Starting phenix.real_space_refine on Sat Mar 16 09:25:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/03_2024/6pc8_20299_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/03_2024/6pc8_20299.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/03_2024/6pc8_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_20299/03_2024/6pc8_20299_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/03_2024/6pc8_20299_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/03_2024/6pc8_20299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/03_2024/6pc8_20299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/03_2024/6pc8_20299_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc8_20299/03_2024/6pc8_20299_neut_updated.pdb" } resolution = 2.9 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= -0.015 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 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. 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-5265/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: 28.43, per 1000 atoms: 0.39 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: 33.62 Conformation dependent library (CDL) restraints added in 2.4 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: 39.63 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: 131.86 Time building geometry restraints manager: 36.04 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 1.802 1.408 0.394 2.00e-02 2.50e+03 3.88e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.410 0.392 2.00e-02 2.50e+03 3.84e+02 bond pdb=" C12 O7Y I3001 " pdb=" C13 O7Y I3001 " ideal model delta sigma weight residual 1.728 1.352 0.376 2.00e-02 2.50e+03 3.54e+02 bond pdb=" C15 O7Y I3001 " pdb=" C16 O7Y I3001 " ideal model delta sigma weight residual 1.715 1.347 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.362 0.273 2.00e-02 2.50e+03 1.86e+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 68.55 120.22 -51.67 3.00e+00 1.11e-01 2.97e+02 angle pdb=" C02 O7Y I3001 " pdb=" C12 O7Y I3001 " pdb=" C13 O7Y I3001 " ideal model delta sigma weight residual 85.85 128.86 -43.01 3.00e+00 1.11e-01 2.06e+02 angle pdb=" C13 O7Y I3001 " pdb=" C15 O7Y I3001 " pdb=" C16 O7Y I3001 " ideal model delta sigma weight residual 85.76 125.19 -39.43 3.00e+00 1.11e-01 1.73e+02 angle pdb=" C15 O7Y I3001 " pdb=" C16 O7Y I3001 " pdb=" C17 O7Y I3001 " ideal model delta sigma weight residual 85.87 124.67 -38.80 3.00e+00 1.11e-01 1.67e+02 angle pdb=" C19 O7Y I3001 " pdb=" C20 O7Y I3001 " pdb=" C21 O7Y I3001 " ideal model delta sigma weight residual 154.23 121.77 32.46 3.00e+00 1.11e-01 1.17e+02 ... (remaining 123230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 44033 35.48 - 70.97: 6715 70.97 - 106.45: 789 106.45 - 141.94: 11 141.94 - 177.42: 8 Dihedral angle restraints: 51556 sinusoidal: 48866 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=" C4* PSU I1911 " pdb=" C3* PSU I1911 " pdb=" C2* PSU I1911 " pdb=" C1* PSU I1911 " ideal model delta sinusoidal sigma weight residual -35.00 34.44 -69.44 1 8.00e+00 1.56e-02 9.73e+01 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 ... (remaining 51553 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 2.96e+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 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: 5.840 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: 0.060 Extract box with map and model: 27.950 Check model and map are aligned: 0.790 Set scattering table: 0.530 Process input model: 278.360 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 327.