Starting phenix.real_space_refine (version: 1.21rc1) on Tue Aug 22 14:55:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/08_2023/7bog_12242_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/08_2023/7bog_12242.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/08_2023/7bog_12242_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/08_2023/7bog_12242_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/08_2023/7bog_12242_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/08_2023/7bog_12242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/08_2023/7bog_12242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/08_2023/7bog_12242_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/08_2023/7bog_12242_updated.pdb" } resolution = 2.75 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= -0.000 sd= 0.003 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1071 5.49 5 Mg 105 5.21 5 S 45 5.16 5 C 16807 2.51 5 N 6235 2.21 5 O 9326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 57": "OE1" <-> "OE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 9": "OD1" <-> "OD2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 52": "OE1" <-> "OE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 100": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 33589 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 23015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 23015 Classifications: {'RNA': 1071} Modifications used: {'rna2p': 1, 'rna2p_pur': 74, 'rna2p_pyr': 53, 'rna3p': 6, 'rna3p_pur': 541, 'rna3p_pyr': 396} Link IDs: {'rna2p': 128, 'rna3p': 942} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "V" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Unusual residues: {' MG': 103} Classifications: {'undetermined': 103} Link IDs: {None: 102} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.58, per 1000 atoms: 0.49 Number of scatterers: 33589 At special positions: 0 Unit cell: (186.9, 150.15, 175.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 45 16.00 P 1071 15.00 Mg 105 11.99 O 9326 8.00 N 6235 7.00 C 16807 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: 17.05 Conformation dependent library (CDL) restraints added in 1.9 seconds 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 12 sheets defined 36.5% alpha, 18.6% beta 363 base pairs and 637 stacking pairs defined. Time for finding SS restraints: 19.26 Creating SS restraints... Processing helix chain 'D' and resid 9 through 14 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 153 through 164 removed outlier: 4.961A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.549A pdb=" N SER D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.577A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 Processing helix chain 'E' and resid 150 through 157 Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'F' and resid 12 through 14 No H-bonds generated for 'chain 'F' and resid 12 through 14' Processing helix chain 'F' and resid 18 through 31 Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 101 through 104 No H-bonds generated for 'chain 'F' and resid 101 through 104' Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 43 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 96 through 98 No H-bonds generated for 'chain 'H' and resid 96 through 98' Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 56 through 58 No H-bonds generated for 'chain 'K' and resid 56 through 58' Processing helix chain 'K' and resid 60 through 73 removed outlier: 3.703A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 77 No H-bonds generated for 'chain 'K' and resid 75 through 77' Processing helix chain 'K' and resid 94 through 101 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 116 No H-bonds generated for 'chain 'L' and resid 114 through 116' Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 removed outlier: 4.059A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 Processing helix chain 'O' and resid 75 through 84 Processing helix chain 'P' and resid 54 through 63 removed outlier: 3.591A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 80 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 26 through 32 removed outlier: 4.177A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'T' and resid 5 through 41 removed outlier: 3.789A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 63 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 86 removed outlier: 3.525A pdb=" N LYS T 85 " --> pdb=" O ALA T 81 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU T 86 " --> pdb=" O GLN T 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 24 Processing helix chain 'V' and resid 62 through 87 removed outlier: 3.914A pdb=" N ALA V 67 " --> pdb=" O ASP V 63 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLY V 77 " --> pdb=" O GLN V 73 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE V 78 " --> pdb=" O GLU V 74 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 123 through 125 removed outlier: 3.835A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 46 through 53 removed outlier: 6.518A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'F' and resid 84 through 92 removed outlier: 7.009A pdb=" N MET F 9 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER F 87 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL F 7 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL F 89 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU F 5 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG F 91 " --> pdb=" O HIS F 3 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N HIS F 3 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 24 through 28 Processing sheet with id= F, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.815A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 106 through 112 removed outlier: 7.771A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE K 110 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL K 86 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP K 112 