Starting phenix.real_space_refine on Thu Feb 22 07:47:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/02_2024/7bog_12242_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/02_2024/7bog_12242.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/02_2024/7bog_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_12242/02_2024/7bog_12242_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/02_2024/7bog_12242_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/02_2024/7bog_12242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/02_2024/7bog_12242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/02_2024/7bog_12242_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bog_12242/02_2024/7bog_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-dev-5238/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: 18.08, per 1000 atoms: 0.54 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: 18.22 Conformation dependent library (CDL) restraints added in 2.6 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: 19.79 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: 30.54 Time building geometry restraints manager: 19.07 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: 20520 35.58 - 71.16: 2502 71.16 - 106.73: 282 106.73 - 142.31: 2 142.31 - 177.89: 5 Dihedral angle restraints: 23311 sinusoidal: 19478 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 23308 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: 4.930 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: 0.030 Extract box with map and model: 15.520 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 119.320 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.120 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:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.080 ------------------------------------------------------------------------------- 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 : 22.777 177.889 20837 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 170 HIS 0.012 0.001 HIS R 74 PHE 0.016 0.001 PHE F 8 TYR 0.011 0.001 TYR Q 34 ARG 0.008 0.000 ARG H 77 *********************** 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 : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 149 SER cc_start: 0.9047 (p) cc_final: 0.8543 (p) REVERT: F 68 GLN cc_start: 0.8602 (mt0) cc_final: 0.8347 (mt0) REVERT: F 72 ASP cc_start: 0.7809 (p0) cc_final: 0.7341 (p0) REVERT: F 97 THR cc_start: 0.7994 (p) cc_final: 0.7381 (p) REVERT: K 27 PHE cc_start: 0.8968 (m-80) cc_final: 0.8666 (m-80) REVERT: K 40 ASN cc_start: 0.9010 (m-40) cc_final: 0.7876 (m110) REVERT: K 68 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8207 (mm-30) REVERT: K 85 MET cc_start: 0.8328 (mtm) cc_final: 0.8017 (mtm) REVERT: L 47 SER cc_start: 0.8695 (t) cc_final: 0.8468 (t) REVERT: L 112 GLN cc_start: 0.9018 (mt0) cc_final: 0.8752 (mt0) REVERT: O 21 ASP cc_start: 0.8576 (t0) cc_final: 0.8307 (t0) REVERT: O 47 LYS cc_start: 0.8587 (ptpp) cc_final: 0.8331 (pttt) REVERT: R 25 ASP cc_start: 0.8636 (t0) cc_final: 0.8372 (t70) REVERT: R 43 ARG cc_start: 0.8641 (ttt-90) cc_final: 0.7840 (ttt-90) REVERT: V 17 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8817 (mtpp) REVERT: V 49 TYR cc_start: 0.8117 (m-80) cc_final: 0.7675 (m-80) REVERT: V 51 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8398 (mtpp) outliers start: 0 outliers final: 1 residues processed: 441 average time/residue: 1.6130 time to fit residues: 834.9917 Evaluate side-chains 383 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 382 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 GLU 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: 10.0000 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: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 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: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 36386 Z= 0.245 Angle : 0.576 13.284 54452 Z= 0.311 Chirality : 0.035 0.353 6939 Planarity : 0.005 0.125 2921 Dihedral : 23.226 178.667 18213 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.82 % Allowed : 17.29 % Favored : 78.89 % 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: -0.76 (0.23), residues: 1309 helix: 0.61 (0.22), residues: 489 sheet: -1.49 (0.31), residues: 245 loop : -0.92 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 42 HIS 0.006 0.001 HIS K 118 PHE 0.015 0.001 PHE F 8 TYR 0.010 0.001 TYR D 65 ARG 0.008 0.001 ARG R 73 *********************** 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 446 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 404 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 65 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7683 (mm-30) REVERT: F 14 GLN cc_start: 0.8633 (mp10) cc_final: 0.8301 (mp10) REVERT: F 24 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7799 (ptp-110) REVERT: F 68 GLN cc_start: 0.8530 (mt0) cc_final: 0.8210 (mt0) REVERT: F 72 ASP cc_start: 0.7738 (p0) cc_final: 0.7486 (p0) REVERT: