Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 16 17:57:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/10_2023/7bog_12242_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/10_2023/7bog_12242.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/10_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_12242/10_2023/7bog_12242_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/10_2023/7bog_12242_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/10_2023/7bog_12242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/10_2023/7bog_12242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/10_2023/7bog_12242_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/10_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-1.21rc1-5097/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: 16.49, 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: 18.07 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: 19.71 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: 28.82 Time building geometry restraints manager: 18.94 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 15.410 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 113.980 Find NCS groups from input model: 0.630 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.720 ------------------------------------------------------------------------------- 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 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (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 : 2.246 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: 1.7380 time to fit residues: 897.5741 Evaluate side-chains 378 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 1.742 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.9875 time to fit residues: 4.2140 ------------------------------------------------------------------------------- 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: 0.8887 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 36386 Z= 0.240 Angle : 0.570 13.896 54452 Z= 0.308 Chirality : 0.034 0.331 6939 Planarity : 0.005 0.129 2921 Dihedral : 13.475 179.053 14297 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.09 % Allowed : 17.65 % Favored : 78.25 % 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: -0.80 (0.22), residues: 1309 helix: 0.57 (0.22), residues: 490 sheet: -1.51 (0.31), residues: 245 loop : -0.93 (0.26), residues: 574 *********************** 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 445 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 400 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 411 average time/residue: 1.7008 time to fit residues: 819.8588 Evaluate side-chains 392 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 370 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 5 residues processed: 17 average time/residue: 0.6393 time to fit residues: 17.5681 ------------------------------------------------------------------------------- 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: 0.8980 chunk 144 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 211 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 O 35 GLN P 26 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: 0.8929 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 36386 Z= 0.444 Angle : 0.641 12.111 54452 Z= 0.341 Chirality : 0.040 0.337 6939 Planarity : 0.006 0.127 2921 Dihedral : 13.566 178.435 14297 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.37 % Allowed : 19.29 % Favored : 75.34 % 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: -0.46 (0.23), residues: 1309 helix: 0.71 (0.23), residues: 495 sheet: -1.17 (0.33), residues: 229 loop : -0.73 (0.26), residues: 585 *********************** 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 430 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 371 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 36 residues processed: 394 average time/residue: 1.6983 time to fit residues: 785.3795 Evaluate side-chains 394 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 358 time to evaluate : 1.847 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 15 residues processed: 22 average time/residue: 0.5046 time to fit residues: 19.2519 ------------------------------------------------------------------------------- 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: 0.6980 chunk 160 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 226 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 202 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 ASN H 38 ASN K 101 ASN K 109 ASN L 73 ASN O 35 GLN Q 9 GLN R 54 GLN V 16 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 36386 Z= 0.181 Angle : 0.576 12.109 54452 Z= 0.310 Chirality : 0.034 0.319 6939 Planarity : 0.006 0.124 2921 Dihedral : 13.542 178.750 14297 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.10 % Allowed : 20.75 % Favored : 74.16 % 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: -0.22 (0.23), residues: 1309 helix: 0.98 (0.23), residues: 493 sheet: -1.05 (0.33), residues: 237 loop : -0.63 (0.26), residues: 579 *********************** 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 442 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 386 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 28 residues processed: 410 average time/residue: 1.6480 time to fit residues: 795.4051 Evaluate side-chains 400 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 372 time to evaluate : 2.167 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 12 residues processed: 17 average time/residue: 0.4319 time to fit residues: 14.4379 ------------------------------------------------------------------------------- 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: 2.9990 chunk 128 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 ASN H 38 ASN K 101 ASN L 73 ASN O 35 GLN Q 9 GLN R 31 ASN R 54 GLN V 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 36386 Z= 0.430 Angle : 0.637 12.095 54452 Z= 0.339 Chirality : 0.039 0.329 6939 Planarity : 0.006 0.125 2921 Dihedral : 13.527 178.980 14297 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.19 % Allowed : 21.75 % Favored : 72.07 % 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: -0.15 (0.23), residues: 1309 helix: 0.96 (0.23), residues: 501 sheet: -0.93 (0.33), residues: 235 loop : -0.58 (0.26), residues: 573 *********************** 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 434 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 366 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 41 residues processed: 387 average time/residue: 1.6941 time to fit residues: 767.6999 Evaluate side-chains 401 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 360 time to evaluate : 1.863 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 12 residues processed: 30 average time/residue: 0.5907 time to fit residues: 28.1692 ------------------------------------------------------------------------------- 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: 6.9990 chunk 44 