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 0.394 80045 Z= 0.366 Angle : 0.502 51.672 123235 Z= 0.227 Chirality : 0.025 0.379 16157 Planarity : 0.023 0.612 4345 Dihedral : 23.734 177.419 49844 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.21 % Favored : 92.69 % Rotamer: Outliers : 2.62 % Allowed : 14.66 % Favored : 82.72 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 78 HIS 0.009 0.001 HIS K 230 PHE 0.006 0.001 PHE N 156 TYR 0.005 0.001 TYR K 103 ARG 0.003 0.000 ARG N 13 *********************** 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 : 2.143 Fit side-chains revert: symmetry clash REVERT: K 84 ASP cc_start: 0.8268 (t0) cc_final: 0.8045 (t0) REVERT: K 194 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7466 (mt-10) REVERT: K 256 LYS cc_start: 0.8377 (mttm) cc_final: 0.8047 (mttt) REVERT: K 261 LYS cc_start: 0.8298 (ttpt) cc_final: 0.8080 (ttmm) REVERT: M 136 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7965 (mm-40) REVERT: N 160 LYS cc_start: 0.8996 (mttt) cc_final: 0.8743 (mttp) REVERT: N 200 ASP cc_start: 0.7559 (m-30) cc_final: 0.7168 (m-30) REVERT: O 12 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7762 (tppt) REVERT: O 44 TYR cc_start: 0.9114 (t80) cc_final: 0.8873 (t80) REVERT: O 58 ASN cc_start: 0.8918 (m-40) cc_final: 0.7991 (m110) REVERT: O 106 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8867 (mtpt) outliers start: 20 outliers final: 12 residues processed: 297 average time/residue: 1.6309 time to fit residues: 633.3882 Evaluate side-chains 217 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 205 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 231 PRO Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN 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 N 49 GLN N 58 ASN N 67 HIS N 126 ASN O 86 GLN O 135 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 80045 Z= 0.486 Angle : 0.773 15.311 123235 Z= 0.398 Chirality : 0.041 0.296 16157 Planarity : 0.007 0.142 4345 Dihedral : 23.593 176.071 48054 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.31 % Favored : 92.48 % Rotamer: Outliers : 6.68 % Allowed : 23.30 % Favored : 70.03 % 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: -2.82 (0.24), residues: 957 helix: -1.77 (0.35), residues: 171 sheet: -1.40 (0.39), residues: 157 loop : -2.13 (0.22), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 78 HIS 0.005 0.001 HIS O 130 PHE 0.020 0.002 PHE L 107 TYR 0.012 0.002 TYR O 16 ARG 0.009 0.001 ARG K 175 *********************** 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 304 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 253 time to evaluate : 2.328 Fit side-chains REVERT: K 100 GLU cc_start: 0.7629 (tt0) cc_final: 0.7341 (tt0) REVERT: K 108 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8229 (ttmm) REVERT: K 114 ASP cc_start: 0.8482 (m-30) cc_final: 0.8183 (m-30) REVERT: K 214 ARG cc_start: 0.8888 (mmt-90) cc_final: 0.8575 (mpt90) REVERT: K 256 LYS cc_start: 0.8764 (mttm) cc_final: 0.8250 (mttt) REVERT: M 10 SER cc_start: 0.8176 (t) cc_final: 0.7946 (p) REVERT: M 116 ASP cc_start: 0.8614 (m-30) cc_final: 0.8321 (m-30) REVERT: M 179 SER cc_start: 0.9103 (m) cc_final: 0.8827 (m) REVERT: N 13 ARG cc_start: 0.5780 (OUTLIER) cc_final: 0.4403 (ptm160) REVERT: N 77 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8726 (ptp90) REVERT: N 114 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9200 (mtmt) REVERT: N 160 LYS cc_start: 0.9135 (mttt) cc_final: 0.8811 (mttp) REVERT: N 174 SER cc_start: 0.9054 (m) cc_final: 0.8347 (p) REVERT: O 1 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6405 (pmt) outliers start: 51 outliers final: 26 residues processed: 282 average time/residue: 1.4143 time to fit residues: 540.3449 Evaluate side-chains 252 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 221 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 77 ARG Chi-restraints excluded: chain N residue 114 LYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 131 ASN 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: 0.9980 chunk 98 optimal weight: 4.9990 chunk 359 optimal weight: 0.7980 chunk 388 optimal weight: 5.9990 chunk 320 optimal weight: 7.9990 chunk 356 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 288 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 115 GLN K 134 ASN K 153 GLN M 41 GLN M 90 GLN M 156 ASN N 36 GLN N 67 HIS N 167 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 80045 Z= 0.323 Angle : 0.618 14.337 123235 Z= 0.327 Chirality : 0.033 0.236 16157 Planarity : 0.007 0.133 4345 Dihedral : 23.587 177.072 48049 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.90 % Favored : 93.00 % Rotamer: Outliers : 7.59 % Allowed : 26.05 % Favored : 66.36 % 