Starting phenix.real_space_refine on Tue Mar 19 12:34:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqb_23941/03_2024/7mqb_23941.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqb_23941/03_2024/7mqb_23941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqb_23941/03_2024/7mqb_23941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqb_23941/03_2024/7mqb_23941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqb_23941/03_2024/7mqb_23941.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqb_23941/03_2024/7mqb_23941.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11544 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 8064 2.51 5 N 2328 2.21 5 O 2304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E ASP 193": "OD1" <-> "OD2" Residue "G ASP 25": "OD1" <-> "OD2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 84": "OD1" <-> "OD2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "I ASP 25": "OD1" <-> "OD2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 84": "OD1" <-> "OD2" Residue "I GLU 124": "OE1" <-> "OE2" Residue "I ASP 155": "OD1" <-> "OD2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I GLU 173": "OE1" <-> "OE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "K ASP 25": "OD1" <-> "OD2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 84": "OD1" <-> "OD2" Residue "K GLU 124": "OE1" <-> "OE2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "K ASP 193": "OD1" <-> "OD2" Residue "M ASP 25": "OD1" <-> "OD2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 84": "OD1" <-> "OD2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "M ASP 155": "OD1" <-> "OD2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M GLU 173": "OE1" <-> "OE2" Residue "M ASP 193": "OD1" <-> "OD2" Residue "O ASP 25": "OD1" <-> "OD2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 84": "OD1" <-> "OD2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "O ASP 155": "OD1" <-> "OD2" Residue "O GLU 167": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "O ASP 193": "OD1" <-> "OD2" 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: 12760 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" 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: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "C" Number of atoms: 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: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "E" Number of atoms: 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: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "F" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "G" Number of atoms: 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: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "I" Number of atoms: 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: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "J" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "K" Number of atoms: 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: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "M" Number of atoms: 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: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "N" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "O" Number of atoms: 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: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "P" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Time building chain proxies: 7.42, per 1000 atoms: 0.58 Number of scatterers: 12760 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 2304 8.00 N 2328 7.00 C 8064 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: 5.30 Conformation dependent library (CDL) restraints added in 2.3 seconds 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 45.4% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.618A 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 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: 3.886A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.619A 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: 3.887A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.618A 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 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: 3.886A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 117 through 127 Processing helix chain 'G' and resid 145 through 155 Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'G' and resid 175 through 196 Proline residue: G 187 - end of helix Processing helix chain 'I' and resid 62 through 71 Processing helix chain 'I' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.619A 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 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: 3.886A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 117 through 127 Processing helix chain 'K' and resid 145 through 155 Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'K' and resid 175 through 196 Proline residue: K 187 - end of helix Processing helix chain 'M' and resid 62 through 71 Processing helix chain 'M' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.619A 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 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: 