Starting phenix.real_space_refine (version: dev) on Sun May 15 04:45:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqf_23945/05_2022/7mqf_23945.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqf_23945/05_2022/7mqf_23945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqf_23945/05_2022/7mqf_23945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqf_23945/05_2022/7mqf_23945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqf_23945/05_2022/7mqf_23945.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqf_23945/05_2022/7mqf_23945.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C ASP 201": "OD1" <-> "OD2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E ASP 201": "OD1" <-> "OD2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G ASP 201": "OD1" <-> "OD2" Residue "I PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 124": "OE1" <-> "OE2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I ASP 201": "OD1" <-> "OD2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 124": "OE1" <-> "OE2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K ASP 201": "OD1" <-> "OD2" Residue "M PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M ASP 201": "OD1" <-> "OD2" Residue "O PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "O GLU 167": "OE1" <-> "OE2" Residue "O ASP 201": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 12288 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1490 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 73 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: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1490 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 73 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: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1490 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 73 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: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1490 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 73 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: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1490 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 73 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: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1490 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 73 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: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1490 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 73 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: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1490 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 73 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: 7.46, per 1000 atoms: 0.61 Number of scatterers: 12288 At special positions: 0 Unit cell: (104.78, 104.78, 86.18, 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 2176 8.00 N 2248 7.00 C 7800 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: 4.92 Conformation dependent library (CDL) restraints added in 2.1 seconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 46.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.993A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.587A 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: 3.624A 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: 3.995A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 145 through 155 removed outlier: 3.624A pdb=" N ASP C 155 " --> pdb=" O TYR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 173 Processing helix chain 'C' and resid 175 through 196 Proline residue: C 187 - end of helix Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.994A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.623A 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: 3.994A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.623A 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: 3.994A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.623A 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: 3.994A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.623A 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: 3.994A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.623A 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: 3.994A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.623A 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: 6.236A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 22 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 22 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.235A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL E 22 " --> pdb=" O ILE E 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL G 22 " --> pdb=" O ILE G 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL I 22 " --> pdb=" O ILE I 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL K 22 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL M 22 " --> pdb=" O ILE M 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL O 22 " --> pdb=" O ILE O 77 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 5.22 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: 4053 1.34 - 1.46: 1823 1.46 - 1.57: 6580 1.57 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 12544 Sorted by residual: bond pdb=" CG LYS A 103 " pdb=" CD LYS A 103 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 bond pdb=" CG LYS M 103 " pdb=" CD LYS M 103 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 bond pdb=" CG LYS I 103 " pdb=" CD LYS I 103 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 bond pdb=" CG LYS K 103 " pdb=" CD LYS K 103 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 bond pdb=" CG LYS O 103 " pdb=" CD LYS O 103 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 ... (remaining 12539 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.05: 384 107.05 - 113.79: 7226 113.79 - 120.53: 4939 120.53 - 127.27: 4411 127.27 - 134.02: 184 Bond angle restraints: 17144 Sorted by residual: angle pdb=" CB LYS E 103 " pdb=" CG LYS E 103 " pdb=" CD LYS E 103 " ideal model delta sigma weight residual 111.30 116.93 -5.63 