H 60 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7888 (tm-30) REVERT: K 27 PHE cc_start: 0.8879 (m-80) cc_final: 0.8545 (m-80) REVERT: K 85 MET cc_start: 0.8315 (mtm) cc_final: 0.8001 (mtm) REVERT: L 47 SER cc_start: 0.8890 (t) cc_final: 0.8659 (t) REVERT: O 21 ASP cc_start: 0.8525 (t0) cc_final: 0.8170 (t0) REVERT: O 47 LYS cc_start: 0.8547 (ptpp) cc_final: 0.8314 (pttt) REVERT: Q 40 ARG cc_start: 0.8897 (mmp-170) cc_final: 0.8671 (mmp-170) REVERT: Q 77 ARG cc_start: 0.8273 (ptm-80) cc_final: 0.8056 (ptm-80) REVERT: R 25 ASP cc_start: 0.8661 (t0) cc_final: 0.8437 (t70) REVERT: R 38 LYS cc_start: 0.9103 (ptmt) cc_final: 0.8886 (ptmm) REVERT: V 17 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8715 (mtpp) REVERT: V 49 TYR cc_start: 0.8292 (m-80) cc_final: 0.7871 (m-80) outliers start: 42 outliers final: 21 residues processed: 415 average time/residue: 1.6495 time to fit residues: 803.6412 Evaluate side-chains 401 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 379 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 43 MET Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 229 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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: 0.8925 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 36386 Z= 0.426 Angle : 0.632 12.074 54452 Z= 0.335 Chirality : 0.039 0.338 6939 Planarity : 0.006 0.127 2921 Dihedral : 23.142 179.133 18210 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.64 % Allowed : 18.74 % Favored : 75.61 % 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: -0.48 (0.23), residues: 1309 helix: 0.76 (0.23), residues: 500 sheet: -1.18 (0.33), residues: 229 loop : -0.80 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 42 HIS 0.005 0.001 HIS K 118 PHE 0.017 0.002 PHE K 61 TYR 0.012 0.002 TYR Q 34 ARG 0.009 0.001 ARG O 88 *********************** 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 442 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 380 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: F 22 ILE cc_start: 0.9168 (mt) cc_final: 0.8948 (mp) REVERT: F 68 GLN cc_start: 0.8562 (mt0) cc_final: 0.8283 (mt0) REVERT: F 72 ASP cc_start: 0.7779 (p0) cc_final: 0.7536 (p0) REVERT: F 96 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8350 (p) REVERT: F 97 THR cc_start: 0.7906 (p) cc_final: 0.7549 (p) REVERT: H 60 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7951 (tm-30) REVERT: L 43 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8506 (mttp) REVERT: L 94 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8207 (mtp85) REVERT: O 21 ASP cc_start: 0.8567 (t0) cc_final: 0.8264 (t0) REVERT: O 47 LYS cc_start: 0.8617 (ptpp) cc_final: 0.8390 (pttt) REVERT: Q 40 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7933 (mmp-170) REVERT: R 25 ASP cc_start: 0.8656 (t0) cc_final: 0.8445 (t70) REVERT: R 38 LYS cc_start: 0.9134 (ptmt) cc_final: 0.8847 (ptmm) REVERT: V 31 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6410 (mtt-85) REVERT: V 49 TYR cc_start: 0.8496 (m-80) cc_final: 0.7993 (m-80) REVERT: V 51 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8294 (mtpt) outliers start: 62 outliers final: 35 residues processed: 399 average time/residue: 1.6346 time to fit residues: 763.8612 Evaluate side-chains 407 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 365 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 47 LEU Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 4.9990 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: 6.9990 chunk 213 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 36386 Z= 0.334 Angle : 0.598 12.079 54452 Z= 0.320 Chirality : 0.037 0.328 6939 Planarity : 0.005 0.124 2921 Dihedral : 23.121 179.229 18210 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 6.19 % Allowed : 20.11 % Favored : 73.70 % 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: -0.24 (0.23), residues: 1309 helix: 0.97 (0.23), residues: 500 sheet: -1.04 (0.33), residues: 235 loop : -0.69 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 42 HIS 0.005 0.001 HIS K 118 PHE 0.014 0.001 PHE F 8 TYR 0.011 0.001 TYR Q 34 ARG 0.012 0.001 ARG V 88 *********************** 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 444 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 376 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: F 24 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7880 (ptp-110) REVERT: F 68 GLN cc_start: 0.8522 (mt0) cc_final: 0.8204 (mt0) REVERT: F 72 ASP cc_start: 0.7747 (p0) cc_final: 0.7450 (p0) REVERT: F 96 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8483 (p) REVERT: H 60 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7878 (tm-30) REVERT: K 94 GLU cc_start: 0.8633 (tp30) cc_final: 0.8321 (tp30) REVERT: L 94 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8247 (mtp85) REVERT: O 21 ASP cc_start: 0.8552 (t0) cc_final: 0.8267 (t0) REVERT: O 47 LYS cc_start: 0.8591 (ptpp) cc_final: 0.8385 (pttt) REVERT: Q 