Starting phenix.real_space_refine on Sat Nov 18 19:06:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqi_23948/11_2023/7mqi_23948.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqi_23948/11_2023/7mqi_23948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqi_23948/11_2023/7mqi_23948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqi_23948/11_2023/7mqi_23948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqi_23948/11_2023/7mqi_23948.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqi_23948/11_2023/7mqi_23948.pdb" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 11339 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 47 5.16 5 C 8025 2.51 5 N 2321 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "I GLU 3": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 120": "OE1" <-> "OE2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "M GLU 3": "OE1" <-> "OE2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "O GLU 120": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 12696 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1513 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1551 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "E" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1548 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1536 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 65 Chain: "I" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1538 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 65 Chain: "K" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1552 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 58 Chain: "M" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1545 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 61 Chain: "O" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1545 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "N" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "P" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Time building chain proxies: 6.96, per 1000 atoms: 0.55 Number of scatterers: 12696 At special positions: 0 Unit cell: (111.6, 114.08, 97.96, 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 47 16.00 P 16 15.00 O 2287 8.00 N 2321 7.00 C 8025 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: 4.76 Conformation dependent library (CDL) restraints added in 2.4 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: 56 helices and 8 sheets defined 45.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.968A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.600A 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 155 removed outlier: 3.657A pdb=" N ASP A 155 " --> pdb=" O TYR A 151 " (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: 3.979A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.627A 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 155 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: 3.948A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.656A 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 155 removed outlier: 3.884A pdb=" N ASP E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 173 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: 4.009A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.573A 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 removed outlier: 3.690A pdb=" N ASP G 155 " --> pdb=" O TYR G 151 " (cutoff:3.500A) 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: 3.956A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.574A 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 145 through 155 removed outlier: 3.550A pdb=" N ASP I 155 " --> pdb=" O TYR I 151 " (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: 3.965A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.597A 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 removed outlier: 3.744A pdb=" N ASP K 155 " --> pdb=" O TYR K 151 " (cutoff:3.500A) 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: 4.029A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.597A 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 155 removed outlier: 3.571A pdb=" N ASP M 155 " --> pdb=" O TYR M 151 " (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: 3.985A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.566A 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 155 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 3 through 8 removed outlier: 6.521A pdb=" N GLU A 3 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL A 52 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU A 27 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL A 41 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASP A 25 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 43 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 23 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 8 removed outlier: 6.586A pdb=" N GLU C 3 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL C 52 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU C 27 " --> pdb=" O CYS C 39 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL C 41 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU C 43 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 23 