Starting phenix.real_space_refine on Tue Mar 19 12:20:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqh_23947/03_2024/7mqh_23947.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqh_23947/03_2024/7mqh_23947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqh_23947/03_2024/7mqh_23947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqh_23947/03_2024/7mqh_23947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqh_23947/03_2024/7mqh_23947.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqh_23947/03_2024/7mqh_23947.pdb" } resolution = 3.1 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= 0.015 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 11504 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 48 5.16 5 C 8040 2.51 5 N 2312 2.21 5 O 2320 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 ASP 36": "OD1" <-> "OD2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 138": "OD1" <-> "OD2" Residue "E TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 138": "OD1" <-> "OD2" Residue "G TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "I GLU 3": "OE1" <-> "OE2" Residue "I ASP 36": "OD1" <-> "OD2" Residue "I PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 138": "OD1" <-> "OD2" Residue "I TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 164": "OD1" <-> "OD2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "K GLU 3": "OE1" <-> "OE2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 138": "OD1" <-> "OD2" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 164": "OD1" <-> "OD2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "M GLU 3": "OE1" <-> "OE2" Residue "M ASP 36": "OD1" <-> "OD2" Residue "M PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 138": "OD1" <-> "OD2" Residue "M TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 164": "OD1" <-> "OD2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "O GLU 3": "OE1" <-> "OE2" Residue "O ASP 36": "OD1" <-> "OD2" Residue "O PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 138": "OD1" <-> "OD2" Residue "O TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 164": "OD1" <-> "OD2" Residue "O GLU 167": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12736 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1546 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "C" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1546 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 64 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "E" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1546 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 64 Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "G" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1546 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 64 Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "I" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1546 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 64 Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "K" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1546 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 64 Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "M" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1546 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 64 Chain: "N" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "O" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1546 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 64 Chain: "P" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Time building chain proxies: 6.98, per 1000 atoms: 0.55 Number of scatterers: 12736 At special positions: 0 Unit cell: (105.4, 105.4, 88.04, 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 48 16.00 P 16 15.00 O 2320 8.00 N 2312 7.00 C 8040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.23 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: 56 helices and 8 sheets defined 45.4% alpha, 12.7% 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: 4.007A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.606A 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: 4.007A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.592A 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 removed outlier: 3.606A pdb=" N ASP C 155 " --> pdb=" O TYR C 151 " (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: 4.007A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.606A 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: 4.007A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.606A 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 