2.30e+00 1.89e-01 5.98e+00 angle pdb=" CB LYS C 103 " pdb=" CG LYS C 103 " pdb=" CD LYS C 103 " ideal model delta sigma weight residual 111.30 116.92 -5.62 2.30e+00 1.89e-01 5.98e+00 angle pdb=" N ARG M 67 " pdb=" CA ARG M 67 " pdb=" CB ARG M 67 " ideal model delta sigma weight residual 110.12 113.71 -3.59 1.47e+00 4.63e-01 5.97e+00 angle pdb=" N ARG A 67 " pdb=" CA ARG A 67 " pdb=" CB ARG A 67 " ideal model delta sigma weight residual 110.12 113.71 -3.59 1.47e+00 4.63e-01 5.97e+00 angle pdb=" CB LYS O 103 " pdb=" CG LYS O 103 " pdb=" CD LYS O 103 " ideal model delta sigma weight residual 111.30 116.90 -5.60 2.30e+00 1.89e-01 5.93e+00 ... (remaining 17139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 6808 15.04 - 30.08: 392 30.08 - 45.12: 104 45.12 - 60.16: 32 60.16 - 75.20: 16 Dihedral angle restraints: 7352 sinusoidal: 2672 harmonic: 4680 Sorted by residual: dihedral pdb=" CA PHE K 78 " pdb=" C PHE K 78 " pdb=" N HIS K 79 " pdb=" CA HIS K 79 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+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 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA PHE M 78 " pdb=" C PHE M 78 " pdb=" N HIS M 79 " pdb=" CA HIS M 79 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 7349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 802 0.028 - 0.056: 625 0.056 - 0.084: 365 0.084 - 0.112: 201 0.112 - 0.140: 87 Chirality restraints: 2080 Sorted by residual: chirality pdb=" CA PRO A 63 " pdb=" N PRO A 63 " pdb=" C PRO A 63 " pdb=" CB PRO A 63 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA PRO C 63 " pdb=" N PRO C 63 " pdb=" C PRO C 63 " pdb=" CB PRO C 63 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA PRO I 63 " pdb=" N PRO I 63 " pdb=" C PRO I 63 " pdb=" CB PRO I 63 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 2077 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE I 83 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C PHE I 83 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE I 83 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP I 84 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 83 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C PHE K 83 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE K 83 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP K 84 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 83 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C PHE C 83 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE C 83 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP C 84 " 0.008 2.00e-02 2.50e+03 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 431 2.72 - 3.26: 11698 3.26 - 3.81: 19601 3.81 - 4.35: 26977 4.35 - 4.90: 44034 Nonbonded interactions: 102741 Sorted by model distance: nonbonded pdb=" NZ LYS G 107 " pdb=" O ALA O 204 " model vdw 2.175 2.520 nonbonded pdb=" O ALA G 204 " pdb=" NZ LYS O 107 " model vdw 2.175 2.520 nonbonded pdb=" NZ LYS E 107 " pdb=" O ALA I 204 " model vdw 2.175 2.520 nonbonded pdb=" NZ LYS A 107 " pdb=" O ALA M 204 " model vdw 2.175 2.520 nonbonded pdb=" O ALA E 204 " pdb=" NZ LYS I 107 " model vdw 2.176 2.520 ... (remaining 102736 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 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 7800 2.51 5 N 2248 2.21 5 O 2176 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 5.820 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.110 Process input model: 35.160 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.030 12544 Z= 0.381 Angle : 0.716 5.625 17144 Z= 0.413 Chirality : 0.055 0.140 2080 Planarity : 0.004 0.025 2120 Dihedral : 11.725 75.197 4296 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.21), residues: 1576 helix: 0.74 (0.19), residues: 704 sheet: 0.56 (0.23), residues: 248 loop : 1.35 (0.28), residues: 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.512 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 1.1280 time to fit residues: 197.4662 Evaluate side-chains 129 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7201 ------------------------------------------------------------------------------- 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: 5.9990 chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 145 optimal weight: 0.0770 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN C 13 ASN E 13 ASN G 13 ASN I 13 ASN K 13 ASN M 13 ASN O 13 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.026 12544 Z= 0.308 Angle : 0.566 4.765 17144 Z= 0.302 Chirality : 0.049 0.153 2080 Planarity : 0.004 0.028 2120 Dihedral : 6.299 34.304 1896 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 0.00 % 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: 1576 helix: 1.75 (0.20), residues: 704 sheet: 0.84 (0.24), residues: 248 loop : 0.73 (0.28), residues: 624 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.307 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 1.0976 time to fit residues: 146.1853 Evaluate side-chains 120 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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: 0.8745 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 12544 Z= 0.157 Angle : 0.438 4.404 17144 Z= 0.240 Chirality : 0.044 0.133 2080 Planarity : 0.003 0.026 2120 Dihedral : 5.884 34.138 1896 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 0.00 % 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: 1.69 (0.21), residues: 1576 helix: 1.85 (0.20), residues: 704 sheet: 0.94 (0.23), residues: 248 loop : 0.49 (0.28), residues: 624 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.422 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.9310 time to fit residues: 141.3646 Evaluate side-chains 136 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 7.9990 chunk 109 optimal weight: 0.0670 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 154 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 13 ASN C 8 GLN C 13 ASN E 8 GLN E 13 ASN G 8 GLN G 13 ASN I 8 GLN I 13 ASN K 8 GLN K 13 ASN M 8 GLN M 13 ASN O 8 GLN O 13 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 12544 Z= 0.223 Angle : 0.477 4.336 17144 Z= 