Starting phenix.real_space_refine (version: dev) on Wed Dec 14 18:33:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/12_2022/6pc8_20299_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/12_2022/6pc8_20299.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/12_2022/6pc8_20299_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/12_2022/6pc8_20299_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/12_2022/6pc8_20299_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/12_2022/6pc8_20299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/12_2022/6pc8_20299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/12_2022/6pc8_20299_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/12_2022/6pc8_20299_neut_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.015 sd= 1.311 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "K GLU 35": "OE1" <-> "OE2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K ASP 187": "OD1" <-> "OD2" Residue "K ARG 189": "NH1" <-> "NH2" Residue "K GLU 199": "OE1" <-> "OE2" Residue "K ARG 203": "NH1" <-> "NH2" Residue "K ARG 212": "NH1" <-> "NH2" Residue "K ARG 221": "NH1" <-> "NH2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ASP 91": "OD1" <-> "OD2" Residue "L PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ARG 170": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N ASP 131": "OD1" <-> "OD2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "O ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 72169 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 62206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62206 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 7, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 14, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 438, 'rna3p': 2458} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "O" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'O7Y': 1} Classifications: {'undetermined': 1} Time building chain proxies: 30.88, per 1000 atoms: 0.43 Number of scatterers: 72169 At special positions: 0 Unit cell: (229.823, 222.963, 189.804, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 3015 15.00 O 22277 8.00 N 13325 7.00 C 33530 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 34.10 Conformation dependent library (CDL) restraints added in 2.2 seconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 11 sheets defined 18.4% alpha, 12.7% beta 878 base pairs and 1657 stacking pairs defined. Time for finding SS restraints: 36.03 Creating SS restraints... Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'K' and resid 208 through 214 removed outlier: 3.965A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.631A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 92 through 98' Processing helix chain 'L' and resid 129 through 138 removed outlier: 3.717A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 39 removed outlier: 3.621A pdb=" N GLN M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 114 removed outlier: 3.516A pdb=" N ALA M 104 " --> pdb=" O MET M 100 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU M 105 " --> pdb=" O TYR M 101 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER M 110 " --> pdb=" O LYS M 106 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL M 113 " --> pdb=" O LEU M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 140 removed outlier: 3.690A pdb=" N GLN M 136 " --> pdb=" O LYS M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 160 removed outlier: 3.733A pdb=" N LEU M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 removed outlier: 3.787A pdb=" N GLN M 195 " --> pdb=" O ASP M 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 71 removed outlier: 3.780A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 121 through 124 No H-bonds generated for 'chain 'N' and resid 121 through 124' Processing helix chain 'O' and resid 25 through 37 removed outlier: 4.238A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 68 through 71 No H-bonds generated for 'chain 'O' and resid 68 through 71' Processing helix chain 'O' and resid 89 through 108 Proline residue: O 97 - end of helix removed outlier: 4.513A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 121 removed outlier: 3.612A pdb=" N PHE O 119 " --> pdb=" O GLY O 115 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 135 No H-bonds generated for 'chain 'O' and resid 133 through 135' Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'K' and resid 101 through 105 removed outlier: 4.002A pdb=" N ARG K 102 " --> pdb=" O VAL K 94 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 129 through 131 Processing sheet with id= E, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.829A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.130A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR M 150 " --> pdb=" O ARG M 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'N' and resid 3 through 7 removed outlier: 7.448A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS N 204 " --> pdb=" O ASP N 108 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'N' and resid 8 through 16 removed outlier: 6.738A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE N 15 " --> pdb=" O VAL N 20 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL N 20 " --> pdb=" O PHE N 15 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL N 189 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP N 181 " --> pdb=" O LEU N 186 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS N 190 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL N 177 " --> pdb=" O LYS N 190 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 80 through 83 removed outlier: 6.016A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.736A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE O 55 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'O' and resid 73 through 76 122 hydrogen bonds defined for protein. 