71 Processing helix chain 'I' and resid 80 through 93 removed outlier: 4.007A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.606A 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: 4.007A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.606A 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: 4.008A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.605A 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: 4.007A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.592A 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 removed outlier: 3.606A pdb=" N ASP O 155 " --> pdb=" O TYR O 151 " (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: 6.163A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU A 27 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL A 41 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP A 25 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 43 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA A 23 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.163A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU C 27 " --> pdb=" O CYS C 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL C 41 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU C 43 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.467A 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: 6.162A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU E 27 " --> pdb=" O CYS E 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL E 41 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP E 25 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU E 43 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA E 23 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.162A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.466A 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: 6.162A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU I 27 " --> pdb=" O CYS I 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL I 41 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP I 25 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU I 43 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA I 23 " --> pdb=" O LEU I 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.163A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU K 27 " --> pdb=" O CYS K 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL K 41 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP K 25 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU K 43 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA K 23 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 4 through 8 removed outlier: 6.161A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU M 27 " --> pdb=" O CYS M 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL M 41 " --> pdb=" O ASP M 25 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP M 25 " --> pdb=" O VAL M 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU M 43 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA M 23 " --> pdb=" O LEU M 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 4 through 8 removed outlier: 6.163A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU O 27 " --> pdb=" O CYS O 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL O 41 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP O 25 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU O 43 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA O 23 " --> pdb=" O LEU O 43 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1656 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: 3.48 Time building geometry restraints manager: 5.60 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: 4237 1.34 - 1.46: 2332 1.46 - 1.58: 6343 1.58 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 13000 Sorted by residual: bond pdb=" N ASP M 47 " pdb=" CA ASP M 47 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.17e-02 7.31e+03 6.05e+00 bond pdb=" N ASP O 47 " pdb=" CA ASP O 47 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.17e-02 7.31e+03 5.99e+00 bond pdb=" N ASP C 47 " pdb=" CA ASP C 47 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.17e-02 7.31e+03 5.99e+00 bond pdb=" N ASP E 47 " pdb=" CA ASP E 47 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.17e-02 7.31e+03 5.99e+00 bond pdb=" N ASP G 47 " pdb=" CA ASP G 47 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.17e-02 7.31e+03 5.99e+00 ... (remaining 12995 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.13: 447 107.13 - 113.85: 7498 113.85 - 120.57: 5296 120.57 - 127.29: 4330 127.29 - 134.01: 189 Bond angle restraints: 17760 Sorted by residual: angle pdb=" C SER M 136 " pdb=" N SER M 137 " pdb=" CA SER M 137 " ideal model delta sigma weight residual 121.87 115.76 6.11 1.64e+00 3.72e-01 1.39e+01 angle pdb=" C SER K 136 " pdb=" N SER K 137 " pdb=" CA SER K 137 " ideal model delta sigma weight residual 121.87 115.80 6.07 1.64e+00 3.72e-01 1.37e+01 angle pdb=" C SER A 136 " pdb=" N SER A 137 " pdb=" CA SER A 137 " ideal model delta sigma weight residual 121.87 115.80 6.07 1.64e+00 3.72e-01 1.37e+01 angle pdb=" C SER C 136 " pdb=" N SER C 137 " pdb=" CA SER C 137 " ideal model delta sigma weight residual 121.87 115.80 6.07 1.64e+00 3.72e-01 1.37e+01 angle pdb=" C SER O 136 " pdb=" N SER O 137 " pdb=" CA SER O 137 " ideal model delta sigma weight residual 121.87 115.80 6.07 1.64e+00 3.72e-01 1.37e+01 ... (remaining 17755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 7055 15.41 - 30.81: 497 30.81 - 46.22: 128 46.22 - 61.62: 48 61.62 - 77.03: 40 Dihedral angle restraints: 7768 sinusoidal: 2984 harmonic: 4784 Sorted by residual: dihedral pdb=" CA PHE M 78 " pdb=" C PHE M 78 " pdb=" N HIS M 79 " pdb=" CA HIS M 79 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+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 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 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 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 804 0.030 - 0.059: 680 0.059 - 0.089: 390 0.089 - 0.119: 205 0.119 - 0.148: 57 Chirality restraints: 2136 Sorted by residual: chirality pdb=" CA ILE E 53 " pdb=" N ILE E 53 " pdb=" C ILE E 53 " pdb=" CB ILE E 53 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE I 53 " pdb=" N ILE I 53 " pdb=" C ILE I 53 " pdb=" CB ILE I 53 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE G 53 " pdb=" N ILE G 53 " pdb=" C ILE G 53 " pdb=" CB ILE G 53 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 2133 not shown) Planarity restraints: 2216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY O 48 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C GLY O 48 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY O 48 " -0.011 2.00e-02 2.50e+03 pdb=" N THR O 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY I 48 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C GLY I 48 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY I 48 " -0.011 2.00e-02 2.50e+03 pdb=" N THR I 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 48 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C GLY E 48 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY E 48 " 0.011 2.00e-02 2.50e+03 pdb=" N THR E 49 " 0.010 2.00e-02 2.50e+03 ... (remaining 2213 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4221 2.86 - 3.37: 11685 3.37 - 3.88: 21260 3.88 - 4.39: 25670 4.39 - 4.90: 42210 Nonbonded interactions: 105046 Sorted by model distance: nonbonded pdb=" OH TYR K 112 " pdb=" OE2 GLU K 124 " model vdw 2.350 2.440 nonbonded pdb=" OH TYR A 112 " pdb=" OE2 GLU A 124 " model vdw 2.350 2.440 nonbonded pdb=" OH TYR G 112 " pdb=" OE2 GLU G 124 " model vdw 2.350 2.440 nonbonded pdb=" OH TYR O 112 " pdb=" OE2 GLU O 124 " model vdw 2.350 2.440 nonbonded pdb=" OH TYR C 112 " pdb=" OE2 GLU C 124 " model vdw 2.350 2.440 ... (remaining 105041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 1.300 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 34.840 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 0.035 13000 Z= 0.478 Angle : 0.808 6.114 17760 Z= 0.499 Chirality : 0.056 0.148 2136 Planarity : 0.005 0.023 2216 Dihedral : 13.706 77.028 4648 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1624 helix: 0.78 (0.19), residues: 704 sheet: 0.48 (0.21), residues: 248 loop : 0.78 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP O 139 HIS 0.007 0.002 HIS E 7 PHE 0.017 0.002 PHE E 78 TYR 0.012 0.003 TYR I 17 ARG 0.008 0.001 ARG M 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 137 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.524 Fit side-chains REVERT: A 27 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7920 (mm-30) REVERT: C 27 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7860 (mm-30) REVERT: E 27 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7827 (mm-30) REVERT: G 27 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7903 (mm-30) REVERT: I 27 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7867 (mm-30) REVERT: K 27 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7903 (mm-30) REVERT: O 27 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7842 (mm-30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2670 