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.314A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.619A 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: 6.342A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA G 23 " --> pdb=" O LEU G 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.158A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.245A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU K 27 " --> pdb=" O CYS K 39 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL K 41 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP K 25 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU K 43 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA K 23 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 8 removed outlier: 6.475A pdb=" N GLU M 3 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL M 52 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.687A 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: 6.720A pdb=" N GLU O 3 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL O 52 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU O 27 " --> pdb=" O CYS O 39 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL O 41 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP O 25 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU O 43 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA O 23 " --> pdb=" O LEU O 43 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1704 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: 3.29 Time building geometry restraints manager: 5.15 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: 4082 1.34 - 1.45: 1805 1.45 - 1.57: 6986 1.57 - 1.69: 24 1.69 - 1.81: 63 Bond restraints: 12960 Sorted by residual: bond pdb=" N LEU C 126 " pdb=" CA LEU C 126 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.06e-02 8.90e+03 1.25e+01 bond pdb=" N ILE I 165 " pdb=" CA ILE I 165 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.44e+00 bond pdb=" N GLN E 42 " pdb=" CA GLN E 42 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.21e-02 6.83e+03 8.75e+00 bond pdb=" N GLN O 42 " pdb=" CA GLN O 42 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.20e+00 bond pdb=" N GLN K 42 " pdb=" CA GLN K 42 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.54e+00 ... (remaining 12955 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.75: 382 106.75 - 113.57: 7344 113.57 - 120.40: 5058 120.40 - 127.22: 4731 127.22 - 134.05: 190 Bond angle restraints: 17705 Sorted by residual: angle pdb=" C SER I 137 " pdb=" N ASP I 138 " pdb=" CA ASP I 138 " ideal model delta sigma weight residual 122.32 129.36 -7.04 1.76e+00 3.23e-01 1.60e+01 angle pdb=" N LEU I 170 " pdb=" CA LEU I 170 " pdb=" C LEU I 170 " ideal model delta sigma weight residual 112.23 107.24 4.99 1.26e+00 6.30e-01 1.57e+01 angle pdb=" C SER A 137 " pdb=" N ASP A 138 " pdb=" CA ASP A 138 " ideal model delta sigma weight residual 122.32 128.91 -6.59 1.76e+00 3.23e-01 1.40e+01 angle pdb=" C ASP E 138 " pdb=" N TRP E 139 " pdb=" CA TRP E 139 " ideal model delta sigma weight residual 121.54 128.30 -6.76 1.91e+00 2.74e-01 1.25e+01 angle pdb=" N VAL O 41 " pdb=" CA VAL O 41 " pdb=" C VAL O 41 " ideal model delta sigma weight residual 108.11 112.92 -4.81 1.40e+00 5.10e-01 1.18e+01 ... (remaining 17700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 7154 17.28 - 34.56: 388 34.56 - 51.85: 73 51.85 - 69.13: 22 69.13 - 86.41: 10 Dihedral angle restraints: 7647 sinusoidal: 2863 harmonic: 4784 Sorted by residual: dihedral pdb=" CA PHE O 78 " pdb=" C PHE O 78 " pdb=" N HIS O 79 " pdb=" CA HIS O 79 " ideal model delta harmonic sigma weight residual 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+01 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 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+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 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 7644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1346 0.048 - 0.095: 590 0.095 - 0.143: 166 0.143 - 0.191: 18 0.191 - 0.238: 4 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA GLU E 27 " pdb=" N GLU E 27 " pdb=" C GLU E 27 " pdb=" CB GLU E 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE C 121 " pdb=" CA ILE C 121 " pdb=" CG1 ILE C 121 " pdb=" CG2 ILE C 121 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ARG A 169 " pdb=" N ARG A 169 " pdb=" C ARG A 169 " pdb=" CB ARG A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.38e-01 ... (remaining 2121 not shown) Planarity restraints: 2213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 152 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C ALA E 152 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA E 152 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA E 153 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS K 122 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C CYS K 122 " 0.031 2.00e-02 2.50e+03 pdb=" O CYS K 122 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY K 123 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS M 122 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C CYS M 122 " -0.029 2.00e-02 2.50e+03 pdb=" O CYS M 122 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY M 123 " 