0.256 Chirality : 0.046 0.141 2080 Planarity : 0.003 0.028 2120 Dihedral : 6.036 33.832 1896 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 0.00 % 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 (0.21), residues: 1576 helix: 1.65 (0.19), residues: 704 sheet: 1.10 (0.24), residues: 248 loop : 0.32 (0.29), residues: 624 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.623 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.9852 time to fit residues: 149.3526 Evaluate side-chains 136 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 13 ASN C 13 ASN E 13 ASN G 13 ASN I 13 ASN K 13 ASN M 13 ASN O 13 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 12544 Z= 0.328 Angle : 0.542 5.568 17144 Z= 0.287 Chirality : 0.049 0.152 2080 Planarity : 0.004 0.030 2120 Dihedral : 6.422 35.015 1896 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 0.00 % 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: 1.05 (0.21), residues: 1576 helix: 1.34 (0.19), residues: 704 sheet: 0.93 (0.24), residues: 248 loop : -0.04 (0.28), residues: 624 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.465 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 1.0183 time to fit residues: 144.5244 Evaluate side-chains 128 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 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 8 GLN C 8 GLN E 8 GLN G 8 GLN I 8 GLN K 8 GLN M 8 GLN O 8 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.018 12544 Z= 0.166 Angle : 0.431 4.362 17144 Z= 0.236 Chirality : 0.044 0.133 2080 Planarity : 0.003 0.027 2120 Dihedral : 5.930 33.234 1896 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 0.00 % 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: 1.22 (0.21), residues: 1576 helix: 1.53 (0.19), residues: 704 sheet: 0.99 (0.24), residues: 248 loop : -0.01 (0.28), residues: 624 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.514 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 1.0331 time to fit residues: 147.0592 Evaluate side-chains 128 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN C 8 GLN E 8 GLN G 8 GLN I 8 GLN K 8 GLN M 8 GLN O 8 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 12544 Z= 0.363 Angle : 0.556 5.862 17144 Z= 0.294 Chirality : 0.050 0.155 2080 Planarity : 0.004 0.030 2120 Dihedral : 6.508 36.262 1896 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 0.00 % 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: 0.82 (0.21), residues: 1576 helix: 1.20 (0.19), residues: 704 sheet: 0.77 (0.24), residues: 248 loop : -0.21 (0.27), residues: 624 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.371 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 1.1999 time to fit residues: 177.4110 Evaluate side-chains 135 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN C 8 GLN E 8 GLN G 8 GLN I 8 GLN K 8 GLN M 8 GLN O 8 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 12544 Z= 0.193 Angle : 0.448 4.331 17144 Z= 0.244 Chirality : 0.045 0.136 2080 Planarity : 0.003 0.027 2120 Dihedral : 6.061 34.417 1896 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 0.00 % 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: 0.99 (0.21), residues: 1576 helix: 1.39 (0.19), residues: 704 sheet: 0.77 (0.24), residues: 248 loop : -0.14 (0.28), residues: 624 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.441 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 1.2383 time to fit residues: 183.2131 Evaluate side-chains 135 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN C 8 GLN E 8 GLN G 8 GLN I 8 GLN K 8 GLN M 8 GLN O 8 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 12544 Z= 0.271 Angle : 0.496 4.779 17144 Z= 0.265 Chirality : 0.047 0.145 2080 Planarity : 0.004 0.029 2120 Dihedral : 6.267 35.589 1896 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 0.00 % 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: 0.85 (0.21), residues: 1576 helix: 1.28 (0.19), residues: 704 sheet: 0.65 (0.25), residues: 248 loop : -0.20 (0.28), residues: 624 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.384 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 1.1587 time to fit residues: 171.5370 Evaluate side-chains 135 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN C 8 GLN E 8 GLN G 8 GLN I 8 GLN K 8 GLN M 8 GLN O 8 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.026 12544 Z= 0.302 Angle : 0.516 5.154 17144 Z= 0.275 Chirality : 0.048 0.149 2080 Planarity : 0.004 0.029 2120 Dihedral : 6.454 36.896 1896 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 0.00 % 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: 0.74 (0.21), residues: 1576 helix: 1.20 (0.19), residues: 704 sheet: 0.59 (0.25), residues: 248 loop : -0.26 (0.27), residues: 624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.452 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 1.1577 time to fit residues: 171.8746 Evaluate side-chains 135 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN C 8 GLN E 8 GLN G 8 GLN I 8 GLN K 8 GLN M 8 GLN O 8 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.111207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.095278 restraints weight = 13260.028| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 0.90 r_work: 0.2864 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 1.08 restraints_weight: 0.2500 r_work: 0.2806 rms_B_bonded: 1.46 restraints_weight: 0.1250 r_work: 0.2750 rms_B_bonded: 2.16 restraints_weight: 0.0625 r_work: 0.2656 rms_B_bonded: 3.50 restraints_weight: 0.0312 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 12544 Z= 0.163 Angle : 0.426 4.373 17144 Z= 0.234 Chirality : 0.044 0.132 2080 Planarity : 0.003 0.027 2120 Dihedral : 5.910 34.307 1896 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 0.00 % 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: 1.02 (0.21), residues: 1576 helix: 1.44 (0.19), residues: 704 sheet: 0.67 (0.25), residues: 248 loop : -0.11 (0.28), residues: 624 =============================================================================== Job complete usr+sys time: 3094.15 seconds wall clock time: 56 minutes 20.49 seconds (3380.49 seconds total)