time to fit residues: 52.5076 Evaluate side-chains 112 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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: 10.0000 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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** M 54 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13000 Z= 0.151 Angle : 0.432 4.518 17760 Z= 0.238 Chirality : 0.042 0.122 2136 Planarity : 0.003 0.024 2216 Dihedral : 10.739 63.759 2040 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.21), residues: 1624 helix: 2.08 (0.20), residues: 704 sheet: 1.06 (0.24), residues: 248 loop : 0.52 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 197 HIS 0.002 0.001 HIS M 7 PHE 0.014 0.001 PHE E 78 TYR 0.007 0.001 TYR O 17 ARG 0.001 0.000 ARG M 169 *********************** 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 167 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.533 Fit side-chains REVERT: A 13 ASN cc_start: 0.8163 (p0) cc_final: 0.7885 (p0) REVERT: A 27 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 120 GLU cc_start: 0.8042 (mp0) cc_final: 0.7679 (mp0) REVERT: C 13 ASN cc_start: 0.8177 (p0) cc_final: 0.7895 (p0) REVERT: C 27 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7995 (mm-30) REVERT: C 120 GLU cc_start: 0.8042 (mp0) cc_final: 0.7679 (mp0) REVERT: E 13 ASN cc_start: 0.8198 (p0) cc_final: 0.7910 (p0) REVERT: E 27 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7990 (mm-30) REVERT: E 120 GLU cc_start: 0.8032 (mp0) cc_final: 0.7677 (mp0) REVERT: G 13 ASN cc_start: 0.8192 (p0) cc_final: 0.7903 (p0) REVERT: G 27 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7832 (mm-30) REVERT: G 120 GLU cc_start: 0.8037 (mp0) cc_final: 0.7679 (mp0) REVERT: I 13 ASN cc_start: 0.8189 (p0) cc_final: 0.7903 (p0) REVERT: I 27 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7827 (mm-30) REVERT: I 120 GLU cc_start: 0.8042 (mp0) cc_final: 0.7678 (mp0) REVERT: K 13 ASN cc_start: 0.8163 (p0) cc_final: 0.7880 (p0) REVERT: K 27 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7846 (mm-30) REVERT: K 120 GLU cc_start: 0.8052 (mp0) cc_final: 0.7689 (mp0) REVERT: M 27 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7638 (mm-30) REVERT: O 13 ASN cc_start: 0.8172 (p0) cc_final: 0.7892 (p0) REVERT: O 27 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8007 (mm-30) REVERT: O 120 GLU cc_start: 0.8036 (mp0) cc_final: 0.7676 (mp0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2637 time to fit residues: 62.4637 Evaluate side-chains 158 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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: 9.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 13000 Z= 0.486 Angle : 0.572 4.466 17760 Z= 0.300 Chirality : 0.049 0.135 2136 Planarity : 0.005 0.045 2216 Dihedral : 10.662 63.772 2040 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.91 % 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: 1.55 (0.20), residues: 696 sheet: 0.96 (0.24), residues: 240 loop : -0.27 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP O 197 HIS 0.005 0.002 HIS I 7 PHE 0.015 0.002 PHE K 78 TYR 0.011 0.003 TYR K 151 ARG 0.004 0.001 ARG M 169 *********************** 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 145 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.433 Fit side-chains REVERT: A 27 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7997 (mm-30) REVERT: A 120 GLU cc_start: 0.7881 (mp0) cc_final: 0.7473 (mp0) REVERT: C 27 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7975 (mm-30) REVERT: C 120 GLU cc_start: 0.7886 (mp0) cc_final: 0.7482 (mp0) REVERT: E 27 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7791 (mm-30) REVERT: E 120 GLU cc_start: 0.7876 (mp0) cc_final: 0.7482 (mp0) REVERT: G 27 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7992 (mm-30) REVERT: G 120 GLU cc_start: 0.7881 (mp0) cc_final: 0.7480 (mp0) REVERT: I 27 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7972 (mm-30) REVERT: I 120 GLU cc_start: 0.7881 (mp0) cc_final: 0.7488 (mp0) REVERT: K 27 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7992 (mm-30) REVERT: K 120 GLU cc_start: 0.7891 (mp0) cc_final: 0.7485 (mp0) REVERT: M 27 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7844 (mm-30) REVERT: O 27 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7936 (mm-30) REVERT: O 120 GLU cc_start: 0.7881 (mp0) cc_final: 0.7481 (mp0) outliers start: 1 outliers final: 1 residues processed: 144 average time/residue: 0.2963 time to fit residues: 59.7651 Evaluate side-chains 