Starting phenix.real_space_refine on Tue Mar 19 01:52:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/03_2024/7mqd_23943.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/03_2024/7mqd_23943.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/7mqd_23943/03_2024/7mqd_23943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/03_2024/7mqd_23943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/03_2024/7mqd_23943.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/03_2024/7mqd_23943.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= 0.001 sd= 0.016 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 10912 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 7632 2.51 5 N 2176 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E ASP 193": "OD1" <-> "OD2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 155": "OD1" <-> "OD2" Residue "I ASP 164": "OD1" <-> "OD2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K ASP 164": "OD1" <-> "OD2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K ASP 193": "OD1" <-> "OD2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 155": "OD1" <-> "OD2" Residue "M ASP 164": "OD1" <-> "OD2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M ASP 193": "OD1" <-> "OD2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 155": "OD1" <-> "OD2" Residue "O ASP 164": "OD1" <-> "OD2" Residue "O GLU 167": "OE1" <-> "OE2" Residue "O ASP 193": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11960 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "C" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "E" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "G" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "I" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "K" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "M" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "N" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "O" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "P" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Time building chain proxies: 6.51, per 1000 atoms: 0.54 Number of scatterers: 11960 At special positions: 0 Unit cell: (105.4, 105.4, 85.56, 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 2088 8.00 N 2176 7.00 C 7632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 2.2 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 46.7% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.911A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.501A pdb=" N ASP A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 175 through 196 Proline residue: A 187 - end of helix Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 80 through 93 removed outlier: 3.912A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.911A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.501A 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: 3.912A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.501A 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: 3.911A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.501A pdb=" N ASP I 155 " --> pdb=" O TYR I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'I' and resid 175 through 196 Proline residue: I 187 - end of helix Processing helix chain 'K' and resid 62 through 71 Processing helix chain 'K' and resid 80 through 93 removed outlier: 3.912A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.501A 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: 3.912A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.501A pdb=" N ASP M 155 " --> pdb=" O TYR M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 173 Processing helix chain 'M' and resid 175 through 196 Proline residue: M 187 - end of helix Processing helix chain 'O' and resid 62 through 71 Processing helix chain 'O' and resid 80 through 93 removed outlier: 3.911A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.501A 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: 6.181A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU A 27 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL A 41 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP A 25 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU A 43 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.181A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU C 27 " --> pdb=" O CYS C 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL C 41 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 43 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.180A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU E 27 " --> pdb=" O CYS E 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL E 41 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP E 25 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU E 43 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.180A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.181A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU I 27 " --> pdb=" O CYS I 39 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL I 41 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP I 25 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU I 43 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 6.649A 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: 6.181A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU K 27 " --> pdb=" O CYS K 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL K 41 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP K 25 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU K 43 