3.886A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.618A 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: 6.483A pdb=" N GLU A 3 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL A 52 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU A 27 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL A 41 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP A 25 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 43 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 6.678A 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: 6.483A pdb=" N GLU C 3 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL C 52 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU C 27 " --> pdb=" O CYS C 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL C 41 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 43 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA C 23 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU E 3 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL E 52 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU E 27 " --> pdb=" O CYS E 39 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL E 41 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP E 25 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU E 43 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA E 23 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU G 3 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL G 52 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA G 23 " --> pdb=" O LEU G 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 3 through 8 removed outlier: 6.484A pdb=" N GLU I 3 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL I 52 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU I 27 " --> pdb=" O CYS I 39 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL I 41 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP I 25 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU I 43 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA I 23 " --> pdb=" O LEU I 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU K 3 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL K 52 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU K 27 " --> pdb=" O CYS K 39 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL K 41 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP K 25 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU K 43 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 6.678A 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: 6.483A pdb=" N GLU M 3 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL M 52 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU M 27 " --> pdb=" O CYS M 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL M 41 " --> pdb=" O ASP M 25 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP M 25 " --> pdb=" O VAL M 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU M 43 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA M 23 " --> pdb=" O LEU M 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU O 3 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL O 52 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU O 27 " --> pdb=" O CYS O 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL O 41 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP O 25 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU O 43 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA O 23 " --> pdb=" O LEU O 43 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1680 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: 5.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4216 1.34 - 1.46: 2302 1.46 - 1.57: 6418 1.57 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 13024 Sorted by residual: bond pdb=" CG LYS C 103 " pdb=" CD LYS C 103 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CG LYS E 103 " pdb=" CD LYS E 103 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CG LYS O 103 " pdb=" CD LYS O 103 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CG LYS I 103 " pdb=" CD LYS I 103 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CG LYS A 103 " pdb=" CD LYS A 103 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 13019 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.97: 376 106.97 - 113.73: 7665 113.73 - 120.49: 5167 120.49 - 127.25: 4392 127.25 - 134.01: 176 Bond angle restraints: 17776 Sorted by residual: angle pdb=" C SER E 61 " pdb=" N ALA E 62 " pdb=" CA ALA E 62 " ideal model delta sigma weight residual 122.28 125.74 -3.46 8.80e-01 1.29e+00 1.55e+01 angle pdb=" C SER C 61 " pdb=" N ALA C 62 " pdb=" CA ALA C 62 " ideal model delta sigma weight residual 122.28 125.74 -3.46 8.80e-01 1.29e+00 1.55e+01 angle pdb=" C SER A 61 " pdb=" N ALA A 62 " pdb=" CA ALA A 62 " ideal model delta sigma weight residual 122.28 125.74 -3.46 8.80e-01 1.29e+00 1.54e+01 angle pdb=" C SER G 61 " pdb=" N ALA G 62 " pdb=" CA ALA G 62 " ideal model delta sigma weight residual 122.28 125.73 -3.45 8.80e-01 1.29e+00 1.54e+01 angle pdb=" C SER I 61 " pdb=" N ALA I 62 " pdb=" CA ALA I 62 " ideal model delta sigma weight residual 122.28 125.72 -3.44 8.80e-01 1.29e+00 1.53e+01 ... (remaining 17771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 