140 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 143 THR 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: 0.9980 chunk 75 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 13000 Z= 0.102 Angle : 0.368 4.417 17760 Z= 0.206 Chirality : 0.041 0.119 2136 Planarity : 0.002 0.025 2216 Dihedral : 10.327 63.765 2040 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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: 1.39 (0.21), residues: 1624 helix: 1.98 (0.20), residues: 704 sheet: 1.44 (0.25), residues: 248 loop : -0.42 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP M 139 HIS 0.001 0.000 HIS E 160 PHE 0.012 0.001 PHE G 78 TYR 0.005 0.001 TYR M 17 ARG 0.001 0.000 ARG C 169 *********************** 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 166 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.613 Fit side-chains REVERT: A 27 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7913 (mm-30) REVERT: A 120 GLU cc_start: 0.7913 (mp0) cc_final: 0.7671 (mp0) REVERT: C 27 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7908 (mm-30) REVERT: C 120 GLU cc_start: 0.7913 (mp0) cc_final: 0.7676 (mp0) REVERT: E 27 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7903 (mm-30) REVERT: E 120 GLU cc_start: 0.7915 (mp0) cc_final: 0.7678 (mp0) REVERT: G 27 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7900 (mm-30) REVERT: G 120 GLU cc_start: 0.7916 (mp0) cc_final: 0.7676 (mp0) REVERT: I 27 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7918 (mm-30) REVERT: I 120 GLU cc_start: 0.7916 (mp0) cc_final: 0.7676 (mp0) REVERT: K 27 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7928 (mm-30) REVERT: K 120 GLU cc_start: 0.7924 (mp0) cc_final: 0.7676 (mp0) REVERT: M 27 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7591 (mm-30) REVERT: M 120 GLU cc_start: 0.7883 (mp0) cc_final: 0.7585 (mp0) REVERT: O 27 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7909 (mm-30) REVERT: O 120 GLU cc_start: 0.7908 (mp0) cc_final: 0.7670 (mp0) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2813 time to fit residues: 66.3405 Evaluate side-chains 146 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 131 optimal weight: 0.0370 chunk 106 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- 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** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 13000 Z= 0.216 Angle : 0.411 4.495 17760 Z= 0.223 Chirality : 0.043 0.124 2136 Planarity : 0.003 0.026 2216 Dihedral : 10.277 63.706 2040 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.66 % Allowed : 6.91 % Favored : 92.43 % 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: 1.93 (0.20), residues: 704 sheet: 1.50 (0.27), residues: 240 loop : -0.52 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 197 HIS 0.002 0.001 HIS O 7 PHE 0.013 0.001 PHE I 78 TYR 0.009 0.002 TYR M 17 ARG 0.002 0.000 ARG I 5 *********************** 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 153 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.489 Fit side-chains REVERT: A 27 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7875 (mm-30) REVERT: A 120 GLU cc_start: 0.7935 (mp0) cc_final: 0.7627 (mp0) REVERT: C 27 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7842 (mm-30) REVERT: C 120 GLU cc_start: 0.7934 (mp0) cc_final: 0.7629 (mp0) REVERT: E 27 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7844 (mm-30) REVERT: E 120 GLU cc_start: 0.7933 (mp0) cc_final: 0.7635 (mp0) REVERT: G 27 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7865 (mm-30) REVERT: G 120 GLU cc_start: 0.7936 (mp0) cc_final: 0.7632 (mp0) REVERT: I 27 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7848 (mm-30) REVERT: I 120 GLU cc_start: 0.7935 (mp0) cc_final: 0.7586 (mp0) REVERT: K 27 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7867 (mm-30) REVERT: K 120 GLU cc_start: 0.7943 (mp0) cc_final: 0.7636 (mp0) REVERT: M 27 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7634 (mm-30) REVERT: M 120 GLU cc_start: 0.7908 (mp0) cc_final: 0.7551 (mp0) REVERT: O 27 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7858 (mm-30) REVERT: O 120 GLU cc_start: 0.7932 (mp0) cc_final: 0.7627 (mp0) outliers start: 8 outliers final: 8 residues processed: 145 average time/residue: 0.2942 time to fit residues: 59.8246 Evaluate side-chains 153 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain O residue 173 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 81 optimal weight: 0.0980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 13000 Z= 0.156 Angle : 0.379 4.476 17760 Z= 0.209 