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.181A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU M 27 " --> pdb=" O CYS M 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL M 41 " --> pdb=" O ASP M 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP M 25 " --> pdb=" O VAL M 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU M 43 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.181A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU O 27 " --> pdb=" O CYS O 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL O 41 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP O 25 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU O 43 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA O 23 " --> pdb=" O LEU O 43 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1659 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: 2.96 Time building geometry restraints manager: 4.55 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: 3841 1.34 - 1.45: 1632 1.45 - 1.57: 6655 1.57 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 12216 Sorted by residual: bond pdb=" N VAL A 156 " pdb=" CA VAL A 156 " ideal model delta sigma weight residual 1.456 1.463 -0.007 1.08e-02 8.57e+03 4.43e-01 bond pdb=" N VAL M 156 " pdb=" CA VAL M 156 " ideal model delta sigma weight residual 1.456 1.463 -0.007 1.08e-02 8.57e+03 4.28e-01 bond pdb=" CB VAL I 40 " pdb=" CG1 VAL I 40 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.13e-01 bond pdb=" CB VAL C 40 " pdb=" CG1 VAL C 40 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.02e-01 bond pdb=" C ARG M 161 " pdb=" O ARG M 161 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.17e-02 7.31e+03 3.94e-01 ... (remaining 12211 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.23: 481 107.23 - 113.93: 7055 113.93 - 120.63: 4916 120.63 - 127.33: 4092 127.33 - 134.03: 168 Bond angle restraints: 16712 Sorted by residual: angle pdb=" CA GLN A 42 " pdb=" CB GLN A 42 " pdb=" CG GLN A 42 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.01e+00 angle pdb=" CA GLN C 42 " pdb=" CB GLN C 42 " pdb=" CG GLN C 42 " ideal model delta sigma weight residual 114.10 119.75 -5.65 2.00e+00 2.50e-01 7.99e+00 angle pdb=" CA GLN M 42 " pdb=" CB GLN M 42 " pdb=" CG GLN M 42 " ideal model delta sigma weight residual 114.10 119.73 -5.63 2.00e+00 2.50e-01 7.92e+00 angle pdb=" CA GLN I 42 " pdb=" CB GLN I 42 " pdb=" CG GLN I 42 " ideal model delta sigma weight residual 114.10 119.72 -5.62 2.00e+00 2.50e-01 7.89e+00 angle pdb=" CA GLN O 42 " pdb=" CB GLN O 42 " pdb=" CG GLN O 42 " ideal model delta sigma weight residual 114.10 119.71 -5.61 2.00e+00 2.50e-01 7.88e+00 ... (remaining 16707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6754 17.83 - 35.66: 318 35.66 - 53.49: 80 53.49 - 71.32: 64 71.32 - 89.15: 16 Dihedral angle restraints: 7232 sinusoidal: 2600 harmonic: 4632 Sorted by residual: 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 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE C 78 " pdb=" C PHE C 78 " pdb=" N HIS C 79 " pdb=" CA HIS C 79 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE G 78 " pdb=" C PHE G 78 " pdb=" N HIS G 79 " pdb=" CA HIS G 79 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1071 0.028 - 0.056: 526 0.056 - 0.083: 256 0.083 - 0.111: 131 0.111 - 0.139: 64 Chirality restraints: 2048 Sorted by residual: chirality pdb=" CA ILE G 4 " pdb=" N ILE G 4 " pdb=" C ILE G 4 " pdb=" CB ILE G 4 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE M 4 " pdb=" N ILE M 4 " pdb=" C ILE M 4 " pdb=" CB ILE M 4 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE I 4 " pdb=" N ILE I 4 " pdb=" C ILE I 4 " pdb=" CB ILE I 4 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 2045 not shown) Planarity restraints: 2048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 83 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.76e+00 pdb=" C PHE G 83 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE G 83 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP G 84 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 83 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C PHE E 83 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE E 83 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP E 84 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE O 83 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C PHE O 83 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE O 83 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP O 84 " -0.008 2.00e-02 2.50e+03 ... (remaining 2045 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.94: 5116 2.94 - 3.43: 11286 3.43 - 3.92: 19745 3.92 - 4.41: 23107 4.41 - 4.90: 37981 Nonbonded interactions: 97235 Sorted by model distance: nonbonded pdb=" O HIS G 205 " pdb=" NZ LYS O 103 " model vdw 2.456 2.520 nonbonded pdb=" NZ LYS E 103 " pdb=" O HIS I 205 " model vdw 2.490 2.520 nonbonded pdb=" OG1 THR G 26 " pdb=" OD1 ASP G 84 " model vdw 2.499 2.440 nonbonded pdb=" OG1 THR C 26 " pdb=" OD1 ASP C 84 " model vdw 2.499 2.440 nonbonded pdb=" OG1 THR I 26 " pdb=" OD1 ASP I 84 " model vdw 2.499 2.440 ... (remaining 97230 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: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 1.260 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 31.560 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.003 0.021 12216 Z= 0.209 Angle : 0.617 5.660 16712 Z= 0.372 Chirality : 0.046 0.139 2048 Planarity : 0.004 0.026 2048 Dihedral : 14.589 89.151 4208 