Starting phenix.real_space_refine on Mon Feb 19 05:08:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqc_23942/02_2024/7mqc_23942.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqc_23942/02_2024/7mqc_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_23942/02_2024/7mqc_23942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqc_23942/02_2024/7mqc_23942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqc_23942/02_2024/7mqc_23942.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqc_23942/02_2024/7mqc_23942.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-dev-5238/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: 7.12, per 1000 atoms: 0.57 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: 4.86 Conformation dependent library (CDL) restraints added in 2.2 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: 1.26 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: 3.04 Time building geometry restraints manager: 5.12 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: 7133 17.97 - 35.94: 360 35.94 - 53.91: 103 53.91 - 71.89: 53 71.89 - 89.86: 15 Dihedral angle restraints: 7664 sinusoidal: 2880 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 7661 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 1.420 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 33.930 Find NCS groups from input model: 0.980 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.790 ------------------------------------------------------------------------------- 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 : 14.358 89.857 4544 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 % Allowed : 1.13 % Favored : 98.26 % 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: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 197 HIS 0.006 0.002 HIS C 116 PHE 0.020 0.002 PHE E 78 TYR 0.033 0.003 TYR E 158 ARG 0.013 0.002 ARG A 37 *********************** 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 : 1.399 Fit side-chains REVERT: A 16 ASN cc_start: 0.7154 (m110) cc_final: 0.6902 (t0) REVERT: A 27 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7944 (mm-30) REVERT: C 51 ASP cc_start: 0.8345 (m-30) cc_final: 0.7941 (m-30) REVERT: C 57 LYS cc_start: 0.7387 (tttp) cc_final: 0.6882 (tptp) REVERT: C 157 LEU cc_start: 0.8141 (mt) cc_final: 0.7917 (mt) REVERT: E 95 MET cc_start: 0.7752 (tpp) cc_final: 0.7353 (tpt) REVERT: G 25 ASP cc_start: 0.7266 (t70) cc_final: 0.6548 (m-30) REVERT: G 26 THR cc_start: 0.8938 (p) cc_final: 0.8649 (p) REVERT: K 39 CYS cc_start: 0.8126 (m) cc_final: 0.7921 (m) REVERT: K 59 GLN cc_start: 0.6805 (tt0) cc_final: 0.6515 (tp40) REVERT: K 184 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7901 (mm-40) REVERT: O 28 THR cc_start: 0.8692 (p) cc_final: 0.8388 (p) REVERT: O 37 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7617 (ptt90) REVERT: O 54 GLN cc_start: 0.7818 (mt0) cc_final: 0.7533 (mt0) REVERT: O 95 MET cc_start: 0.7503 (tpp) cc_final: 0.6956 (tpp) outliers start: 7 outliers final: 1 residues processed: 195 average time/residue: 0.2320 time to fit residues: 66.5897 Evaluate side-chains 150 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 184 GLN Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 178 VAL 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: 10.0000 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 145 optimal weight: 0.0050 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 54 GLN E 54 GLN G 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12820 Z= 0.307 Angle : 0.540 5.515 17511 Z= 0.291 Chirality : 0.048 0.141 2103 Planarity : 0.004 0.031 2164 Dihedral : 11.918 75.546 2045 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.48 % Allowed : 5.05 % Favored : 93.47 % 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: 1.78 (0.20), residues: 696 sheet: 0.63 (0.26), residues: 240 loop : 0.75 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 197 HIS 0.007 0.001 HIS O 79 PHE 0.015 0.002 PHE C 78 TYR 0.011 0.001 TYR A 158 ARG 0.004 0.001 ARG C 172 *********************** 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: 17 poor density : 168 time to evaluate : 1.601 Fit side-chains REVERT: A 16 ASN cc_start: 0.7270 (m110) cc_final: 0.6742 (t0) REVERT: A 54 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6662 (mt0) REVERT: A 127 ASN cc_start: 0.8062 (m110) cc_final: 0.6452 (t0) REVERT: E 11 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7796 (mt) REVERT: G 25 ASP cc_start: 0.7348 (t70) cc_final: 0.6836 (m-30) REVERT: G 26 THR cc_start: 0.8723 (p) cc_final: 0.8354 (p) REVERT: G 155 ASP cc_start: 0.7238 (t70) cc_final: 0.6903 (t0) REVERT: G 206 SER cc_start: 0.7236 (m) cc_final: 0.7034 (t) REVERT: I 200 ILE cc_start: 0.7860 (mm) cc_final: 0.7290 (tt) REVERT: K 134 GLN cc_start: 0.7512 (mm-40) cc_final: 0.6859 (mp10) REVERT: K 184 GLN cc_start: 0.8256 (mp-120) cc_final: 0.8003 (mm-40) REVERT: M 176 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6888 (mt-10) outliers start: 17 outliers final: 10 residues processed: 179 average time/residue: 0.2205 time to fit residues: 59.2869 Evaluate side-chains 162 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain O residue 128 VAL Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 54 GLN G 64 ASN G 184 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 GLN O 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12820 Z= 0.328 Angle : 0.536 6.625 17511 Z= 0.286 Chirality : 0.048 0.282 2103 Planarity : 0.004 0.035 2164 Dihedral : 11.836 64.126 2037 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.91 % Allowed : 6.44 % Favored : 91.64 % 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: 1.16 (0.21), residues: 1624 helix: 1.17 (0.19), residues: 752 sheet: 0.66 (0.28), residues: 240 loop : 0.53 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 197 HIS 0.008 0.001 HIS O 79 PHE 0.013 0.002 PHE A 78 TYR 0.009 0.001 TYR A 158 ARG 0.005 0.001 ARG G 67 *********************** 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 188 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.333 Fit side-chains REVERT: A 16 ASN cc_start: 0.7229 (m110) cc_final: 0.6742 (t0) REVERT: A 127 ASN cc_start: 0.8090 (m110) cc_final: 0.6347 (t0) REVERT: E 25 ASP cc_start: 0.7394 (t0) cc_final: 0.6802 (t70) REVERT: E 95 MET cc_start: 0.7710 (tpt) cc_final: 0.7472 (tpp) REVERT: G 25 ASP cc_start: 0.7767 (t70) cc_final: 0.6889 (m-30) REVERT: G 26 THR cc_start: 0.8933 (p) cc_final: 0.8625 (p) REVERT: G 54 GLN cc_start: 0.8382 (mt0) cc_final: 0.8113 (mt0) REVERT: G 155 ASP cc_start: 0.7366 (t70) cc_final: 0.6512 (t0) REVERT: G 193 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6867 (t0) REVERT: I 200 ILE cc_start: 0.7935 (mm) cc_final: 0.7332 (tt) REVERT: K 134 GLN cc_start: 0.7461 (mm-40) cc_final: 0.7035 (mp10) REVERT: K 154 SER cc_start: 0.7845 (t) cc_final: 0.7446 (p) REVERT: K 184 GLN cc_start: 0.8302 (mp-120) cc_final: 0.8032 (mm-40) REVERT: M 27 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7558 (mm-30) REVERT: M 206 SER cc_start: 0.7208 (m) cc_final: 0.6753 (p) outliers start: 22 outliers final: 17 residues processed: 177 average time/residue: 0.2056 time to fit residues: 55.9053 Evaluate side-chains 176 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 184 GLN Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 128 VAL Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 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 32 GLN 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: 0.7628 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12820 Z= 0.217 Angle : 0.451 6.043 17511 Z= 0.244 Chirality : 0.045 0.160 2103 Planarity : 0.003 0.035 2164 Dihedral : 11.653 64.034 2037 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.13 % Allowed : 8.53 % Favored : 90.34 % 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 (0.21), residues: 1624 helix: 1.14 (0.19), residues: 768 sheet: 0.80 (0.29), residues: 240 loop : 0.40 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 197 HIS 0.005 0.001 HIS O 79 PHE 0.013 0.001 PHE O 78 TYR 0.008 0.001 TYR A 17 ARG 0.005 0.000 ARG I 67 *********************** 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 178 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 1.497 Fit side-chains REVERT: A 16 ASN cc_start: 0.7168 (m110) cc_final: 0.6725 (t0) REVERT: A 39 CYS cc_start: 0.8431 (m) cc_final: 0.8176 (m) REVERT: A 127 ASN cc_start: 0.8048 (m110) cc_final: 0.6291 (t0) REVERT: A 155 ASP cc_start: 0.7380 (t0) cc_final: 0.7081 (t0) REVERT: E 25 ASP cc_start: 0.7402 (t0) cc_final: 0.6729 (t70) REVERT: E 27 GLU cc_start: 0.7892 (mp0) cc_final: 0.7064 (mp0) REVERT: G 25 ASP cc_start: 0.7799 (t70) cc_final: 0.7114 (m-30) REVERT: G 26 THR cc_start: 