345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2176 hydrogen bonds 3572 hydrogen bond angles 0 basepair planarities 878 basepair parallelities 1657 stacking parallelities Total time for adding SS restraints: 139.47 Time building geometry restraints manager: 36.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5745 1.31 - 1.43: 39664 1.43 - 1.56: 28548 1.56 - 1.68: 6046 1.68 - 1.81: 42 Bond restraints: 80045 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.805 1.408 0.397 2.00e-02 2.50e+03 3.94e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.805 1.410 0.395 2.00e-02 2.50e+03 3.90e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.638 1.362 0.276 2.00e-02 2.50e+03 1.90e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.638 1.368 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C20 O7Y I3001 " pdb=" C21 O7Y I3001 " ideal model delta sigma weight residual 1.602 1.349 0.253 2.00e-02 2.50e+03 1.61e+02 ... (remaining 80040 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.42: 17532 106.42 - 113.53: 48463 113.53 - 120.64: 33264 120.64 - 127.75: 18891 127.75 - 134.86: 5085 Bond angle restraints: 123235 Sorted by residual: angle pdb=" C14 O7Y I3001 " pdb=" C13 O7Y I3001 " pdb=" C15 O7Y I3001 " ideal model delta sigma weight residual 68.61 120.22 -51.61 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C19 O7Y I3001 " pdb=" C20 O7Y I3001 " pdb=" C21 O7Y I3001 " ideal model delta sigma weight residual 154.31 121.77 32.54 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C12 O7Y I3001 " pdb=" C13 O7Y I3001 " pdb=" C14 O7Y I3001 " ideal model delta sigma weight residual 154.34 122.39 31.95 3.00e+00 1.11e-01 1.13e+02 angle pdb=" C12 O7Y I3001 " pdb=" C13 O7Y I3001 " pdb=" C15 O7Y I3001 " ideal model delta sigma weight residual 85.73 117.39 -31.66 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C15 O7Y I3001 " pdb=" C16 O7Y I3001 " pdb=" C17 O7Y I3001 " ideal model delta sigma weight residual 154.30 124.67 29.63 3.00e+00 1.11e-01 9.75e+01 ... (remaining 123230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 39469 35.48 - 70.97: 1112 70.97 - 106.45: 104 106.45 - 141.94: 11 141.94 - 177.42: 5 Dihedral angle restraints: 40701 sinusoidal: 38011 harmonic: 2690 Sorted by residual: dihedral pdb=" CA THR N 151 " pdb=" C THR N 151 " pdb=" N PRO N 152 " pdb=" CA PRO N 152 " ideal model delta harmonic sigma weight residual 180.00 122.16 57.84 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" C5* PSU I1911 " pdb=" C4* PSU I1911 " pdb=" C3* PSU I1911 " pdb=" O3* PSU I1911 " ideal model delta sinusoidal sigma weight residual 147.00 79.38 67.62 1 8.00e+00 1.56e-02 9.29e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 49.42 -177.42 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 40698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 16002 0.076 - 0.152: 144 0.152 - 0.227: 5 0.227 - 0.303: 2 0.303 - 0.379: 4 Chirality restraints: 16157 Sorted by residual: chirality pdb=" CA MET K 225 " pdb=" N MET K 225 " pdb=" C MET K 225 " pdb=" CB MET K 225 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA ASP K 229 " pdb=" N ASP K 229 " pdb=" C ASP K 229 " pdb=" CB ASP K 229 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C22 O7Y I3001 " pdb=" C21 O7Y I3001 " pdb=" C23 O7Y I3001 " pdb=" C24 O7Y I3001 " both_signs ideal model delta sigma weight residual False -2.78 -2.44 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 16154 not shown) Planarity restraints: 4345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.040 2.00e-02 2.50e+03 6.12e-01 8.43e+03 pdb=" C4' 2MG I2445 " -0.471 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.791 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.589 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.232 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.893 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.184 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.973 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.037 2.00e-02 2.50e+03 5.94e-01 7.94e+03 pdb=" C4' OMG I2251 " 0.446 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.714 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.598 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.585 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.217 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.912 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.210 