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 1.04 (0.21), residues: 1560 helix: 0.79 (0.19), residues: 704 sheet: 0.50 (0.22), residues: 240 loop : 0.94 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 197 HIS 0.002 0.001 HIS E 116 PHE 0.013 0.002 PHE K 78 TYR 0.005 0.001 TYR M 17 ARG 0.009 0.002 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.042 Fit side-chains REVERT: A 137 SER cc_start: 0.8402 (t) cc_final: 0.8122 (p) REVERT: A 146 ARG cc_start: 0.7689 (tpt170) cc_final: 0.7413 (tpp-160) REVERT: C 146 ARG cc_start: 0.7610 (tpt170) cc_final: 0.7176 (tpp-160) REVERT: E 146 ARG cc_start: 0.7698 (tpt170) cc_final: 0.7277 (tpp-160) REVERT: G 146 ARG cc_start: 0.7808 (tpt170) cc_final: 0.7471 (tpp-160) REVERT: I 146 ARG cc_start: 0.7775 (tpt170) cc_final: 0.7423 (tpp-160) REVERT: K 137 SER cc_start: 0.8430 (t) cc_final: 0.8148 (p) REVERT: M 146 ARG cc_start: 0.7579 (tpt170) cc_final: 0.7288 (tpp-160) REVERT: O 146 ARG cc_start: 0.7612 (tpt170) cc_final: 0.7170 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2450 time to fit residues: 49.1775 Evaluate side-chains 137 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 61 optimal weight: 10.0000 chunk 119 optimal weight: 0.4980 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 54 GLN K 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12216 Z= 0.325 Angle : 0.517 4.675 16712 Z= 0.273 Chirality : 0.046 0.131 2048 Planarity : 0.004 0.030 2048 Dihedral : 11.203 63.815 1968 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.76 % Allowed : 0.57 % Favored : 98.67 % 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 (0.22), residues: 1560 helix: 1.78 (0.20), residues: 704 sheet: 0.94 (0.26), residues: 240 loop : 0.92 (0.29), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 197 HIS 0.004 0.001 HIS K 116 PHE 0.017 0.002 PHE A 78 TYR 0.010 0.002 TYR G 17 ARG 0.003 0.001 ARG G 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.388 Fit side-chains REVERT: C 27 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7765 (mm-30) REVERT: G 27 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7751 (mm-30) REVERT: O 27 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7764 (mm-30) outliers start: 8 outliers final: 8 residues processed: 134 average time/residue: 0.2448 time to fit residues: 47.8112 Evaluate side-chains 131 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain O residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12216 Z= 0.409 Angle : 0.534 4.585 16712 Z= 0.280 Chirality : 0.047 0.130 2048 Planarity : 0.004 0.034 2048 Dihedral : 11.280 63.762 1968 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.85 % Allowed : 2.46 % Favored : 96.69 % 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: 1.38 (0.22), residues: 1560 helix: 1.27 (0.20), residues: 704 sheet: 1.38 (0.29), residues: 240 loop : 0.46 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 197 HIS 0.004 0.001 HIS M 116 PHE 0.012 0.002 PHE K 78 TYR 0.013 0.002 TYR O 17 ARG 0.003 0.001 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.325 Fit side-chains REVERT: G 146 ARG cc_start: 0.8084 (tpt-90) cc_final: 0.7430 (tpp-160) REVERT: K 146 ARG cc_start: 0.7542 (tpp-160) cc_final: 0.7280 (tpp-160) REVERT: O 146 ARG cc_start: 0.8060 (tpt-90) cc_final: 0.7375 (tpp-160) outliers start: 9 outliers final: 0 residues processed: 121 average time/residue: 0.2459 time to fit residues: 43.3086 Evaluate side-chains 120 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 12216 Z= 0.141 Angle : 0.394 4.449 16712 Z= 0.214 Chirality : 0.042 0.120 2048 Planarity : 0.003 0.029 2048 Dihedral : 11.054 63.852 1968 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.22), residues: 1560 helix: 1.61 (0.20), residues: 704 sheet: 1.59 (0.29), residues: 240 loop : 0.54 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 139 HIS 0.001 0.000 HIS O 116 PHE 0.012 0.001 PHE K 78 TYR 0.005 0.001 TYR K 17 ARG 0.001 0.000 ARG O 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.399 Fit side-chains REVERT: I 27 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7679 (mm-30) REVERT: M 27 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7580 (mm-30) REVERT: O 27 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7636 (mm-30) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1716 time to fit residues: 33.4119 Evaluate side-chains 112 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 12216 Z= 0.462 Angle : 0.544 4.587 16712 Z= 0.284 Chirality : 0.047 0.131 2048 Planarity : 0.004 0.035 2048 Dihedral : 11.232 63.748 1968 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % 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: 1.25 (0.21), residues: 1560 helix: 1.13 (0.20), residues: 704 sheet: 1.50 (0.29), residues: 240 loop : 0.35 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 197 HIS 0.004 0.001 HIS A 116 PHE 0.010 0.002 PHE M 78 TYR 0.015 0.002 TYR K 17 ARG 0.002 0.001 ARG M 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2435 time to fit residues: 42.1981 Evaluate side-chains 119 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12216 Z= 0.192 Angle : 0.412 4.409 16712 Z= 0.223 Chirality : 0.043 0.122 2048 Planarity : 0.003 0.031 2048 Dihedral : 11.128 63.778 1968 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.19 % Allowed : 3.79 % Favored : 96.02 % 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: 1.58 (0.22), residues: 1560 helix: 1.40 (0.20), residues: 704 sheet: 1.81 (0.29), residues: 240 loop : 0.47 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 