Chirality : 0.042 0.122 2136 Planarity : 0.003 0.025 2216 Dihedral : 10.174 63.697 2040 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.16 % Allowed : 7.73 % Favored : 92.11 % 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: 2.03 (0.20), residues: 704 sheet: 1.48 (0.27), residues: 248 loop : -0.55 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 139 HIS 0.002 0.000 HIS M 7 PHE 0.012 0.001 PHE A 78 TYR 0.007 0.001 TYR I 17 ARG 0.001 0.000 ARG M 5 *********************** 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 155 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 1.464 Fit side-chains REVERT: A 27 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8028 (mm-30) REVERT: A 61 SER cc_start: 0.8757 (p) cc_final: 0.8411 (t) REVERT: A 120 GLU cc_start: 0.7909 (mp0) cc_final: 0.7646 (mp0) REVERT: C 27 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8004 (mm-30) REVERT: C 61 SER cc_start: 0.8762 (p) cc_final: 0.8420 (t) REVERT: C 120 GLU cc_start: 0.7906 (mp0) cc_final: 0.7646 (mp0) REVERT: E 27 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8008 (mm-30) REVERT: E 61 SER cc_start: 0.8763 (p) cc_final: 0.8422 (t) REVERT: E 120 GLU cc_start: 0.7907 (mp0) cc_final: 0.7653 (mp0) REVERT: G 27 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8019 (mm-30) REVERT: G 61 SER cc_start: 0.8760 (p) cc_final: 0.8421 (t) REVERT: G 120 GLU cc_start: 0.7909 (mp0) cc_final: 0.7649 (mp0) REVERT: I 27 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8015 (mm-30) REVERT: I 61 SER cc_start: 0.8759 (p) cc_final: 0.8416 (t) REVERT: I 120 GLU cc_start: 0.7909 (mp0) cc_final: 0.7651 (mp0) REVERT: K 27 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8020 (mm-30) REVERT: K 61 SER cc_start: 0.8760 (p) cc_final: 0.8419 (t) REVERT: K 120 GLU cc_start: 0.7917 (mp0) cc_final: 0.7655 (mp0) REVERT: M 27 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7566 (mm-30) REVERT: M 120 GLU cc_start: 0.7892 (mp0) cc_final: 0.7627 (mp0) REVERT: O 27 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8017 (mm-30) REVERT: O 61 SER cc_start: 0.8758 (p) cc_final: 0.8415 (t) REVERT: O 120 GLU cc_start: 0.7906 (mp0) cc_final: 0.7647 (mp0) outliers start: 2 outliers final: 1 residues processed: 154 average time/residue: 0.2948 time to fit residues: 65.1101 Evaluate side-chains 184 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 173 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.0770 chunk 17 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- 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** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN M 54 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13000 Z= 0.288 Angle : 0.449 4.495 17760 Z= 0.239 Chirality : 0.044 0.128 2136 Planarity : 0.003 0.027 2216 Dihedral : 10.307 63.715 2040 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.74 % Allowed : 7.24 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.21), residues: 1624 helix: 1.79 (0.20), residues: 704 sheet: 1.19 (0.29), residues: 240 loop : -0.74 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 197 HIS 0.003 0.001 HIS O 7 PHE 0.014 0.002 PHE I 78 TYR 0.009 0.002 TYR M 17 ARG 0.002 0.000 ARG A 5 *********************** 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 176 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 167 time to evaluate : 1.454 Fit side-chains REVERT: A 27 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 120 GLU cc_start: 0.7909 (mp0) cc_final: 0.7677 (mp0) REVERT: C 27 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7854 (mm-30) REVERT: C 120 GLU cc_start: 0.7909 (mp0) cc_final: 0.7679 (mp0) REVERT: C 138 ASP cc_start: 0.8913 (t70) cc_final: 0.8693 (t70) REVERT: E 27 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7845 (mm-30) REVERT: E 120 GLU cc_start: 0.7933 (mp0) cc_final: 0.7714 (mp0) REVERT: E 138 ASP cc_start: 0.8912 (t70) cc_final: 0.8686 (t70) REVERT: G 27 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7871 (mm-30) REVERT: G 120 GLU cc_start: 0.7932 (mp0) cc_final: 0.7709 (mp0) REVERT: G 138 ASP cc_start: 0.8912 (t70) cc_final: 0.8685 (t70) REVERT: I 27 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7854 (mm-30) REVERT: I 120 GLU cc_start: 0.7937 (mp0) cc_final: 0.7712 (mp0) REVERT: I 138 ASP cc_start: 0.8915 (t70) cc_final: 0.8689 (t70) REVERT: K 27 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7872 (mm-30) REVERT: K 120 GLU cc_start: 0.7919 (mp0) cc_final: 0.7687 (mp0) REVERT: K 138 ASP cc_start: 0.8914 (t70) cc_final: 0.8690 (t70) REVERT: M 27 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7676 (mm-30) REVERT: M 120 GLU cc_start: 0.7873 (mp0) cc_final: 0.7431 (mp0) REVERT: O 27 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7854 (mm-30) REVERT: O 120 GLU cc_start: 0.7909 (mp0) cc_final: 0.7680 (mp0) REVERT: O 138 ASP cc_start: 0.8915 (t70) cc_final: 0.8685 (t70) outliers start: 9 outliers final: 8 residues processed: 168 average time/residue: 0.2659 time to fit residues: 63.6432 Evaluate side-chains 169 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain O residue 173 GLU 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: 0.4980 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 13000 Z= 0.194 Angle : 0.402 4.447 17760 Z= 0.218 Chirality : 0.042 0.124 2136 Planarity : 0.003 0.026 2216 Dihedral : 10.218 63.699 2040 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.58 % Allowed : 7.65 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1624 helix: 1.89 (0.20), residues: 704 sheet: 1.10 (0.29), residues: 248 loop : -0.75 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 197 HIS 0.002 0.001 HIS K 7 PHE 0.013 0.001 PHE M 78 TYR 0.008 0.001 TYR E 17 ARG 0.001 0.000 ARG I 5 *********************** 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 168 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 1.512 Fit side-chains REVERT: A 27 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7852 (mm-30) REVERT: A 120 GLU cc_start: 0.7883 (mp0) cc_final: 0.7548 (mp0) REVERT: C 27 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7819 (mm-30) REVERT: C 120 GLU cc_start: 0.7881 (mp0) cc_final: 0.7551 (mp0) REVERT: E 27 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7813 (mm-30) REVERT: E 120 GLU cc_start: 0.7886 (mp0) cc_final: 0.7559 (mp0) REVERT: E 138 ASP cc_start: 0.8920 (t70) cc_final: 0.8719 (t70) REVERT: G 27 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7840 (mm-30) REVERT: G 120 GLU cc_start: 0.7887 (mp0) cc_final: 0.7555 (mp0) REVERT: G 138 ASP cc_start: 0.8919 (t70) cc_final: 0.8718 (t70) REVERT: I 27 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7819 (mm-30) REVERT: I 120 GLU cc_start: 0.7888 (mp0) cc_final: 0.7559 (mp0) REVERT: K 27 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7841 (mm-30) REVERT: K 120 GLU cc_start: 0.7895 (mp0) cc_final: 0.7559 (mp0) REVERT: M 27 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7610 (mm-30) REVERT: M 120 GLU cc_start: 0.7813 (mp0) cc_final: 0.7443 (mp0) REVERT: O 27 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7823 (mm-30) REVERT: O 120 GLU cc_start: 0.7882 (mp0) cc_final: 0.7550 (mp0) REVERT: O 138 ASP cc_start: 0.8923 (t70) cc_final: 0.8718 (t70) outliers start: 7 outliers final: 6 residues processed: 162 average time/residue: 0.2754 time to fit residues: 63.6816 Evaluate side-chains 168 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain O residue 173 GLU 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: 5.9990 chunk 143 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- 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** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 13000 Z= 0.363 Angle : 0.489 4.471 17760 Z= 0.257 Chirality : 0.046 0.133 2136 Planarity : 0.004 0.029 2216 Dihedral : 10.375 63.724 2040 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.74 % Allowed : 7.24 % Favored : 92.02 % 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: 0.67 (0.21), residues: 1624 helix: 1.62 (0.20), residues: 704 sheet: 0.67 (0.30), residues: 240 loop : -0.90 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 139 HIS 0.003 0.001 HIS A 7 PHE 0.014 0.002 PHE M 78 TYR 0.010 0.002 TYR M 17 ARG 0.002 0.001 ARG C 5 *********************** 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 153 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 1.166 Fit side-chains REVERT: A 27 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7913 (mm-30) REVERT: A 120 GLU cc_start: 0.7929 (mp0) cc_final: 0.7518 (mp0) REVERT: A 173 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: C 27 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7891 (mm-30) REVERT: C 120 GLU cc_start: 0.7927 (mp0) cc_final: 0.7521 (mp0) REVERT: C 173 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7023 (mt-10) REVERT: E 27 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7881 (mm-30) REVERT: E 120 GLU cc_start: 0.7930 (mp0) cc_final: 0.7529 (mp0) REVERT: E 138 ASP cc_start: 0.8926 (t70) cc_final: 0.8716 (t70) REVERT: E 173 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: G 27 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7907 (mm-30) REVERT: G 120 GLU cc_start: 