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.918 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I1835 " -0.039 2.00e-02 2.50e+03 5.80e-01 7.56e+03 pdb=" C4' 2MG I1835 " -0.438 2.00e-02 2.50e+03 pdb=" O4' 2MG I1835 " -0.651 2.00e-02 2.50e+03 pdb=" C3' 2MG I1835 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG I1835 " 0.580 2.00e-02 2.50e+03 pdb=" C2' 2MG I1835 " 0.206 2.00e-02 2.50e+03 pdb=" O2' 2MG I1835 " -0.914 2.00e-02 2.50e+03 pdb=" C1' 2MG I1835 " -0.226 2.00e-02 2.50e+03 pdb=" N9 2MG I1835 " 0.887 2.00e-02 2.50e+03 ... (remaining 4342 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 432 2.52 - 3.12: 50399 3.12 - 3.71: 142495 3.71 - 4.31: 205628 4.31 - 4.90: 269100 Nonbonded interactions: 668054 Sorted by model distance: nonbonded pdb=" O2' 2MA I2503 " pdb=" OP2 G I2505 " model vdw 1.931 2.440 nonbonded pdb=" O2' A I2799 " pdb=" OP2 G I2801 " model vdw 1.949 2.440 nonbonded pdb=" O2' U I1061 " pdb=" OP2 G I1063 " model vdw 1.952 2.440 nonbonded pdb=" O2' A I1508 " pdb=" O4' A I1509 " model vdw 1.966 2.440 nonbonded pdb=" OG1 THR N 110 " pdb=" OG1 THR N 171 " model vdw 1.981 2.440 ... (remaining 668049 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3015 5.49 5 S 22 5.16 5 C 33530 2.51 5 N 13325 2.21 5 O 22277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 30.010 Check model and map are aligned: 0.840 Convert atoms to be neutral: 0.490 Process input model: 287.290 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 339.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.397 80045 Z= 0.359 Angle : 0.484 51.612 123235 Z= 0.223 Chirality : 0.025 0.379 16157 Planarity : 0.023 0.612 4345 Dihedral : 12.746 177.419 38989 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.21 % Favored : 92.69 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -4.11 (0.22), residues: 957 helix: -3.41 (0.26), residues: 160 sheet: -2.42 (0.38), residues: 142 loop : -2.79 (0.21), residues: 655 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 282 time to evaluate : 2.226 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 297 average time/residue: 1.5492 time to fit residues: 608.8271 Evaluate side-chains 213 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 201 time to evaluate : 2.208 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 3 average time/residue: 0.5521 time to fit residues: 4.7211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 1.9990 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 201 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 309 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 358 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 60 GLN M 41 GLN N 49 GLN N 58 ASN N 67 HIS N 126 ASN O 58 ASN O 86 GLN O 135 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.073 80045 Z= 0.474 Angle : 0.735 14.937 123235 Z= 0.378 Chirality : 0.039 0.291 16157 Planarity : 0.007 0.139 4345 Dihedral : 13.469 176.252 37183 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.21 % Favored : 92.58 % Rotamer Outliers : 6.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.11 % 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: -2.88 (0.24), residues: 957 helix: -1.89 (0.34), residues: 174 sheet: -1.29 (0.42), residues: 138 loop : -2.19 (0.21), residues: 645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 246 time to evaluate : 2.240 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 28 residues processed: 276 average time/residue: 1.3504 time to fit residues: 511.7104 Evaluate side-chains 258 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 230 time to evaluate : 2.196 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 14 residues processed: 14 average time/residue: 0.9983 time to fit residues: 22.3063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 359 optimal weight: 0.9980 chunk 388 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 356 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 288 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 60 GLN K 115 GLN K 153 GLN M 90 GLN M 156 ASN N 67 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 80045 Z= 0.215 Angle : 0.613 14.615 123235 Z= 0.328 Chirality : 0.031 0.282 16157 Planarity : 0.007 0.130 4345 Dihedral : 13.442 176.556 37183 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.79 % Favored : 93.10 % Rotamer Outliers : 6.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.11 % 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: -2.39 (0.25), residues: 957 helix: -1.38 (0.37), residues: 161 sheet: -1.33 (0.38), residues: 166 loop : -1.79 (0.23), residues: 630 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 243 time to evaluate : 2.231 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 25 residues processed: 267 average time/residue: 1.3087 time to fit residues: 482.9398 Evaluate side-chains 255 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 230 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 10 average time/residue: 0.6397 time to fit residues: 12.8332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 7.9990 chunk 270 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 360 optimal weight: 0.9990 chunk 381 optimal weight: 0.6980 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 0.0270 chunk 102 optimal weight: 8.9990 overall best weight: 3.