.29 (0.28), residues: 608 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 1.648 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 162 average time/residue: 0.2206 time to fit residues: 54.8416 Evaluate side-chains 161 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 1.480 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1215 time to fit residues: 3.7128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 32 GLN G 64 ASN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 12820 Z= 0.218 Angle : 0.439 4.976 17511 Z= 0.238 Chirality : 0.044 0.128 2103 Planarity : 0.003 0.035 2164 Dihedral : 6.471 58.644 1941 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.78 % 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: 1.12 (0.22), residues: 1624 helix: 1.15 (0.19), residues: 776 sheet: 0.97 (0.30), residues: 248 loop : 0.27 (0.28), residues: 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 1.587 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 160 average time/residue: 0.2182 time to fit residues: 54.2778 Evaluate side-chains 154 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1226 time to fit residues: 3.6964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN G 64 ASN G 184 GLN K 184 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 12820 Z= 0.283 Angle : 0.475 5.088 17511 Z= 0.256 Chirality : 0.046 0.131 2103 Planarity : 0.003 0.036 2164 Dihedral : 6.554 57.207 1941 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 0.61 % 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 (0.22), residues: 1624 helix: 1.03 (0.19), residues: 776 sheet: 0.80 (0.31), residues: 248 loop : 0.14 (0.28), residues: 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 1.692 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 154 average time/residue: 0.2241 time to fit residues: 52.5068 Evaluate side-chains 152 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.494 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1183 time to fit residues: 3.3427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 64 ASN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 12820 Z= 0.360 Angle : 0.525 5.208 17511 Z= 0.280 Chirality : 0.047 0.135 2103 Planarity : 0.004 0.039 2164 Dihedral : 6.732 55.730 1941 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.78 % 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: 0.58 (0.21), residues: 1624 helix: 0.82 (0.19), residues: 776 sheet: 0.56 (0.31), residues: 248 loop : -0.11 (0.27), residues: 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.685 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 156 average time/residue: 0.2181 time to fit residues: 51.8942 Evaluate side-chains 154 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1119 time to fit residues: 3.3721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN G 64 ASN K 184 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 12820 Z= 0.193 Angle : 0.429 5.022 17511 Z= 0.233 Chirality : 0.044 0.127 2103 Planarity : 0.003 0.037 2164 Dihedral : 6.351 58.262 1941 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1624 helix: 1.12 (0.19), residues: 776 sheet: 0.76 (0.31), residues: 248 loop : -0.06 (0.28), residues: 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.523 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 155 average time/residue: 0.2161 time to fit residues: 51.5985 Evaluate side-chains 151 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1135 time to fit residues: 2.6975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS G 32 GLN G 64 ASN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 12820 Z= 0.177 Angle : 0.417 4.974 17511 Z= 0.227 Chirality : 0.044 0.164 2103 Planarity : 0.003 0.035 2164 Dihedral : 6.215 58.366 1941 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.09 % 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: 1.03 (0.22), residues: 1624 helix: 1.27 (0.19), residues: 776 sheet: 0.88 (0.31), residues: 248 loop : -0.04 (0.28), residues: 600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.552 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 153 average time/residue: 0.2285 time to fit residues: 53.6089 Evaluate side-chains 149 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.507 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1153 time to fit residues: 2.2550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 135 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.092963 restraints weight = 18414.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094311 restraints weight = 12987.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.095522 restraints weight = 10212.435| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 12820 Z= 0.169 Angle : 0.418 9.162 17511 Z= 0.226 Chirality : 0.043 0.134 2103 Planarity : 0.003 0.035 2164 Dihedral : 6.143 58.411 1941 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.35 % 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: 1.13 (0.22), residues: 1624 helix: 1.35 (0.19), residues: 776 sheet: 0.96 (0.31), residues: 248 loop : -0.01 (0.28), residues: 600 =============================================================================== Job complete usr+sys time: 1932.42 seconds wall clock time: 36 minutes 31.62 seconds (2191.62 seconds total)