0.8915 (p) cc_final: 0.8648 (p) REVERT: G 54 GLN cc_start: 0.8355 (mt0) cc_final: 0.8103 (mt0) REVERT: G 155 ASP cc_start: 0.7343 (t70) cc_final: 0.6720 (t0) REVERT: G 193 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.6892 (t0) REVERT: I 200 ILE cc_start: 0.7889 (mm) cc_final: 0.7337 (tt) REVERT: K 154 SER cc_start: 0.8021 (t) cc_final: 0.7729 (p) REVERT: K 184 GLN cc_start: 0.8297 (mp-120) cc_final: 0.8012 (mm-40) REVERT: M 206 SER cc_start: 0.7452 (m) cc_final: 0.6931 (p) outliers start: 13 outliers final: 11 residues processed: 169 average time/residue: 0.2135 time to fit residues: 55.5320 Evaluate side-chains 170 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 9.9990 chunk 87 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 63 optimal weight: 0.0030 chunk 131 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 overall best weight: 2.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7625 moved from start: 0.2385 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= 0.208 Angle : 0.433 4.901 17511 Z= 0.235 Chirality : 0.044 0.128 2103 Planarity : 0.003 0.034 2164 Dihedral : 11.556 64.028 2037 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.57 % Allowed : 8.79 % Favored : 89.64 % 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: 1.17 (0.21), residues: 1624 helix: 1.15 (0.19), residues: 776 sheet: 0.87 (0.30), residues: 240 loop : 0.43 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 197 HIS 0.005 0.001 HIS O 79 PHE 0.013 0.001 PHE O 78 TYR 0.008 0.001 TYR E 158 ARG 0.005 0.000 ARG I 67 *********************** 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 179 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 1.391 Fit side-chains REVERT: A 16 ASN cc_start: 0.7175 (m110) cc_final: 0.6714 (t0) REVERT: A 39 CYS cc_start: 0.8459 (m) cc_final: 0.8226 (m) REVERT: A 127 ASN cc_start: 0.8046 (m110) cc_final: 0.6304 (t0) REVERT: A 155 ASP cc_start: 0.7438 (t0) cc_final: 0.7115 (t0) REVERT: E 25 ASP cc_start: 0.7449 (t70) cc_final: 0.6793 (t70) REVERT: E 27 GLU cc_start: 0.7876 (mp0) cc_final: 0.6997 (mp0) REVERT: G 25 ASP cc_start: 0.7764 (t70) cc_final: 0.7033 (m-30) REVERT: G 54 GLN cc_start: 0.8346 (mt0) cc_final: 0.8091 (mt0) REVERT: G 155 ASP cc_start: 0.7198 (t70) cc_final: 0.6528 (t0) REVERT: G 193 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6833 (t0) REVERT: I 65 LEU cc_start: 0.7601 (tp) cc_final: 0.7386 (tp) REVERT: K 184 GLN cc_start: 0.8285 (mp-120) cc_final: 0.7989 (mm-40) REVERT: M 206 SER cc_start: 0.7567 (m) cc_final: 0.7042 (p) outliers start: 18 outliers final: 17 residues processed: 170 average time/residue: 0.2120 time to fit residues: 55.4266 Evaluate side-chains 171 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 184 GLN Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12820 Z= 0.293 Angle : 0.482 5.110 17511 Z= 0.259 Chirality : 0.046 0.133 2103 Planarity : 0.004 0.036 2164 Dihedral : 11.669 64.022 2037 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.26 % Allowed : 9.92 % Favored : 87.82 % 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 (0.21), residues: 1624 helix: 0.98 (0.19), residues: 776 sheet: 0.71 (0.30), residues: 240 loop : 0.26 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 197 HIS 0.007 0.001 HIS O 79 PHE 0.014 0.001 PHE O 78 TYR 0.011 0.001 TYR A 158 ARG 0.006 0.000 ARG I 67 *********************** 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 180 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 1.322 Fit side-chains REVERT: A 16 ASN cc_start: 0.7204 (m110) cc_final: 0.6675 (t0) REVERT: A 39 CYS cc_start: 0.8494 (m) cc_final: 0.8246 (m) REVERT: A 127 ASN cc_start: 0.8105 (m110) cc_final: 0.6388 (t0) REVERT: A 155 ASP cc_start: 0.7412 (t0) cc_final: 0.7092 (t0) REVERT: E 25 ASP cc_start: 0.7535 (t70) cc_final: 0.6851 (t70) REVERT: E 27 GLU cc_start: 0.7955 (mp0) cc_final: 0.7049 (mp0) REVERT: G 25 ASP cc_start: 0.7851 (t70) cc_final: 0.6945 (m-30) REVERT: G 155 ASP cc_start: 0.7263 (t70) cc_final: 0.6660 (t0) REVERT: G 193 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6838 (t0) REVERT: K 184 GLN cc_start: 0.8321 (mp-120) cc_final: 0.8039 (mm-40) REVERT: M 206 SER cc_start: 0.7552 (m) cc_final: 0.7201 (m) outliers start: 26 outliers final: 25 residues processed: 165 average time/residue: 0.2065 time to fit residues: 52.1568 Evaluate side-chains 178 