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 25 HIS K 60 GLN K 86 ASN K 134 ASN M 62 GLN N 36 GLN N 67 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 80045 Z= 0.318 Angle : 0.619 14.368 123235 Z= 0.330 Chirality : 0.033 0.239 16157 Planarity : 0.007 0.132 4345 Dihedral : 13.803 176.306 37183 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.52 % Favored : 92.37 % Rotamer Outliers : 7.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.11 % 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: -2.00 (0.25), residues: 957 helix: -1.13 (0.36), residues: 176 sheet: -0.96 (0.42), residues: 145 loop : -1.53 (0.23), residues: 636 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 236 time to evaluate : 2.258 Fit side-chains outliers start: 58 outliers final: 25 residues processed: 263 average time/residue: 1.3146 time to fit residues: 476.6388 Evaluate side-chains 252 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 227 time to evaluate : 2.199 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 13 residues processed: 12 average time/residue: 0.6053 time to fit residues: 14.6526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 0.9980 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 6.9990 chunk 284 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 263 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 342 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 25 HIS K 60 GLN K 115 GLN M 62 GLN N 36 GLN N 167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 80045 Z= 0.419 Angle : 0.681 14.747 123235 Z= 0.358 Chirality : 0.037 0.280 16157 Planarity : 0.007 0.136 4345 Dihedral : 14.072 176.345 37183 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.15 % Favored : 91.75 % Rotamer Outliers : 7.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.11 % 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: -2.02 (0.25), residues: 957 helix: -1.07 (0.37), residues: 177 sheet: -0.86 (0.41), residues: 154 loop : -1.62 (0.23), residues: 626 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 228 time to evaluate : 2.234 Fit side-chains outliers start: 56 outliers final: 31 residues processed: 256 average time/residue: 1.3217 time to fit residues: 464.7682 Evaluate side-chains 254 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 223 time to evaluate : 2.171 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 16 residues processed: 15 average time/residue: 0.8143 time to fit residues: 21.0024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 6.9990 chunk 343 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 382 optimal weight: 6.9990 chunk 317 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 25 HIS K 60 GLN K 200 HIS M 62 GLN N 167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 80045 Z= 0.339 Angle : 0.643 14.747 123235 Z= 0.343 Chirality : 0.035 0.271 16157 Planarity : 0.007 0.134 4345 Dihedral : 14.054 176.458 37183 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.73 % Favored : 92.16 % Rotamer Outliers : 5.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.25), residues: 957 helix: -0.81 (0.37), residues: 177 sheet: -0.82 (0.41), residues: 154 loop : -1.53 (0.23), residues: 626 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 231 time to evaluate : 2.260 Fit side-chains outliers start: 40 outliers final: 30 residues processed: 251 average time/residue: 1.3055 time to fit residues: 454.9767 Evaluate side-chains 247 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 217 time to evaluate : 2.193 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 16 residues processed: 14 average time/residue: 0.8207 time to fit residues: 19.8788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 217 optimal weight: 30.0000 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 40.0000 chunk 321 optimal weight: 2.9990 chunk 213 optimal weight: 30.0000 chunk 380 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 25 HIS K 60 GLN M 62 GLN N 167 ASN O 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.054 80045 Z= 0.515 Angle : 0.739 14.708 123235 Z= 0.384 Chirality : 0.041 0.307 16157 Planarity : 0.007 0.138 4345 Dihedral : 14.339 176.927 37183 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.99 % Favored : 90.80 % Rotamer Outliers : 5.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.11 % 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: -1.92 (0.25), residues: 957 helix: -0.81 (0.38), residues: 172 sheet: -0.87 (0.39), residues: 168 loop : -1.59 (0.23), residues: 617 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 214 time to evaluate : 2.262 Fit side-chains outliers start: 45 outliers final: 29 residues processed: 242 average time/residue: 1.3244 time to fit residues: 444.9102 Evaluate side-chains 237 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 208 time to evaluate : 2.243 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 20 residues processed: 10 average time/residue: 0.5597 time to fit residues: 12.1693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 299 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 25 HIS K 60 GLN M 62 GLN N 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 80045 Z= 0.438 Angle : 0.701 14.764 123235 Z= 0.369 Chirality : 0.039 0.294 16157 Planarity : 0.007 0.137 4345 Dihedral : 14.314 177.069 37183 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.57 % Favored : 91.33 % Rotamer Outliers : 5.