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY K 19 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N MET K 85 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA K 21 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LYS K 87 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE K 23 " --> pdb=" O LYS K 87 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY K 43 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASP K 36 " --> pdb=" O ALA K 41 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA K 41 " --> pdb=" O ASP K 36 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.843A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'P' and resid 2 through 11 removed outlier: 3.673A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'Q' and resid 7 through 11 removed outlier: 9.267A pdb=" N SER Q 72 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N HIS Q 45 " --> pdb=" O SER Q 72 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N THR Q 74 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N HIS Q 47 " --> pdb=" O THR Q 74 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA Q 24 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL Q 12 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLU Q 26 " --> pdb=" O GLY Q 10 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY Q 10 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.508A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'V' and resid 94 through 99 removed outlier: 3.817A pdb=" N GLY V 40 " --> pdb=" O TYR V 53 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR V 55 " --> pdb=" O VAL V 38 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL V 38 " --> pdb=" O THR V 55 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 903 hydrogen bonds 1406 hydrogen bond angles 0 basepair planarities 363 basepair parallelities 637 stacking parallelities Total time for adding SS restraints: 28.36 Time building geometry restraints manager: 18.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5879 1.33 - 1.45: 14797 1.45 - 1.58: 13493 1.58 - 1.70: 2138 1.70 - 1.82: 79 Bond restraints: 36386 Sorted by residual: bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.462 1.309 0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.348 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C2 5MC A1407 " pdb=" N3 5MC A1407 " ideal model delta sigma weight residual 1.493 1.352 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" N3 G7M A 527 " pdb=" C4 G7M A 527 " ideal model delta sigma weight residual 1.492 1.358 0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C2 2MG A1516 " pdb=" N2 2MG A1516 " ideal model delta sigma weight residual 1.475 1.346 0.129 2.00e-02 2.50e+03 4.17e+01 ... (remaining 36381 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.97: 4927 104.97 - 112.91: 22179 112.91 - 120.85: 16770 120.85 - 128.78: 9424 128.78 - 136.72: 1152 Bond angle restraints: 54452 Sorted by residual: angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 129.31 -34.35 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C4 G7M A 527 " ideal model delta sigma weight residual 142.80 125.22 17.58 3.00e+00 1.11e-01 3.44e+01 angle pdb=" N LYS P 46 " pdb=" CA LYS P 46 " pdb=" C LYS P 46 " ideal model delta sigma weight residual 113.17 106.03 7.14 1.26e+00 6.30e-01 3.21e+01 angle pdb=" C4' G7M A 527 " pdb=" C3' G7M A 527 " pdb=" C2' G7M A 527 " ideal model delta sigma weight residual 102.60 97.03 5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" C1' 2MG A1516 " pdb=" N9 2MG A1516 " pdb=" C8 2MG A1516 " ideal model delta sigma weight residual 110.07 126.41 -16.34 3.00e+00 1.11e-01 2.97e+01 ... (remaining 54447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 18749 35.58 - 71.16: 598 71.16 - 106.73: 44 106.73 - 142.31: 2 142.31 - 177.89: 5 Dihedral angle restraints: 19398 sinusoidal: 15565 harmonic: 3833 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 52.20 147.80 1 1.50e+01 4.44e-03 7.88e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 63.93 136.07 1 1.50e+01 4.44e-03 7.34e+01 dihedral pdb=" O4' U A 85 " pdb=" C1' U A 85 " pdb=" N1 U A 85 " pdb=" C2 U A 85 " ideal model delta sinusoidal sigma weight residual 232.00 54.11 177.89 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 19395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 6065 0.048 - 0.096: 664 0.096 - 0.145: 137 0.145 - 0.193: 62 0.193 - 0.241: 11 Chirality restraints: 6939 Sorted by residual: chirality pdb=" C3' A A1534 " pdb=" C4' A A1534 " pdb=" O3' A A1534 " pdb=" C2' A A1534 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE P 42 " pdb=" N ILE P 42 " pdb=" C ILE P 42 " pdb=" CB ILE P 42 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3' C A 841 " pdb=" C4' C A 841 " pdb=" O3' C A 841 " pdb=" C2' C A 841 " both_signs ideal model delta sigma weight residual False -2.48 -2.70 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 6936 not shown) Planarity restraints: 2921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " 0.045 2.00e-02 2.50e+03 5.77e-01 7.50e+03 pdb=" C4' 5MC A1407 " 0.434 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " 0.604 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " -0.597 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " -0.194 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " 0.940 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " 0.232 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " -0.873 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.025 2.00e-02 2.50e+03 5.47e-01 6.74e+03 pdb=" C4' 2MG A1516 " 0.423 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.577 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.587 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.530 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.218 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.886 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.242 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.818 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " 0.131 2.00e-02 2.50e+03 2.15e-01 4.63e+02 pdb=" N6 MA6 A1519 " -0.373 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " 0.122 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " 0.120 2.00e-02 2.50e+03 ... (remaining 2918 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 215 2.53 - 3.12: 23499 3.12 - 3.71: 65316 3.71 - 4.31: 96419 4.31 - 4.90: 126336 Nonbonded interactions: 311785 Sorted by model distance: nonbonded pdb=" O4 U A 180 " pdb="MG MG A1643 " model vdw 1.937 2.170 nonbonded pdb=" OP2 G A 760 " pdb="MG MG A1660 " model vdw 1.971 2.170 nonbonded pdb=" OP1 G A 450 " pdb="MG MG A1637 " model vdw 1.974 2.170 nonbonded pdb=" OP2 A A 441 " pdb="MG MG A1626 " model vdw 1.993 2.170 nonbonded pdb=" O6 G A 299 " pdb="MG MG A1619 " model vdw 2.005 2.170 ... (remaining 311780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 16.310 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 112.150 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.153 36386 Z= 0.400 Angle : 0.619 34.351 54452 Z= 0.343 Chirality : 0.037 0.241 6939 Planarity : 0.016 0.577 2921 Dihedral : 13.915 177.889 16924 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: -1.93 (0.21), residues: 1309 helix: -0.64 (0.20), residues: 502 sheet: -1.89 (0.31), residues: 226 loop : -1.47 (0.25), residues: 581 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 441 average time/residue: 1.6719 time to fit residues: 865.3220 Evaluate side-chains 378 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.9086 time to fit residues: 4.0703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN D 41 HIS D 54 GLN D 126 ASN D 152 GLN D 164 GLN E 12 GLN E 83 HIS E 122 ASN E 135 ASN E 146 ASN E 148 ASN F 3 HIS F 17 GLN F 37 HIS K 15 GLN K 28 ASN K 40 ASN K 109 ASN L 112 GLN O 28 GLN O 35 GLN O 46 HIS P 18 GLN P 29 ASN P 40 ASN Q 9 GLN R 54 GLN T 70 ASN T 84 ASN V 58 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 36386 Z= 0.238 Angle : 0.568 13.317 54452 Z= 0.307 Chirality : 0.034 0.335 6939 Planarity : 0.005 0.128 2921 Dihedral : 13.480 178.844 14297 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 4.19 % 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: -0.78 (0.23), residues: 1309 helix: 0.59 (0.22), residues: 489 sheet: -1.50 (0.31), residues: 245 loop : -0.92 (0.26), residues: 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 401 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 23 residues processed: 412 average time/residue: 1.6976 time to fit residues: 819.1697 Evaluate side-chains 399 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 376 time to evaluate : 1.957 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 5 residues processed: 18 average time/residue: 0.6101 time to fit residues: 18.0457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 146 ASN H 38 ASN H 76 GLN K 101 ASN K 109 ASN L 73 ASN O 35 GLN P 26 ASN Q 9 GLN R 54 GLN V 16 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.053 36386 Z= 0.482 Angle : 0.656 12.026 54452 Z= 0.347 Chirality : 0.041 0.340 6939 Planarity : 0.006 0.127 2921 Dihedral : 13.593 178.576 14297 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 5.28 % 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: -0.53 (0.23), residues: 1309 helix: 0.71 (0.23), residues: 499 sheet: -1.18 (0.33), residues: 229 loop : -0.85 (0.26), residues: 581 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 375 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 35 residues processed: 398 average time/residue: 1.6552 time to fit residues: 773.1176 Evaluate side-chains 401 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 366 time to evaluate : 1.936 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 14 residues processed: 21 average time/residue: 0.5091 time to fit residues: 18.5814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 ASN D 164 GLN E 146 ASN H 38 ASN K 101 ASN K 109 ASN L 73 ASN Q 9 GLN R 54 GLN V 16 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 36386 Z= 0.261 Angle : 0.589 12.068 54452 Z= 0.317 Chirality : 0.035 0.323 6939 Planarity : 0.005 0.125 2921 Dihedral : 13.548 178.938 14297 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 5.55 % 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: -0.20 (0.23), residues: 1309 helix: 1.04 (0.23), residues: 492 sheet: -1.03 (0.33), residues: 235 loop : -0.68 (0.26), residues: 582 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 382 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 31 residues processed: 405 average time/residue: 1.6218 time to fit residues: 773.2744 Evaluate side-chains 399 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 368 time to evaluate : 1.976 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 14 residues processed: 19 average time/residue: 0.5324 time to fit residues: 17.5794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 193 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN F 46 GLN H 38 ASN L 73 ASN O 35 GLN Q 9 GLN R 54 GLN V 16 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.086 36386 Z= 0.445 Angle : 0.648 12.106 54452 Z= 0.344 Chirality : 0.040 0.329 6939 Planarity : 0.006 0.125 2921 Dihedral : 13.572 179.075 14297 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 6.19 % 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: -0.17 (0.23), residues: 1309 helix: 1.04 (0.23), residues: 499 sheet: -0.98 (0.33), residues: 235 loop : -0.67 (0.26), residues: 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 369 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 41 residues processed: 388 average time/residue: 1.6843 time to fit residues: 766.0989 Evaluate side-chains 404 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 363 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 13 residues processed: 30 average time/residue: 0.6646 time to fit residues: 30.8349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 ASN D 164 GLN E 146 ASN H 38 ASN K 101 ASN L 73 ASN O 35 GLN O 80 GLN Q 9 GLN R 54 GLN V 16 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 