139 HIS 0.002 0.000 HIS A 116 PHE 0.011 0.001 PHE M 78 TYR 0.007 0.001 TYR I 17 ARG 0.001 0.000 ARG M 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.382 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 114 average time/residue: 0.1887 time to fit residues: 34.2358 Evaluate side-chains 112 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 12216 Z= 0.445 Angle : 0.531 4.583 16712 Z= 0.278 Chirality : 0.047 0.129 2048 Planarity : 0.004 0.035 2048 Dihedral : 11.239 63.743 1968 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.85 % Allowed : 3.60 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.21), residues: 1560 helix: 1.05 (0.19), residues: 704 sheet: 1.57 (0.30), residues: 240 loop : 0.26 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 197 HIS 0.004 0.001 HIS I 116 PHE 0.010 0.002 PHE I 78 TYR 0.015 0.002 TYR K 17 ARG 0.002 0.001 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.282 Fit side-chains REVERT: A 146 ARG cc_start: 0.8054 (tpt170) cc_final: 0.7334 (tpp-160) REVERT: E 146 ARG cc_start: 0.8059 (tpt170) cc_final: 0.7498 (tpp-160) REVERT: I 146 ARG cc_start: 0.8054 (tpt170) cc_final: 0.7336 (tpp-160) REVERT: M 146 ARG cc_start: 0.7888 (tpt-90) cc_final: 0.7267 (tpp-160) outliers start: 9 outliers final: 5 residues processed: 127 average time/residue: 0.2279 time to fit residues: 42.8070 Evaluate side-chains 123 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain K residue 42 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12216 Z= 0.208 Angle : 0.419 4.426 16712 Z= 0.226 Chirality : 0.043 0.123 2048 Planarity : 0.003 0.032 2048 Dihedral : 11.160 63.781 1968 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.76 % Allowed : 3.88 % Favored : 95.36 % 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: 1.52 (0.22), residues: 1560 helix: 1.33 (0.20), residues: 704 sheet: 1.77 (0.30), residues: 240 loop : 0.45 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 139 HIS 0.002 0.000 HIS K 116 PHE 0.011 0.001 PHE C 78 TYR 0.008 0.001 TYR K 17 ARG 0.001 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.305 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 115 average time/residue: 0.1795 time to fit residues: 33.3928 Evaluate side-chains 110 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain O residue 42 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 7.9990 chunk 136 optimal weight: 0.0070 chunk 140 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 0.3980 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 overall best weight: 2.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12216 Z= 0.218 Angle : 0.421 4.444 16712 Z= 0.226 Chirality : 0.043 0.128 2048 Planarity : 0.003 0.032 2048 Dihedral : 11.138 63.773 1968 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.76 % Allowed : 3.88 % Favored : 95.36 % 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: 1.54 (0.22), residues: 1560 helix: 1.37 (0.20), residues: 704 sheet: 1.82 (0.30), residues: 240 loop : 0.41 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 139 HIS 0.002 0.000 HIS I 116 PHE 0.010 0.001 PHE O 78 TYR 0.008 0.001 TYR K 17 ARG 0.001 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.393 Fit side-chains REVERT: C 146 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7489 (tpp-160) outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 0.1931 time to fit residues: 35.0957 Evaluate side-chains 111 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain O residue 42 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12216 Z= 0.241 Angle : 0.432 4.468 16712 Z= 0.231 Chirality : 0.044 0.123 2048 Planarity : 0.003 0.032 2048 Dihedral : 11.134 63.760 1968 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.95 % Allowed : 3.69 % Favored : 95.36 % 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: 1.50 (0.22), residues: 1560 helix: 1.34 (0.20), residues: 704 sheet: 1.86 (0.30), residues: 240 loop : 0.36 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 139 HIS 0.002 0.001 HIS E 116 PHE 0.011 0.001 PHE M 78 TYR 0.008 0.001 TYR K 17 ARG 0.001 0.000 ARG G 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.294 Fit side-chains REVERT: C 146 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7447 (tpp-160) REVERT: M 42 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8078 (mp10) outliers start: 10 outliers final: 6 residues processed: 116 average time/residue: 0.1864 time to fit residues: 34.6437 Evaluate side-chains 114 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain O residue 42 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.123234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.103698 restraints weight = 13672.610| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.49 r_work: 0.2980 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 12216 Z= 0.117 Angle : 0.370 4.394 16712 Z= 0.203 Chirality : 0.042 0.119 2048 Planarity : 0.003 0.030 2048 Dihedral : 10.996 63.790 1968 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Rotamer: Outliers : 0.85 % Allowed : 3.79 % Favored : 95.36 % 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: 1.82 (0.22), residues: 1560 helix: 1.61 (0.20), residues: 704 sheet: 2.10 (0.30), residues: 240 loop : 0.49 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 139 HIS 0.001 0.000 HIS K 116 PHE 0.011 0.001 PHE C 78 TYR 0.005 0.001 TYR C 151 ARG 0.001 0.000 ARG C 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1927.38 seconds wall clock time: 35 minutes 46.30 seconds (2146.30 seconds total)