0.010 2.00e-02 2.50e+03 ... (remaining 2210 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1245 2.74 - 3.28: 11813 3.28 - 3.82: 20516 3.82 - 4.36: 26121 4.36 - 4.90: 43889 Nonbonded interactions: 103584 Sorted by model distance: nonbonded pdb=" OH TYR E 17 " pdb=" OD2 ASP E 51 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR O 112 " pdb=" OE2 GLU O 124 " model vdw 2.298 2.440 nonbonded pdb=" O THR M 28 " pdb=" O2' G N 604 " model vdw 2.349 2.440 nonbonded pdb=" OD1 ASP M 25 " pdb=" N THR M 26 " model vdw 2.354 2.520 nonbonded pdb=" OE1 GLU I 173 " pdb=" NH1 ARG I 175 " model vdw 2.359 2.520 ... (remaining 103579 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 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 46 or (resid 47 and (n \ ame N or name CA or name C or name O or name CB )) or resid 48 through 56 or (re \ sid 57 and (name N or name CA or name C or name O or name CB )) or resid 58 thro \ ugh 70 or (resid 71 through 73 and (name N or name CA or name C or name O or nam \ e CB )) or resid 74 through 129 or (resid 130 through 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 (n \ ame N or name CA or name C or name O or name CB )) or resid 144 through 153 or ( \ resid 154 through 155 and (name N or name CA or name C or name O or name CB )) o \ r resid 156 through 163 or (resid 164 and (name N or name CA or name C or name O \ or name CB )) or resid 165 through 176 or (resid 177 and (name N or name CA or \ name C or name O or name CB )) or resid 178 through 206)) selection = (chain 'C' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 38 or (resid 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 through 46 or (resid 47 and \ (name N or name CA or name C or name O or name CB )) or resid 48 through 70 or ( \ resid 71 through 73 and (name N or name CA or name C or name O or name CB )) or \ resid 74 through 113 or (resid 114 and (name N or name CA or name C or name O or \ name CB )) or resid 115 through 118 or (resid 119 through 120 and (name N or na \ me CA or name C or name O or name CB )) or resid 121 through 128 or (resid 129 t \ hrough 138 and (name N or name CA or name C or name O or name CB )) or resid 139 \ through 153 or (resid 154 through 155 and (name N or name CA or name C or name \ O or name CB )) or resid 156 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 \ 172 or (resid 173 through 174 and (name N or name CA or name C or name O or nam \ e CB )) or resid 175 through 176 or (resid 177 and (name N or name CA or name C \ or name O or name CB )) or resid 178 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 183 or \ (resid 184 and (name N or name CA or name C or name O or name CB )) or resid 185 \ through 198 or (resid 199 and (name N or name CA or name C or name O or name CB \ )) or resid 200 through 206)) selection = (chain 'E' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 38 or (resid 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 through 46 or (resid 47 and \ (name N or name CA or name C or name O or name CB )) or resid 48 through 56 or ( \ resid 57 and (name N or name CA or name C or name O or name CB )) or resid 58 th \ rough 60 or (resid 61 through 62 and (name N or name CA or name C or name O or n \ ame CB )) or resid 63 through 69 or (resid 70 through 73 and (name N or name CA \ or name C or name O or name CB )) or resid 74 through 113 or (resid 114 and (nam \ e N or name CA or name C or name O or name CB )) or resid 115 through 118 or (re \ sid 119 through 120 and (name N or name CA or name C or name O or name CB )) or \ resid 121 through 128 or (resid 129 through 138 and (name N or name CA or name C \ or name O or name CB )) or resid 139 through 153 or (resid 154 through 155 and \ (name N or name CA or name C or name O or name CB )) or resid 156 through 163 or \ (resid 164 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 5 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 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 176 or (resid \ 177 and (name N or name CA or name C or name O or name CB )) or resid 178 throug \ h 206)) selection = (chain 'G' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 17 or (resid 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 35 or (resid 36 and (n \ ame N or name CA or name C or name O or name CB )) or resid 37 through 38 or (re \ sid 39 and (name N or name CA or name C or name O or name CB )) or resid 40 thro \ ugh 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or \ resid 58 through 70 or (resid 71 through 73 and (name N or name CA or name C or \ name O or name CB )) or resid 74 through 113 or (resid 114 and (name N or name C \ A 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 128 or \ (resid 129 through 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 name CA or name C or name \ O or name CB )) or resid 144 through 153 or (resid 154 through 155 and (name N o \ r name CA or name C or name O or name CB )) or resid 156 through 166 or (resid 1 \ 67 through 168 and (name N or name CA or name C or name O or name CB )) or resid \ 169 through 183 or (resid 184 and (name N or name CA or name C or name O or nam \ e CB )) or resid 185 through 198 or (resid 199 and (name N or name CA or name C \ or name O or name CB )) or resid 200 through 206)) selection = (chain 'I' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 17 or (resid 18 and (name N or name CA or name C or name O \ or name CB )) or resid 19 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 38 or (resid 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 through 46 or (resid 47 and \ (name N or name CA or name C or name O or name CB )) or resid 48 or (resid 49 th \ rough 50 and (name N or name CA or name C or name O or name CB )) or resid 51 th \ rough 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) o \ r resid 58 through 69 or (resid 70 through 73 and (name N or name CA or name C o \ r name O or name CB )) or resid 74 through 113 or (resid 114 and (name N or name \ CA or name C or name O or name CB )) or resid 115 through 128 or (resid 129 thr \ ough 138 and (name N or name CA or name C or name O or name CB )) or resid 139 t \ hrough 154 or (resid 155 and (name N or name CA or name C or name O or name CB ) \ ) or resid 156 through 166 or (resid 167 through 168 and (name N or name CA or n \ ame C or name O or name CB )) or resid 169 through 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 1 \ 76 or (resid 177 and (name N or name CA or name C or name O or name CB )) or res \ id 178 through 183 or (resid 184 and (name N or name CA or name C or name O or n \ ame CB )) or resid 185 through 206)) selection = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 35 or (resid 36 and (name N or na \ me CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and \ (name N or name CA or name C or name O or name CB )) or resid 40 through 46 or ( \ resid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 or \ (resid 49 through 50 and (name N or name CA or name C or name O or name CB )) o \ r resid 51 through 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB )) or resid 58 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 118 or (resid 119 throug \ h 120 and (name N or name CA or name C or name O or name CB )) or resid 121 thro \ ugh 128 or (resid 129 through 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 name CA or name \ C or name O or name CB )) or resid 144 through 153 or (resid 154 through 155 an \ d (name N or name CA or name C or name O or name CB )) or resid 156 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 na \ me O or name CB )) or resid 169 through 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 176 or (resi \ d 177 and (name N or name CA or name C or name O or name CB )) or resid 178 thro \ ugh 183 or (resid 184 and (name N or name CA or name C or name O or name CB )) o \ r resid 185 through 206)) selection = (chain 'M' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 35 or (resid 36 and (name N or na \ me CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and \ (name N or name CA or name C or name O or name CB )) or resid 40 through 46 or ( \ resid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 or \ (resid 49 through 50 and (name N or name CA or name C or name O or name CB )) o \ r resid 51 through 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB )) or resid 58 through 69 or (resid 70 through 73 and (name N or name C \ A or name C or name O or name CB )) or resid 74 through 119 or (resid 120 and (n \ ame N or name CA or name C or name O or name CB )) or resid 121 through 129 or ( \ resid 130 through 138 and (name N or name CA or name C or name O or name CB )) o \ r 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 153 or (resid 154 through 155 and (name N or \ name CA or name C or name O or name CB )) or resid 156 through 166 or (resid 16 \ 7 through 168 and (name N or name CA or name C or name O or name CB )) or resid \ 169 through 172 or (resid 173 through 174 and (name N or name CA or name C or na \ me O or name CB )) or resid 175 through 176 or (resid 177 and (name N or name CA \ or name C or name O or name CB )) or resid 178 through 183 or (resid 184 and (n \ ame N or name CA or name C or name O or name CB )) or resid 185 through 206)) selection = (chain 'O' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 38 or (resid 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 through 46 or (resid 47 and \ (name N or name CA or name C or name O or name CB )) or resid 48 through 56 or ( \ resid 57 and (name N or name CA or name C or name O or name CB )) or resid 58 th \ rough 60 or (resid 61 through 62 and (name N or name CA or name C or name O or n \ ame CB )) or resid 63 through 69 or (resid 70 through 73 and (name N or name CA \ or name C or name O or name CB )) or resid 74 through 118 or (resid 119 through \ 120 and (name N or name CA or name C or name O or name CB )) or resid 121 throug \ h 128 or (resid 129 through 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 153 or (resid 154 through 155 and \ (name N or name CA or name C or name O or name CB )) or resid 156 through 163 or \ (resid 164 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 5 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 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 176 or (resid \ 177 and (name N or name CA or name C or name O or name CB )) or resid 178 throug \ h 179 or (resid 180 through 