7169 17.25 - 34.50: 459 34.50 - 51.75: 116 51.75 - 69.00: 48 69.00 - 86.25: 16 Dihedral angle restraints: 7808 sinusoidal: 3024 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 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE K 78 " pdb=" C PHE K 78 " pdb=" N HIS K 79 " pdb=" CA HIS K 79 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE A 78 " pdb=" C PHE A 78 " pdb=" N HIS A 79 " pdb=" CA HIS A 79 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 7805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 978 0.030 - 0.061: 617 0.061 - 0.091: 339 0.091 - 0.121: 157 0.121 - 0.152: 37 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CA VAL E 40 " pdb=" N VAL E 40 " pdb=" C VAL E 40 " pdb=" CB VAL E 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA VAL I 40 " pdb=" N VAL I 40 " pdb=" C VAL I 40 " pdb=" CB VAL I 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA VAL O 40 " pdb=" N VAL O 40 " pdb=" C VAL O 40 " pdb=" CB VAL O 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2125 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 83 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C PHE K 83 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE K 83 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP K 84 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE O 83 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C PHE O 83 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE O 83 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP O 84 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 83 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C PHE C 83 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE C 83 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP C 84 " 0.009 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3579 2.82 - 3.34: 11494 3.34 - 3.86: 21299 3.86 - 4.38: 25619 4.38 - 4.90: 43455 Nonbonded interactions: 105446 Sorted by model distance: nonbonded pdb=" NE2 HIS K 79 " pdb=" OP1 G L 603 " model vdw 2.302 2.520 nonbonded pdb=" NE2 HIS A 79 " pdb=" OP1 G B 603 " model vdw 2.341 2.520 nonbonded pdb=" OH TYR M 17 " pdb=" OD2 ASP M 51 " model vdw 2.341 2.440 nonbonded pdb=" OH TYR O 17 " pdb=" OD2 ASP O 51 " model vdw 2.341 2.440 nonbonded pdb=" OH TYR C 17 " pdb=" OD2 ASP C 51 " model vdw 2.341 2.440 ... (remaining 105441 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 1.490 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 36.220 Find NCS groups from input model: 0.830 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 0.034 13024 Z= 0.436 Angle : 0.721 4.752 17776 Z= 0.456 Chirality : 0.052 0.152 2128 Planarity : 0.004 0.021 2200 Dihedral : 14.343 86.249 4688 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.66 % Allowed : 1.32 % Favored : 98.03 % 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: 1.28 (0.20), residues: 1624 helix: 0.73 (0.19), residues: 704 sheet: 0.72 (0.23), residues: 248 loop : 1.33 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP G 197 HIS 0.004 0.001 HIS G 79 PHE 0.018 0.002 PHE E 78 TYR 0.006 0.002 TYR M 17 ARG 0.009 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 249 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 241 time to evaluate : 1.623 Fit side-chains REVERT: A 51 ASP cc_start: 0.7822 (m-30) cc_final: 0.7490 (m-30) REVERT: A 119 LYS cc_start: 0.8624 (tttm) cc_final: 0.8314 (tttp) REVERT: C 119 LYS cc_start: 0.8704 (tttm) cc_final: 0.8405 (tttp) REVERT: I 51 ASP cc_start: 0.7900 (m-30) cc_final: 0.7616 (m-30) REVERT: K 51 ASP cc_start: 0.7863 (m-30) cc_final: 0.7541 (m-30) REVERT: K 119 LYS cc_start: 0.8611 (tttm) cc_final: 0.8295 (tttp) REVERT: K 138 ASP cc_start: 0.8546 (t0) cc_final: 0.8340 (t0) REVERT: O 119 LYS cc_start: 0.8787 (tttm) cc_final: 0.8481 (tttt) outliers start: 8 outliers final: 0 residues processed: 241 average time/residue: 0.2557 time to fit residues: 89.1436 Evaluate side-chains 193 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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: 9.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN E 8 GLN E 16 ASN G 8 GLN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 8 GLN O 16 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 13024 Z= 0.435 Angle : 0.547 4.640 17776 Z= 0.294 Chirality : 0.049 0.138 2128 Planarity : 0.004 0.030 2200 Dihedral : 10.117 63.863 2040 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.32 % Allowed : 6.74 % Favored : 91.94 % 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 (0.21), residues: 1624 helix: 1.79 (0.20), residues: 704 sheet: 0.86 (0.24), residues: 240 loop : 0.72 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 197 HIS 0.005 0.001 HIS O 79 PHE 0.015 0.002 PHE G 78 TYR 0.008 0.002 TYR I 17 ARG 0.005 0.001 ARG O 189 *********************** 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 212 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 196 time to evaluate : 1.405 Fit side-chains REVERT: A 119 LYS cc_start: 0.8891 (tttm) cc_final: 0.8547 (tttt) REVERT: C 119 LYS cc_start: 0.8945 (tttm) cc_final: 0.8615 (tttt) REVERT: E 17 TYR cc_start: 0.8983 (m-80) cc_final: 0.8723 (m-80) REVERT: I 16 