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 184 GLN Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 39 CYS Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 0.0020 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7604 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12820 Z= 0.150 Angle : 0.398 4.910 17511 Z= 0.217 Chirality : 0.043 0.125 2103 Planarity : 0.003 0.034 2164 Dihedral : 11.362 64.882 2037 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.74 % Allowed : 11.14 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.22), residues: 1624 helix: 1.27 (0.19), residues: 776 sheet: 1.05 (0.31), residues: 240 loop : 0.30 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 197 HIS 0.003 0.001 HIS G 79 PHE 0.016 0.001 PHE G 185 TYR 0.009 0.001 TYR E 158 ARG 0.007 0.000 ARG I 67 *********************** 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 180 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 1.577 Fit side-chains REVERT: A 16 ASN cc_start: 0.7252 (m110) cc_final: 0.6792 (t0) REVERT: A 39 CYS cc_start: 0.8459 (m) cc_final: 0.8198 (m) REVERT: A 42 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8172 (pt0) REVERT: A 127 ASN cc_start: 0.8040 (m110) cc_final: 0.6238 (t0) REVERT: E 25 ASP cc_start: 0.7490 (t70) cc_final: 0.6864 (t70) REVERT: E 27 GLU cc_start: 0.7874 (mp0) cc_final: 0.6972 (mp0) REVERT: G 25 ASP cc_start: 0.7775 (t70) cc_final: 0.6902 (m-30) REVERT: G 155 ASP cc_start: 0.7175 (t70) cc_final: 0.6540 (t0) REVERT: G 193 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.6934 (t0) REVERT: K 154 SER cc_start: 0.8001 (t) cc_final: 0.7776 (p) REVERT: K 184 GLN cc_start: 0.8288 (mp-120) cc_final: 0.7993 (mm-40) REVERT: M 206 SER cc_start: 0.7537 (m) cc_final: 0.7201 (m) outliers start: 20 outliers final: 16 residues processed: 171 average time/residue: 0.2191 time to fit residues: 57.1477 Evaluate side-chains 172 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain M residue 184 GLN Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12820 Z= 0.389 Angle : 0.541 5.259 17511 Z= 0.287 Chirality : 0.048 0.136 2103 Planarity : 0.004 0.039 2164 Dihedral : 11.702 64.043 2037 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.79 % Allowed : 10.44 % Favored : 86.77 % 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: 0.66 (0.21), residues: 1624 helix: 0.81 (0.19), residues: 776 sheet: 0.71 (0.31), residues: 248 loop : -0.00 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 197 HIS 0.008 0.001 HIS O 79 PHE 0.017 0.002 PHE A 78 TYR 0.013 0.002 TYR A 158 ARG 0.007 0.001 ARG I 67 *********************** 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 181 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 1.418 Fit side-chains REVERT: A 16 ASN cc_start: 0.7285 (m110) cc_final: 0.6670 (t0) REVERT: A 39 CYS cc_start: 0.8507 (m) cc_final: 0.8206 (m) REVERT: A 42 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8153 (pt0) REVERT: E 25 ASP cc_start: 0.7538 (t70) cc_final: 0.6808 (t70) REVERT: E 27 GLU cc_start: 0.8008 (mp0) cc_final: 0.7056 (mp0) REVERT: G 25 ASP cc_start: 0.7862 (t70) cc_final: 0.6878 (m-30) REVERT: G 155 ASP cc_start: 0.7294 (t70) cc_final: 0.6655 (t0) REVERT: G 193 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6839 (t0) REVERT: K 134 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6989 (mp10) REVERT: K 184 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8159 (mm-40) REVERT: M 206 SER cc_start: 0.7557 (m) cc_final: 0.7287 (m) outliers start: 32 outliers final: 29 residues processed: 164 average time/residue: 0.2070 time to fit residues: 51.9998 Evaluate side-chains 182 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 184 GLN Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 184 GLN Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 39 CYS Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 206 SER 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: 5.9990 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 0.0970 chunk 44 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12820 Z= 0.238 Angle : 0.448 5.060 17511 Z= 0.242 Chirality : 0.045 0.129 2103 Planarity : 0.003 0.037 2164 Dihedral : 11.560 64.491 2037 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.18 % Allowed : 11.40 % Favored : 86.42 % 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: 0.80 (0.21), residues: 