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** H 38 ASN K 101 ASN L 73 ASN O 35 GLN O 80 GLN Q 9 GLN R 54 GLN V 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 36386 Z= 0.407 Angle : 0.631 12.411 54452 Z= 0.337 Chirality : 0.039 0.325 6939 Planarity : 0.006 0.123 2921 Dihedral : 13.528 179.443 14297 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.55 % Allowed : 23.75 % Favored : 70.70 % 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: -0.13 (0.23), residues: 1309 helix: 1.01 (0.23), residues: 503 sheet: -0.91 (0.33), residues: 238 loop : -0.60 (0.26), residues: 568 *********************** 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 423 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 362 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 33 residues processed: 380 average time/residue: 1.7338 time to fit residues: 773.3561 Evaluate side-chains 387 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 354 time to evaluate : 1.935 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 12 residues processed: 22 average time/residue: 0.4713 time to fit residues: 18.9837 ------------------------------------------------------------------------------- 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: 4.9990 chunk 25 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 225 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 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 85 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 36386 Z= 0.250 Angle : 0.593 12.066 54452 Z= 0.319 Chirality : 0.035 0.312 6939 Planarity : 0.006 0.122 2921 Dihedral : 13.509 179.222 14297 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.46 % Allowed : 25.57 % Favored : 69.97 % 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: -0.01 (0.23), residues: 1309 helix: 1.13 (0.23), residues: 503 sheet: -0.84 (0.33), residues: 238 loop : -0.57 (0.26), residues: 568 *********************** 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 412 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 363 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 29 residues processed: 380 average time/residue: 1.6812 time to fit residues: 751.1830 Evaluate side-chains 385 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 356 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 12 residues processed: 18 average time/residue: 0.4890 time to fit residues: 15.8414 ------------------------------------------------------------------------------- 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: 7.9990 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 205 optimal weight: 0.2980 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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** 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 36386 Z= 0.399 Angle : 0.637 12.038 54452 Z= 0.340 Chirality : 0.039 0.319 6939 Planarity : 0.006 0.122 2921 Dihedral : 13.494 179.324 14297 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.82 % Allowed : 26.66 % Favored : 69.52 % 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: -0.05 (0.23), residues: 1309 helix: 1.04 (0.23), residues: 500 sheet: -0.81 (0.33), residues: 239 loop : -0.55 (0.26), residues: 570 *********************** 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 407 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 365 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 28 residues processed: 380 average time/residue: 1.7073 time to fit residues: 761.9505 Evaluate side-chains 387 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 359 time to evaluate : 1.860 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 11 residues processed: 17 average time/residue: 0.5075 time to fit residues: 15.5208 ------------------------------------------------------------------------------- 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: 3.9990 chunk 197 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 chunk 126 optimal weight: 0.0670 chunk 91 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 189 optimal weight: 0.0570 chunk 198 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 36386 Z= 0.162 Angle : 0.605 13.512 54452 Z= 0.323 Chirality : 0.033 0.295 6939 Planarity : 0.006 0.120 2921 Dihedral : 13.524 179.110 14297 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.09 % Allowed : 28.12 % Favored : 68.79 % 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 (0.23), residues: 1309 helix: 1.10 (0.23), residues: 503 sheet: -0.76 (0.33), residues: 239 loop : -0.51 (0.26), 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 404 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 370 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 384 average time/residue: 1.6569 time to fit residues: 749.7803 Evaluate side-chains 375 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 358 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 7 average time/residue: 1.2223 time to fit residues: 12.4737 ------------------------------------------------------------------------------- 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: 0.7980 chunk 135 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36386 Z= 0.202 Angle : 0.585 12.200 54452 Z= 0.315 Chirality : 0.033 0.300 6939 Planarity : 0.006 0.120 2921 Dihedral : 13.398 178.935 14297 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.73 % Allowed : 29.85 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.23), residues: 1309 helix: 1.18 (0.24), residues: 496 sheet: -0.72 (0.33), residues: 239 loop : -0.42 (0.26), residues: 574 ********************** 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 383 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 364 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 376 average time/residue: 1.7082 time to fit residues: 754.3088 Evaluate side-chains 373 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 359 time to evaluate : 1.888 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 4 average time/residue: 0.6929 time to fit residues: 5.9527 ------------------------------------------------------------------------------- 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: 0.0980 chunk 27 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.067396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.045612 restraints weight = 84051.561| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 1.20 r_work: 0.2480 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2379 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 36386 Z= 0.357 Angle : 0.630 13.287 54452 Z= 0.336 Chirality : 0.037 0.304 6939 Planarity : 0.006 0.121 2921 Dihedral : 13.409 179.068 14297 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.09 % Allowed : 29.57 % Favored : 68.33 % 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: 1.17 (0.24), residues: 502 sheet: -0.67 (0.33), residues: 237 loop : -0.51 (0.26), residues: 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12057.45 seconds wall clock time: 215 minutes 51.23 seconds (12951.23 seconds total)