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.11 % 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: -1.96 (0.25), residues: 957 helix: -0.78 (0.38), residues: 177 sheet: -1.03 (0.39), residues: 170 loop : -1.59 (0.23), residues: 610 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 225 time to evaluate : 3.117 Fit side-chains outliers start: 45 outliers final: 33 residues processed: 250 average time/residue: 1.3038 time to fit residues: 456.8817 Evaluate side-chains 257 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 224 time to evaluate : 2.257 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 23 residues processed: 12 average time/residue: 0.7024 time to fit residues: 16.1680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.8980 chunk 364 optimal weight: 3.9990 chunk 332 optimal weight: 0.7980 chunk 354 optimal weight: 5.9990 chunk 213 optimal weight: 30.0000 chunk 154 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 2.9990 chunk 335 optimal weight: 0.4980 chunk 353 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 60 GLN M 62 GLN M 156 ASN N 36 GLN N 42 ASN N 167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 80045 Z= 0.185 Angle : 0.612 14.932 123235 Z= 0.330 Chirality : 0.031 0.254 16157 Planarity : 0.007 0.128 4345 Dihedral : 14.237 177.502 37183 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.63 % Favored : 92.27 % Rotamer Outliers : 4.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.11 % 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: -1.78 (0.26), residues: 957 helix: -0.61 (0.38), residues: 176 sheet: -0.95 (0.40), residues: 172 loop : -1.46 (0.24), residues: 609 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 221 time to evaluate : 2.341 Fit side-chains outliers start: 38 outliers final: 27 residues processed: 246 average time/residue: 1.2575 time to fit residues: 434.1662 Evaluate side-chains 244 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 217 time to evaluate : 2.226 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 6 average time/residue: 0.7094 time to fit residues: 8.8271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 7.9990 chunk 375 optimal weight: 2.9990 chunk 228 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 393 optimal weight: 0.0970 chunk 362 optimal weight: 7.9990 chunk 313 optimal weight: 0.1980 chunk 32 optimal weight: 8.9990 chunk 242 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 overall best weight: 3.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 25 HIS K 60 GLN K 153 GLN M 62 GLN N 36 GLN N 42 ASN N 167 ASN O 86 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 80045 Z= 0.324 Angle : 0.627 14.686 123235 Z= 0.335 Chirality : 0.034 0.274 16157 Planarity : 0.007 0.133 4345 Dihedral : 14.155 177.036 37183 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.46 % Favored : 91.43 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.11 % 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: -1.71 (0.26), residues: 957 helix: -0.46 (0.39), residues: 175 sheet: -0.95 (0.39), residues: 172 loop : -1.43 (0.24), residues: 610 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 2.355 Fit side-chains outliers start: 29 outliers final: 26 residues processed: 240 average time/residue: 1.2592 time to fit residues: 423.1679 Evaluate side-chains 236 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 210 time to evaluate : 2.209 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 23 residues processed: 5 average time/residue: 0.5768 time to fit residues: 7.0063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 7.9990 chunk 333 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 322 optimal weight: 0.0770 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 25 HIS K 60 GLN M 62 GLN M 136 GLN N 36 GLN N 42 ASN N 167 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.105155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.081234 restraints weight = 153172.204| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 0.66 r_work: 0.2910 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 80045 Z= 0.263 Angle : 0.611 14.687 123235 Z= 0.328 Chirality : 0.032 0.260 16157 Planarity : 0.007 0.132 4345 Dihedral : 14.150 176.996 37183 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.05 % Favored : 91.85 % Rotamer Outliers : 4.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.11 % 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: -1.66 (0.26), residues: 957 helix: -0.40 (0.39), residues: 175 sheet: -0.98 (0.39), residues: 172 loop : -1.39 (0.24), residues: 610 =============================================================================== Job complete usr+sys time: 10592.69 seconds wall clock time: 190 minutes 23.62 seconds (11423.62 seconds total)