40 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.7913 (mmp-170) REVERT: Q 77 ARG cc_start: 0.8239 (ptm-80) cc_final: 0.7992 (ptm-80) REVERT: R 38 LYS cc_start: 0.9125 (ptmt) cc_final: 0.8836 (ptmm) REVERT: V 31 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6348 (mtt-85) REVERT: V 49 TYR cc_start: 0.8481 (m-80) cc_final: 0.8000 (m-80) REVERT: V 51 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8570 (mtpt) outliers start: 68 outliers final: 36 residues processed: 401 average time/residue: 1.5966 time to fit residues: 752.2513 Evaluate side-chains 406 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 364 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 69 ILE Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 F 46 GLN H 38 ASN L 73 ASN O 80 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: 0.8942 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 36386 Z= 0.542 Angle : 0.696 12.483 54452 Z= 0.365 Chirality : 0.043 0.331 6939 Planarity : 0.006 0.125 2921 Dihedral : 23.107 179.407 18210 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 6.28 % Allowed : 21.75 % Favored : 71.97 % 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: -0.30 (0.23), residues: 1309 helix: 0.84 (0.23), residues: 506 sheet: -0.97 (0.33), residues: 234 loop : -0.72 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 42 HIS 0.005 0.001 HIS K 118 PHE 0.020 0.002 PHE K 61 TYR 0.013 0.002 TYR R 51 ARG 0.010 0.001 ARG V 88 *********************** 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 427 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 358 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: F 24 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7923 (ptp-110) REVERT: F 68 GLN cc_start: 0.8619 (mt0) cc_final: 0.8226 (mt0) REVERT: F 96 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8499 (p) REVERT: H 60 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7921 (tm-30) REVERT: K 79 ILE cc_start: 0.8438 (mp) cc_final: 0.7912 (tp) REVERT: L 94 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8183 (mtp85) REVERT: O 21 ASP cc_start: 0.8541 (t0) cc_final: 0.8270 (t0) REVERT: Q 40 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7931 (mmp-170) REVERT: Q 77 ARG cc_start: 0.8264 (ptm-80) cc_final: 0.8042 (ptm-80) REVERT: R 38 LYS cc_start: 0.9169 (ptmt) cc_final: 0.8891 (ptmm) REVERT: V 31 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6542 (mtt-85) REVERT: V 36 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9120 (p) REVERT: V 49 TYR cc_start: 0.8559 (m-80) cc_final: 0.8064 (m-80) outliers start: 69 outliers final: 39 residues processed: 379 average time/residue: 1.6686 time to fit residues: 740.4281 Evaluate side-chains 401 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 355 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 69 ILE Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 F 68 GLN H 38 ASN K 101 ASN K 109 ASN L 73 ASN O 35 GLN O 80 GLN Q 9 GLN R 54 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 36386 Z= 0.209 Angle : 0.593 12.054 54452 Z= 0.318 Chirality : 0.034 0.315 6939 Planarity : 0.005 0.122 2921 Dihedral : 23.184 179.456 18210 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.46 % Allowed : 24.11 % Favored : 71.43 % 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: -0.05 (0.23), residues: 1309 helix: 1.09 (0.23), residues: 503 sheet: -0.95 (0.33), residues: 237 loop : -0.55 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 42 HIS 0.005 0.001 HIS K 118 PHE 0.014 0.001 PHE F 8 TYR 0.011 0.001 TYR D 4 ARG 0.013 0.001 ARG Q 11 *********************** 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 421 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 372 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: F 24 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7798 (ptp-170) REVERT: F 68 GLN cc_start: 0.8476 (mt0) cc_final: 0.8223 (mt0) REVERT: F 96 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8466 (p) REVERT: H 52 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7264 (mt-10) REVERT: H 60 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7855 (tm-30) REVERT: K 79 ILE cc_start: 0.8429 (mp) cc_final: 0.7904 (tp) REVERT: K 94 GLU cc_start: 0.8620 (tp30) cc_final: 0.8363 (tp30) REVERT: L 94 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8399 (mtp85) REVERT: O 21 ASP cc_start: 0.8528 (t0) cc_final: 0.8247 (t0) REVERT: Q 77 ARG cc_start: 0.8250 (ptm-80) cc_final: 0.7996 (ptm-80) REVERT: R 30 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8933 (mtpt) REVERT: R 38 LYS cc_start: 0.9101 (ptmt) cc_final: 0.8816 (ptmm) REVERT: V 17 LYS cc_start: 0.9000 (mtpm) cc_final: 0.8756 (mtpp) REVERT: V 31 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6313 (mtt180) REVERT: V 49 TYR cc_start: 0.8497 (m-80) cc_final: 0.8013 (m-80) REVERT: V 51 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8352 (mtpt) outliers start: 49 outliers final: 26 residues processed: 390 average