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.8066 (t0) REVERT: K 119 LYS cc_start: 0.8907 (tttm) cc_final: 0.8563 (tttt) REVERT: K 164 ASP cc_start: 0.7058 (m-30) cc_final: 0.6696 (m-30) REVERT: O 115 ARG cc_start: 0.8486 (mtm180) cc_final: 0.8196 (mtm180) REVERT: O 119 LYS cc_start: 0.8902 (tttm) cc_final: 0.8589 (tttt) outliers start: 16 outliers final: 8 residues processed: 204 average time/residue: 0.2452 time to fit residues: 73.1311 Evaluate side-chains 191 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN C 59 GLN E 16 ASN E 59 GLN G 16 ASN G 59 GLN I 16 ASN I 59 GLN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 13024 Z= 0.368 Angle : 0.486 4.568 17776 Z= 0.263 Chirality : 0.047 0.131 2128 Planarity : 0.003 0.030 2200 Dihedral : 10.017 63.849 2040 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.64 % Allowed : 7.98 % Favored : 90.38 % 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: 1.37 (0.21), residues: 1624 helix: 1.62 (0.20), residues: 704 sheet: 0.98 (0.27), residues: 240 loop : 0.23 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 197 HIS 0.004 0.001 HIS M 79 PHE 0.012 0.002 PHE C 78 TYR 0.009 0.001 TYR I 17 ARG 0.003 0.001 ARG G 189 *********************** 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 216 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 1.675 Fit side-chains REVERT: A 119 LYS cc_start: 0.8909 (tttm) cc_final: 0.8602 (tttt) REVERT: C 119 LYS cc_start: 0.8909 (tttm) cc_final: 0.8603 (tttt) REVERT: I 16 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7843 (t0) REVERT: K 119 LYS cc_start: 0.8879 (tttm) cc_final: 0.8563 (tttt) REVERT: O 17 TYR cc_start: 0.8919 (m-80) cc_final: 0.8618 (m-80) REVERT: O 119 LYS cc_start: 0.8910 (tttm) cc_final: 0.8603 (tttt) outliers start: 20 outliers final: 11 residues processed: 205 average time/residue: 0.2301 time to fit residues: 69.8738 Evaluate side-chains 195 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 183 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 59 GLN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN K 59 GLN M 16 ASN M 59 GLN O 16 ASN O 59 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13024 Z= 0.232 Angle : 0.420 4.547 17776 Z= 0.229 Chirality : 0.044 0.126 2128 Planarity : 0.003 0.027 2200 Dihedral : 9.900 63.805 2040 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.32 % Allowed : 8.31 % Favored : 90.38 % 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: 1.67 (0.20), residues: 704 sheet: 1.26 (0.29), residues: 240 loop : 0.03 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP O 197 HIS 0.003 0.001 HIS A 79 PHE 0.010 0.001 PHE K 78 TYR 0.008 0.001 TYR I 17 ARG 0.002 0.000 ARG I 175 *********************** 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 222 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 1.569 Fit side-chains REVERT: A 119 LYS cc_start: 0.8920 (tttm) cc_final: 0.8606 (tttt) REVERT: C 119 LYS cc_start: 0.8922 (tttm) cc_final: 0.8610 (tttt) REVERT: O 119 LYS cc_start: 0.8923 (tttm) cc_final: 0.8610 (tttt) outliers start: 16 outliers final: 8 residues processed: 214 average time/residue: 0.2161 time to fit residues: 69.0472 Evaluate side-chains 197 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 13024 Z= 0.182 Angle : 0.393 4.574 17776 Z= 0.215 Chirality : 0.043 0.128 2128 Planarity : 0.003 0.026 2200 Dihedral : 9.809 63.787 2040 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.48 % Allowed : 9.62 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.21), residues: 1624 helix: 1.76 (0.20), residues: 704 sheet: 1.61 (0.29), residues: 240 loop : -0.09 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP O 197 HIS 0.002 0.001 HIS G 79 PHE 0.009 0.001 PHE K 78 TYR 0.003 0.001 TYR C 158 ARG 0.001 0.000 ARG I 175 *********************** 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 230 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 212 time to evaluate : 1.590 Fit side-chains REVERT: E 51 ASP cc_start: 0.7820 (m-30) cc_final: 0.7605 (m-30) REVERT: I 16 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8074 (t0) outliers start: 18 outliers final: 9 residues processed: 221 average time/residue: 0.2617 time to fit residues: 82.4691 Evaluate side-chains 197 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 13024 Z= 0.348 Angle : 0.461 4.625 17776 Z= 0.247 Chirality : 0.046 0.132 2128 Planarity : 0.003 0.029 2200 Dihedral : 9.963 63.848 2040 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.81 % Allowed : 10.20 % Favored : 87.99 % 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: 1.19 (0.21), residues: 1624 helix: 1.58 (0.20), residues: 704 sheet: 1.52 (0.29), residues: 240 loop : -0.28 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 197 HIS 0.004 0.001 HIS K 79 PHE 0.011 0.002 PHE K 78 TYR 0.005 0.001 TYR E 17 ARG 0.002 0.001 ARG C 189 *********************** 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 228 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 1.456 Fit side-chains REVERT: C 119 LYS cc_start: 0.8887 (tttm) cc_final: 0.8593 (tttt) REVERT: I 16 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7965 (t0) outliers start: 22 outliers final: 14 residues processed: 214 average