181 and (name N or name CA or name C or name O or na \ me CB )) or resid 182 through 183 or (resid 184 and (name N or name CA or name C \ or name O or name CB )) or resid 185 through 206)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.190 Set scattering table: 0.130 Process input model: 34.130 Find NCS groups from input model: 0.930 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.006 0.046 12960 Z= 0.418 Angle : 0.791 9.035 17705 Z= 0.482 Chirality : 0.055 0.238 2124 Planarity : 0.004 0.029 2213 Dihedral : 12.228 86.408 4527 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.59 % Allowed : 0.59 % Favored : 98.82 % 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: 0.80 (0.20), residues: 1624 helix: 0.50 (0.19), residues: 704 sheet: 0.59 (0.22), residues: 248 loop : 0.81 (0.26), residues: 672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 203 time to evaluate : 1.559 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 206 average time/residue: 0.2692 time to fit residues: 79.3747 Evaluate side-chains 163 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 ASN K 16 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12960 Z= 0.199 Angle : 0.472 7.632 17705 Z= 0.256 Chirality : 0.044 0.132 2124 Planarity : 0.003 0.027 2213 Dihedral : 6.232 55.522 1949 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.01 % Allowed : 3.37 % Favored : 95.62 % 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: 1.75 (0.21), residues: 1624 helix: 1.78 (0.20), residues: 704 sheet: 1.12 (0.25), residues: 248 loop : 0.66 (0.26), residues: 672 *********************** 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 193 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 1.307 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 188 average time/residue: 0.2541 time to fit residues: 68.8289 Evaluate side-chains 185 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 175 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1468 time to fit residues: 4.3713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN K 16 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12960 Z= 0.263 Angle : 0.480 5.653 17705 Z= 0.257 Chirality : 0.045 0.128 2124 Planarity : 0.003 0.031 2213 Dihedral : 6.045 55.886 1949 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.42 % Allowed : 5.31 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.21), residues: 1624 helix: 1.64 (0.20), residues: 704 sheet: 1.12 (0.27), residues: 256 loop : 0.25 (0.26), residues: 664 *********************** 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 182 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 1.470 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 179 average time/residue: 0.2402 time to fit residues: 62.9673 Evaluate side-chains 171 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1220 time to fit residues: 2.2424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12960 Z= 0.243 Angle : 0.447 5.048 17705 Z= 0.241 Chirality : 0.044 0.126 2124 Planarity : 0.003 0.033 2213 Dihedral : 5.932 54.690 1949 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.93 % Allowed : 5.73 % Favored : 93.34 % 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: 1.30 (0.21), residues: 1624 helix: 1.60 (0.20), residues: 704 sheet: 1.18 (0.28), residues: 256 loop : 0.00 (0.26), residues: 664 *********************** 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 177 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 1.503 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 171 average time/residue: 0.2514 time to fit residues: 62.2277 Evaluate side-chains 174 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 166 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1152 time to fit residues: 3.6605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12960 Z= 0.288 Angle : 0.466 6.061 17705 Z= 0.250 Chirality : 0.045 0.129 2124 Planarity : 0.003 0.034 2213 Dihedral : 6.034 53.445 1949 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.34 % Allowed : 7.41 % Favored : 92.25 % 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: 1.14 (0.21), residues: 1624 helix: 1.51 (0.20), residues: 704 sheet: 1.30 (0.28), residues: 248 loop : -0.19 (0.25), residues: 672 *********************** 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 175 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.503 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 173 average time/residue: 0.2632 time to fit residues: 65.7565 Evaluate side-chains 170 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.469 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1388 time to fit residues: 2.5205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 81 optimal weight: 0.0040 overall best weight: 2.