time/residue: 1.5894 time to fit residues: 729.2142 Evaluate side-chains 392 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 360 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 225 optimal weight: 0.2980 chunk 141 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 H 38 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: 0.8849 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 36386 Z= 0.153 Angle : 0.564 13.602 54452 Z= 0.304 Chirality : 0.032 0.303 6939 Planarity : 0.005 0.120 2921 Dihedral : 23.133 179.119 18210 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.55 % Allowed : 25.57 % Favored : 69.88 % 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: 0.11 (0.24), residues: 1309 helix: 1.23 (0.24), residues: 498 sheet: -0.82 (0.33), residues: 243 loop : -0.46 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 42 HIS 0.004 0.001 HIS K 118 PHE 0.029 0.002 PHE K 61 TYR 0.008 0.001 TYR D 4 ARG 0.028 0.001 ARG V 88 *********************** 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 430 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 380 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: F 24 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7902 (ptp-110) REVERT: F 68 GLN cc_start: 0.8431 (mt0) cc_final: 0.8091 (mt0) REVERT: F 96 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8450 (p) REVERT: H 52 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7256 (mt-10) REVERT: K 79 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7912 (tp) REVERT: K 94 GLU cc_start: 0.8568 (tp30) cc_final: 0.8234 (tp30) REVERT: L 94 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8379 (mtp85) REVERT: O 21 ASP cc_start: 0.8479 (t0) cc_final: 0.8199 (t0) REVERT: R 30 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8896 (mtpt) REVERT: V 31 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6234 (mtt180) REVERT: V 49 TYR cc_start: 0.8436 (m-80) cc_final: 0.7918 (m-80) REVERT: V 51 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8074 (mtpt) REVERT: V 96 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8479 (p) REVERT: V 98 PHE cc_start: 0.8265 (m-10) cc_final: 0.7850 (m-10) outliers start: 50 outliers final: 28 residues processed: 391 average time/residue: 1.6326 time to fit residues: 750.0674 Evaluate side-chains 402 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 366 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 96 THR 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: 7.9990 chunk 143 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 177 optimal weight: 0.5980 chunk 205 optimal weight: 0.7980 overall best weight: 4.2786 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 36386 Z= 0.432 Angle : 0.653 12.424 54452 Z= 0.345 Chirality : 0.039 0.305 6939 Planarity : 0.006 0.122 2921 Dihedral : 23.049 179.182 18210 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.19 % Allowed : 25.75 % Favored : 69.06 % 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: 0.04 (0.24), residues: 1309 helix: 1.11 (0.23), residues: 501 sheet: -0.80 (0.33), residues: 238 loop : -0.47 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 42 HIS 0.005 0.001 HIS K 118 PHE 0.013 0.002 PHE O 43 TYR 0.013 0.002 TYR Q 34 ARG 0.013 0.001 ARG Q 11 *********************** 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 419 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 362 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 24 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7842 (ptp-110) REVERT: F 68 GLN cc_start: 0.8462 (mt0) cc_final: 0.8198 (mt0) REVERT: F 72 ASP cc_start: 0.7681 (p0) cc_final: 0.7472 (p0) REVERT: F 96 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8498 (p) REVERT: K 79 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7882 (tp) REVERT: K 94 GLU cc_start: 0.8600 (tp30) cc_final: 0.8238 (tp30) REVERT: L 94 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8233 (mtp85) REVERT: O 21 ASP cc_start: 0.8529 (t0) cc_final: 0.8260 (t0) REVERT: O 77 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.8073 (ttp-110) REVERT: Q 11 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7586 (mtp85) REVERT: R 38 LYS cc_start: 0.9102 (ptmt) cc_final: 0.8901 (ptmm) REVERT: V 17 LYS cc_start: 0.9003 (mtpm) cc_final: 0.8693 (mtpp) REVERT: V 31 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6353 (mtt-85) REVERT: V 49 TYR cc_start: 0.8515 (m-80) cc_final: 0.8094 (m-80) REVERT: V 51 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8400 (mtpt) outliers start: 57 outliers final: 37 residues processed: 374 average time/residue: 1.6358 time to fit residues: 717.0021 Evaluate side-chains 399 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 357 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 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 164 GLN 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: 0.8882 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36386 Z= 0.184 Angle : 0.593 