1624 helix: 0.97 (0.19), residues: 776 sheet: 0.78 (0.31), residues: 248 loop : -0.01 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 197 HIS 0.005 0.001 HIS O 79 PHE 0.013 0.001 PHE O 78 TYR 0.009 0.001 TYR A 158 ARG 0.007 0.000 ARG I 67 *********************** 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 178 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.355 Fit side-chains REVERT: A 16 ASN cc_start: 0.7350 (m110) cc_final: 0.6716 (t0) REVERT: A 39 CYS cc_start: 0.8509 (m) cc_final: 0.8213 (m) REVERT: A 42 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8150 (pt0) REVERT: A 127 ASN cc_start: 0.8128 (m110) cc_final: 0.6409 (t0) REVERT: E 25 ASP cc_start: 0.7464 (t70) cc_final: 0.6770 (t70) REVERT: E 27 GLU cc_start: 0.7960 (mp0) cc_final: 0.7009 (mp0) REVERT: G 25 ASP cc_start: 0.7832 (t70) cc_final: 0.6882 (m-30) REVERT: G 155 ASP cc_start: 0.7270 (t70) cc_final: 0.6568 (t0) REVERT: G 193 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6817 (t0) REVERT: K 184 GLN cc_start: 0.8327 (mp-120) cc_final: 0.8040 (mm-40) REVERT: M 206 SER cc_start: 0.7588 (m) cc_final: 0.7351 (m) outliers start: 25 outliers final: 23 residues processed: 165 average time/residue: 0.2098 time to fit residues: 52.9658 Evaluate side-chains 178 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 184 GLN Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 39 CYS Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS C 42 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: 0.7594 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12820 Z= 0.133 Angle : 0.390 4.914 17511 Z= 0.213 Chirality : 0.043 0.122 2103 Planarity : 0.003 0.035 2164 Dihedral : 11.210 65.546 2037 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.83 % Allowed : 11.84 % Favored : 86.34 % 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: 1.18 (0.22), residues: 1624 helix: 1.29 (0.19), residues: 776 sheet: 1.13 (0.31), residues: 248 loop : 0.09 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 197 HIS 0.003 0.000 HIS O 79 PHE 0.012 0.001 PHE G 183 TYR 0.006 0.001 TYR E 158 ARG 0.007 0.000 ARG I 67 ********************** 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 183 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.640 Fit side-chains REVERT: A 16 ASN cc_start: 0.7271 (m110) cc_final: 0.6781 (t0) REVERT: A 39 CYS cc_start: 0.8473 (m) cc_final: 0.8185 (m) REVERT: A 42 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8169 (pt0) REVERT: A 127 ASN cc_start: 0.8120 (m110) cc_final: 0.6240 (t0) REVERT: E 25 ASP cc_start: 0.7493 (t70) cc_final: 0.6788 (t70) REVERT: E 27 GLU cc_start: 0.7854 (mp0) cc_final: 0.6945 (mp0) REVERT: G 25 ASP cc_start: 0.7775 (t70) cc_final: 0.6866 (m-30) REVERT: G 155 ASP cc_start: 0.7150 (t70) cc_final: 0.6462 (t0) REVERT: G 193 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.6916 (t0) REVERT: I 171 LYS cc_start: 0.7264 (ttpp) cc_final: 0.7019 (ttpp) REVERT: K 154 SER cc_start: 0.7926 (t) cc_final: 0.7715 (p) REVERT: K 184 GLN cc_start: 0.8268 (mp-120) cc_final: 0.7969 (mm-40) outliers start: 21 outliers final: 17 residues processed: 174 average time/residue: 0.2160 time to fit residues: 57.6025 Evaluate side-chains 172 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 184 GLN Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 184 GLN M 135 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.101638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.090385 restraints weight = 18657.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.091716 restraints weight = 13243.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.092654 restraints weight = 10388.499| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12820 Z= 0.278 Angle : 0.478 10.133 17511 Z= 0.254 Chirality : 0.046 0.130 2103 Planarity : 0.003 0.039 2164 Dihedral : 11.458 64.370 2037 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.18 % Allowed : 11.92 % Favored : 85.90 % 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: 1.09 (0.19), residues: 776 sheet: 0.88 (0.31), residues: 248 loop : 0.01 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 139 HIS 0.006 0.001 HIS O 79 PHE 0.014 0.001 PHE O 78 TYR 0.009 0.001 TYR M 151 ARG 0.007 0.000 ARG I 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2042.46 seconds wall clock time: 38 minutes 30.40 seconds (2310.40 seconds total)