0.7929 (mp0) cc_final: 0.7523 (mp0) REVERT: G 138 ASP cc_start: 0.8927 (t70) cc_final: 0.8716 (t70) REVERT: G 173 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7023 (mt-10) REVERT: I 27 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7891 (mm-30) REVERT: I 120 GLU cc_start: 0.7932 (mp0) cc_final: 0.7530 (mp0) REVERT: I 173 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7088 (mt-10) REVERT: K 27 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7908 (mm-30) REVERT: K 120 GLU cc_start: 0.7937 (mp0) cc_final: 0.7528 (mp0) REVERT: K 173 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7020 (mt-10) REVERT: M 27 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7764 (mm-30) REVERT: M 120 GLU cc_start: 0.7891 (mp0) cc_final: 0.7691 (mp0) REVERT: M 173 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: O 27 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7889 (mm-30) REVERT: O 120 GLU cc_start: 0.7927 (mp0) cc_final: 0.7518 (mp0) REVERT: O 138 ASP cc_start: 0.8930 (t70) cc_final: 0.8718 (t70) REVERT: O 173 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7081 (mt-10) outliers start: 9 outliers final: 0 residues processed: 145 average time/residue: 0.2779 time to fit residues: 57.0043 Evaluate side-chains 152 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain O residue 173 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 13000 Z= 0.273 Angle : 0.439 4.433 17760 Z= 0.236 Chirality : 0.044 0.128 2136 Planarity : 0.003 0.027 2216 Dihedral : 10.317 63.712 2040 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.74 % Allowed : 7.24 % Favored : 92.02 % 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: 0.70 (0.21), residues: 1624 helix: 1.69 (0.20), residues: 704 sheet: 0.61 (0.30), residues: 240 loop : -0.92 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 139 HIS 0.003 0.001 HIS M 7 PHE 0.013 0.002 PHE E 78 TYR 0.009 0.002 TYR M 17 ARG 0.001 0.000 ARG M 169 ********************** 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 160 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 1.504 Fit side-chains REVERT: A 27 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7849 (mm-30) REVERT: A 120 GLU cc_start: 0.7907 (mp0) cc_final: 0.7670 (mp0) REVERT: C 27 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7630 (mm-30) REVERT: C 120 GLU cc_start: 0.7905 (mp0) cc_final: 0.7670 (mp0) REVERT: E 27 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7646 (mm-30) REVERT: E 120 GLU cc_start: 0.7912 (mp0) cc_final: 0.7676 (mp0) REVERT: G 27 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7840 (mm-30) REVERT: G 120 GLU cc_start: 0.7911 (mp0) cc_final: 0.7674 (mp0) REVERT: I 27 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7621 (mm-30) REVERT: I 120 GLU cc_start: 0.7912 (mp0) cc_final: 0.7678 (mp0) REVERT: K 27 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7845 (mm-30) REVERT: K 120 GLU cc_start: 0.7917 (mp0) cc_final: 0.7679 (mp0) REVERT: M 27 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7675 (mm-30) REVERT: M 120 GLU cc_start: 0.7833 (mp0) cc_final: 0.7469 (mp0) REVERT: O 27 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7663 (mm-30) REVERT: O 120 GLU cc_start: 0.7906 (mp0) cc_final: 0.7669 (mp0) outliers start: 9 outliers final: 8 residues processed: 152 average time/residue: 0.2844 time to fit residues: 61.4631 Evaluate side-chains 159 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain O residue 173 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 111 optimal weight: 0.3980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN ** O 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 = 0.3111 r_free = 0.3111 target = 0.102995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.091294 restraints weight = 14850.417| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 0.93 r_work: 0.2857 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 13000 Z= 0.140 Angle : 0.374 4.454 17760 Z= 0.206 Chirality : 0.041 0.122 2136 Planarity : 0.003 0.025 2216 Dihedral : 10.104 63.710 2040 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.74 % Allowed : 7.24 % Favored : 92.02 % 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: 0.98 (0.21), residues: 1624 helix: 2.01 (0.20), residues: 704 sheet: 0.76 (0.30), residues: 248 loop : -0.89 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 139 HIS 0.001 0.000 HIS M 90 PHE 0.012 0.001 PHE M 78 TYR 0.007 0.001 TYR E 17 ARG 0.001 0.000 ARG O 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2220.19 seconds wall clock time: 41 minutes 6.51 seconds (2466.51 seconds total)