12.151 54452 Z= 0.318 Chirality : 0.034 0.300 6939 Planarity : 0.006 0.121 2921 Dihedral : 23.140 178.962 18210 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.00 % Allowed : 26.84 % Favored : 69.15 % 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: 0.12 (0.24), residues: 1309 helix: 1.22 (0.24), residues: 494 sheet: -0.76 (0.33), residues: 238 loop : -0.44 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 42 HIS 0.005 0.001 HIS K 118 PHE 0.035 0.002 PHE K 61 TYR 0.011 0.001 TYR O 78 ARG 0.014 0.001 ARG F 79 *********************** 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 408 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 364 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 65 GLU cc_start: 0.8361 (tt0) cc_final: 0.7458 (tp30) REVERT: F 68 GLN cc_start: 0.8413 (mt0) cc_final: 0.8121 (mt0) REVERT: K 79 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.7907 (tp) REVERT: K 94 GLU cc_start: 0.8551 (tp30) cc_final: 0.8178 (tp30) REVERT: L 94 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8199 (mtp85) REVERT: O 21 ASP cc_start: 0.8519 (t0) cc_final: 0.8242 (t0) REVERT: Q 11 ARG cc_start: 0.7827 (mtp-110) cc_final: 0.7488 (mtp85) REVERT: V 17 LYS cc_start: 0.8984 (mtpm) cc_final: 0.8669 (mtpp) REVERT: V 31 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6229 (mtt180) REVERT: V 49 TYR cc_start: 0.8475 (m-80) cc_final: 0.8050 (m-80) REVERT: V 51 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8225 (mtpt) outliers start: 44 outliers final: 31 residues processed: 373 average time/residue: 1.6355 time to fit residues: 715.0172 Evaluate side-chains 393 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 359 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 43 MET Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 154 optimal weight: 0.7980 chunk 233 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 113 optimal weight: 0.0970 chunk 147 optimal weight: 1.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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: 0.8873 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 36386 Z= 0.200 Angle : 0.596 12.269 54452 Z= 0.319 Chirality : 0.033 0.294 6939 Planarity : 0.006 0.120 2921 Dihedral : 23.086 178.897 18210 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.55 % Allowed : 27.75 % Favored : 68.70 % 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: 0.20 (0.24), residues: 1309 helix: 1.33 (0.24), residues: 496 sheet: -0.75 (0.34), residues: 239 loop : -0.45 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 42 HIS 0.004 0.001 HIS K 118 PHE 0.022 0.001 PHE V 98 TYR 0.010 0.001 TYR Q 34 ARG 0.013 0.001 ARG F 79 ********************** 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 400 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 361 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 65 GLU cc_start: 0.8380 (tt0) cc_final: 0.7510 (tp30) REVERT: F 68 GLN cc_start: 0.8432 (mt0) cc_final: 0.7979 (mt0) REVERT: K 79 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7869 (tp) REVERT: K 94 GLU cc_start: 0.8554 (tp30) cc_final: 0.8183 (tp30) REVERT: L 94 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8399 (mtp85) REVERT: O 21 ASP cc_start: 0.8509 (t0) cc_final: 0.8230 (t0) REVERT: Q 11 ARG cc_start: 0.7815 (mtp-110) cc_final: 0.7480 (mtp85) REVERT: V 17 LYS cc_start: 0.8978 (mtpm) cc_final: 0.8666 (mtpp) REVERT: V 31 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6222 (mtt180) REVERT: V 49 TYR cc_start: 0.8468 (m-80) cc_final: 0.7989 (m-80) REVERT: V 51 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8476 (mtpt) REVERT: V 98 PHE cc_start: 0.8340 (m-10) cc_final: 0.8066 (m-10) outliers start: 39 outliers final: 30 residues processed: 369 average time/residue: 1.6129 time to fit residues: 698.9034 Evaluate side-chains 390 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 357 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 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: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.066255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.044395 restraints weight = 84498.124| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 1.34 r_work: 0.2444 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2342 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 36386 Z= 0.507 Angle : 0.701 13.468 54452 Z= 0.368 Chirality : 0.042 0.310 6939 Planarity : 0.006 0.123 2921 Dihedral : 23.036 178.831 18210 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.73 % Allowed : 28.03 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1309 helix: 1.06 (0.23), residues: 502 sheet: -0.79 (0.33), residues: 242 loop : -0.48 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 42 HIS 0.005 0.001 HIS K 118 PHE 0.028 0.002 PHE K 61 TYR 0.012 0.002 TYR R 51 ARG 0.014 0.001 ARG F 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11671.11 seconds wall clock time: 208 minutes 26.02 seconds (12506.02 seconds total)