36386 Z= 0.355 Angle : 0.614 12.246 54452 Z= 0.330 Chirality : 0.037 0.322 6939 Planarity : 0.005 0.123 2921 Dihedral : 13.530 179.273 14297 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 5.37 % 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: -0.09 (0.24), residues: 1309 helix: 1.06 (0.23), residues: 504 sheet: -0.89 (0.33), residues: 235 loop : -0.60 (0.27), residues: 570 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 367 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 36 residues processed: 389 average time/residue: 1.6619 time to fit residues: 761.1108 Evaluate side-chains 397 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 361 time to evaluate : 2.047 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 14 residues processed: 24 average time/residue: 0.6988 time to fit residues: 25.7779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 126 optimal weight: 0.0870 chunk 225 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 ASN D 164 GLN E 146 ASN H 38 ASN K 101 ASN L 73 ASN O 35 GLN O 80 GLN Q 9 GLN R 31 ASN R 54 GLN V 16 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 36386 Z= 0.171 Angle : 0.585 12.559 54452 Z= 0.316 Chirality : 0.033 0.304 6939 Planarity : 0.006 0.122 2921 Dihedral : 13.535 179.076 14297 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 4.09 % 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: 0.03 (0.24), residues: 1309 helix: 1.11 (0.23), residues: 504 sheet: -0.78 (0.33), residues: 235 loop : -0.52 (0.27), residues: 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 377 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 25 residues processed: 393 average time/residue: 1.6511 time to fit residues: 764.8550 Evaluate side-chains 389 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 364 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 13 residues processed: 13 average time/residue: 0.7535 time to fit residues: 15.7201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 GLN E 97 GLN E 146 ASN H 38 ASN K 101 ASN L 73 ASN O 35 GLN O 80 GLN Q 9 GLN R 31 ASN R 54 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.097 36386 Z= 0.466 Angle : 0.665 12.523 54452 Z= 0.354 Chirality : 0.040 0.325 6939 Planarity : 0.006 0.123 2921 Dihedral : 13.535 179.263 14297 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 4.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1309 helix: 1.00 (0.23), residues: 505 sheet: -0.86 (0.33), residues: 239 loop : -0.50 (0.27), residues: 565 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 364 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 37 residues processed: 381 average time/residue: 1.6826 time to fit residues: 750.8380 Evaluate side-chains 394 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 357 time to evaluate : 2.042 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 13 residues processed: 26 average time/residue: 0.5760 time to fit residues: 24.6542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 GLN E 97 GLN E 146 ASN H 38 ASN K 40 ASN K 101 ASN L 73 ASN O 35 GLN O 80 GLN Q 9 GLN R 31 ASN R 54 GLN V 16 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 36386 Z= 0.171 Angle : 0.617 12.880 54452 Z= 0.330 Chirality : 0.033 0.300 6939 Planarity : 0.006 0.122 2921 Dihedral : 13.562 179.060 14297 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 2.64 % 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: 0.06 (0.24), residues: 1309 helix: 1.11 (0.23), residues: 503 sheet: -0.80 (0.33), residues: 239 loop : -0.45 (0.27), residues: 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 372 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 385 average time/residue: 1.7038 time to fit residues: 770.3802 Evaluate side-chains 384 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 365 time to evaluate : 1.926 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 12 residues processed: 9 average time/residue: 0.7850 time to fit residues: 11.6296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 214 optimal weight: 0.4980 chunk 185 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 143 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 GLN H 38 ASN K 40 ASN K 101 ASN K 109 ASN L 73 ASN O 35 GLN O 80 GLN Q 9 GLN R 31 ASN R 54 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 36386 Z= 0.191 Angle : 0.590 13.414 54452 Z= 0.318 Chirality : 0.033 0.300 6939 Planarity : 0.006 0.120 2921 Dihedral : 13.449 179.116 14297 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1309 helix: 1.21 (0.24), residues: 497 sheet: -0.72 (0.34), residues: 239 loop : -0.37 (0.27), residues: 573 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 368 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 380 average time/residue: 1.7014 time to fit residues: 758.6684 Evaluate side-chains 374 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 363 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.3287 time to fit residues: 3.9535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 171 optimal weight: 0.0060 chunk 27 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 GLN H 38 ASN K 40 ASN K 101 ASN L 73 ASN O 80 GLN Q 9 GLN R 31 ASN R 54 GLN V 13 GLN V 16 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.067153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.045394 restraints weight = 84079.964| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 1.22 r_work: 0.2473 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 36386 Z= 0.377 Angle : 0.639 12.097 54452 Z= 0.341 Chirality : 0.038 0.306 6939 Planarity : 0.006 0.122 2921 Dihedral : 13.441 179.029 14297 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 2.18 % 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: 0.16 (0.24), residues: 1309 helix: 1.16 (0.24), residues: 503 sheet: -0.66 (0.33), residues: 237 loop : -0.40 (0.27), residues: 569 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11766.64 seconds wall clock time: 210 minutes 31.67 seconds (12631.67 seconds total)