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12960 Z= 0.210 Angle : 0.418 6.583 17705 Z= 0.227 Chirality : 0.043 0.125 2124 Planarity : 0.003 0.033 2213 Dihedral : 5.789 50.579 1949 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.67 % Allowed : 8.00 % Favored : 91.32 % 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: 1.23 (0.21), residues: 1624 helix: 1.64 (0.20), residues: 704 sheet: 1.38 (0.28), residues: 248 loop : -0.23 (0.25), residues: 672 *********************** 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 182 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 1.549 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 178 average time/residue: 0.2786 time to fit residues: 70.6444 Evaluate side-chains 179 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 1.485 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2013 time to fit residues: 3.1952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 0.0070 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 154 optimal weight: 0.0370 chunk 96 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 overall best weight: 1.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12960 Z= 0.169 Angle : 0.397 7.492 17705 Z= 0.216 Chirality : 0.042 0.124 2124 Planarity : 0.003 0.032 2213 Dihedral : 5.555 48.575 1949 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.59 % Allowed : 8.68 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.21), residues: 1624 helix: 1.77 (0.20), residues: 704 sheet: 1.49 (0.29), residues: 248 loop : -0.22 (0.25), residues: 672 *********************** 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 187 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 180 time to evaluate : 1.479 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 182 average time/residue: 0.2456 time to fit residues: 65.3782 Evaluate side-chains 180 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1135 time to fit residues: 3.1808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.0050 chunk 98 optimal weight: 0.3980 chunk 105 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 121 optimal weight: 0.0970 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN O 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.017 12960 Z= 0.094 Angle : 0.357 5.928 17705 Z= 0.196 Chirality : 0.041 0.122 2124 Planarity : 0.003 0.031 2213 Dihedral : 5.041 46.461 1949 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.34 % Allowed : 8.59 % Favored : 91.07 % 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: 1.72 (0.22), residues: 1624 helix: 2.07 (0.20), residues: 704 sheet: 1.81 (0.29), residues: 248 loop : -0.10 (0.26), residues: 672 *********************** 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 196 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 1.384 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 195 average time/residue: 0.2584 time to fit residues: 72.6153 Evaluate side-chains 178 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.428 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 10.0000 chunk 147 optimal weight: 0.0270 chunk 134 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12960 Z= 0.159 Angle : 0.392 7.694 17705 Z= 0.213 Chirality : 0.042 0.121 2124 Planarity : 0.003 0.030 2213 Dihedral : 5.219 45.441 1949 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.17 % Allowed : 9.77 % Favored : 90.06 % 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: 1.63 (0.22), residues: 1624 helix: 2.03 (0.20), residues: 704 sheet: 1.62 (0.30), residues: 256 loop : -0.14 (0.26), residues: 664 *********************** 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 174 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 1.376 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 172 average time/residue: 0.2552 time to fit residues: 63.5320 Evaluate side-chains 172 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1147 time to fit residues: 2.1417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12960 Z= 0.413 Angle : 0.531 10.795 17705 Z= 0.279 Chirality : 0.048 0.136 2124 Planarity : 0.004 0.034 2213 Dihedral : 6.055 47.309 1949 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.34 % Allowed : 9.86 % Favored : 89.81 % 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: 0.97 (0.21), residues: 1624 helix: 1.44 (0.19), residues: 712 sheet: 1.34 (0.29), residues: 248 loop : -0.45 (0.25), residues: 664 ********************** 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 173 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 169 time to evaluate : 1.517 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 172 average time/residue: 0.2617 time to fit residues: 65.1613 Evaluate side-chains 168 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1307 time to fit residues: 2.7584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 111 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.113691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.098581 restraints weight = 15446.711| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.32 r_work: 0.2876 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12960 Z= 0.123 Angle : 0.381 8.146 17705 Z= 0.209 Chirality : 0.042 0.124 2124 Planarity : 0.003 0.032 2213 Dihedral : 5.391 42.740 1949 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.17 % Allowed : 9.86 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.21), residues: 1624 helix: 1.80 (0.20), residues: 712 sheet: 1.67 (0.30), residues: 248 loop : -0.29 (0.26), residues: 664 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2406.60 seconds wall clock time: 44 minutes 30.50 seconds (2670.50 seconds total)