time/residue: 0.2327 time to fit residues: 73.8989 Evaluate side-chains 203 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 13024 Z= 0.187 Angle : 0.404 4.524 17776 Z= 0.219 Chirality : 0.043 0.122 2128 Planarity : 0.003 0.027 2200 Dihedral : 9.816 63.796 2040 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.32 % Allowed : 11.76 % Favored : 86.92 % 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: 1.29 (0.21), residues: 1624 helix: 1.64 (0.20), residues: 712 sheet: 1.61 (0.29), residues: 240 loop : -0.24 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP I 197 HIS 0.003 0.001 HIS A 79 PHE 0.009 0.001 PHE A 78 TYR 0.003 0.001 TYR I 17 ARG 0.001 0.000 ARG M 189 *********************** 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 211 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 1.447 Fit side-chains REVERT: A 17 TYR cc_start: 0.9099 (m-80) cc_final: 0.8824 (m-80) REVERT: I 16 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7845 (t0) outliers start: 16 outliers final: 8 residues processed: 203 average time/residue: 0.2293 time to fit residues: 68.8115 Evaluate side-chains 201 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 13024 Z= 0.265 Angle : 0.429 4.586 17776 Z= 0.232 Chirality : 0.045 0.124 2128 Planarity : 0.003 0.028 2200 Dihedral : 9.878 63.819 2040 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.48 % Allowed : 12.25 % Favored : 86.27 % 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: 1.10 (0.21), residues: 1624 helix: 1.58 (0.20), residues: 704 sheet: 1.52 (0.29), residues: 240 loop : -0.45 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 197 HIS 0.003 0.001 HIS A 79 PHE 0.011 0.001 PHE M 78 TYR 0.003 0.001 TYR E 158 ARG 0.002 0.000 ARG C 189 *********************** 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 215 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 1.652 Fit side-chains REVERT: A 17 TYR cc_start: 0.9037 (m-80) cc_final: 0.8818 (m-80) REVERT: I 16 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7678 (t0) outliers start: 18 outliers final: 10 residues processed: 205 average time/residue: 0.2298 time to fit residues: 70.1319 Evaluate side-chains 202 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 135 optimal weight: 0.0970 chunk 94 optimal weight: 10.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 13024 Z= 0.402 Angle : 0.483 4.630 17776 Z= 0.259 Chirality : 0.047 0.130 2128 Planarity : 0.003 0.030 2200 Dihedral : 10.004 63.867 2040 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.81 % Allowed : 12.42 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1624 helix: 1.43 (0.20), residues: 704 sheet: 1.21 (0.28), residues: 240 loop : -0.60 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 139 HIS 0.004 0.001 HIS K 79 PHE 0.012 0.002 PHE K 78 TYR 0.006 0.001 TYR I 17 ARG 0.003 0.001 ARG G 169 *********************** 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 206 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 1.468 Fit side-chains REVERT: I 16 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7808 (t0) outliers start: 22 outliers final: 13 residues processed: 193 average time/residue: 0.2366 time to fit residues: 68.1298 Evaluate side-chains 198 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 13024 Z= 0.182 Angle : 0.403 4.983 17776 Z= 0.219 Chirality : 0.043 0.120 2128 Planarity : 0.003 0.027 2200 Dihedral : 9.798 63.791 2040 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.40 % Allowed : 12.83 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1624 helix: 1.49 (0.20), residues: 720 sheet: 1.50 (0.29), residues: 240 loop : -0.50 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 197 HIS 0.002 0.001 HIS A 79 PHE 0.009 0.001 PHE K 78 TYR 0.003 0.001 TYR G 158 ARG 0.001 0.000 ARG M 37 ********************** 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 224 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 207 time to evaluate : 1.561 Fit side-chains REVERT: I 16 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7867 (t0) outliers start: 17 outliers final: 9 residues processed: 215 average time/residue: 0.2597 time to fit residues: 79.8654 Evaluate side-chains 207 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.0270 chunk 38 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 127 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.088162 restraints weight = 16203.359| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.72 r_work: 0.2785 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 13024 Z= 0.104 Angle : 0.376 4.642 17776 Z= 0.206 Chirality : 0.042 0.117 2128 Planarity : 0.002 0.025 2200 Dihedral : 9.698 63.753 2040 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.74 % Allowed : 13.49 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.21), residues: 1624 helix: 1.78 (0.20), residues: 712 sheet: 1.89 (0.31), residues: 240 loop : -0.48 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP O 197 HIS 0.002 0.000 HIS A 79 PHE 0.008 0.001 PHE M 78 TYR 0.007 0.001 TYR I 17 ARG 0.001 0.000 ARG C 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2461.74 seconds wall clock time: 45 minutes 28.17 seconds (2728.17 seconds total)