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: -2.19 (0.25), residues: 957 helix: -1.26 (0.37), residues: 171 sheet: -1.14 (0.41), residues: 151 loop : -1.66 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 78 HIS 0.005 0.001 HIS K 25 PHE 0.015 0.002 PHE L 107 TYR 0.010 0.002 TYR O 75 ARG 0.005 0.001 ARG K 175 *********************** 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 295 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 237 time to evaluate : 2.153 Fit side-chains revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7600 (tt0) cc_final: 0.7318 (tt0) REVERT: K 153 GLN cc_start: 0.8672 (mt0) cc_final: 0.8464 (mt0) REVERT: L 55 MET cc_start: 0.8690 (tpp) cc_final: 0.8465 (tpp) REVERT: L 110 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8297 (t) REVERT: M 10 SER cc_start: 0.8306 (t) cc_final: 0.8048 (p) REVERT: M 116 ASP cc_start: 0.8616 (m-30) cc_final: 0.8356 (m-30) REVERT: M 179 SER cc_start: 0.8941 (m) cc_final: 0.8623 (m) REVERT: M 191 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7500 (p0) REVERT: M 198 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8391 (mp0) REVERT: N 13 ARG cc_start: 0.5477 (OUTLIER) cc_final: 0.4327 (ptm160) REVERT: N 114 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.8888 (mtmm) REVERT: N 131 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7884 (p0) REVERT: N 160 LYS cc_start: 0.9120 (mttt) cc_final: 0.8819 (mttp) REVERT: O 1 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6233 (pmt) REVERT: O 81 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8102 (mp) outliers start: 58 outliers final: 24 residues processed: 266 average time/residue: 1.4513 time to fit residues: 519.8681 Evaluate side-chains 264 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 233 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 114 LYS Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 360 optimal weight: 0.9990 chunk 381 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 N 36 GLN N 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 80045 Z= 0.336 Angle : 0.636 14.657 123235 Z= 0.339 Chirality : 0.034 0.260 16157 Planarity : 0.007 0.131 4345 Dihedral : 23.617 176.765 48047 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.90 % Favored : 93.00 % Rotamer: Outliers : 7.46 % Allowed : 26.96 % Favored : 65.58 % 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: -1.09 (0.37), residues: 177 sheet: -0.94 (0.39), residues: 173 loop : -1.58 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 78 HIS 0.005 0.001 HIS K 25 PHE 0.015 0.002 PHE M 19 TYR 0.010 0.002 TYR O 75 ARG 0.011 0.001 ARG K 214 *********************** 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 286 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 229 time to evaluate : 2.142 Fit side-chains REVERT: K 100 GLU cc_start: 0.7560 (tt0) cc_final: 0.7230 (tt0) REVERT: K 256 LYS cc_start: 0.8827 (mttm) cc_final: 0.8355 (mttt) REVERT: M 116 ASP cc_start: 0.8640 (m-30) cc_final: 0.8394 (m-30) REVERT: M 136 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8511 (tp-100) REVERT: M 157 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8585 (pt) REVERT: M 179 SER cc_start: 0.9020 (m) cc_final: 0.8771 (m) REVERT: M 191 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7565 (p0) REVERT: M 195 GLN cc_start: 0.8891 (mt0) cc_final: 0.8675 (mt0) REVERT: M 198 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8404 (mp0) REVERT: N 13 ARG cc_start: 0.5542 (OUTLIER) cc_final: 0.4354 (ptm160) REVERT: N 88 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: N 91 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8444 (p) REVERT: N 114 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9191 (mtmt) REVERT: N 131 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7887 (p0) REVERT: N 174 SER cc_start: 0.9061 (m) cc_final: 0.8334 (p) REVERT: N 186 LEU cc_start: 0.9000 (mt) cc_final: 0.8796 (mp) REVERT: O 1 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6393 (pmt) REVERT: O 31 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7860 (mm-30) outliers start: 57 outliers final: 33 residues processed: 257 average time/residue: 1.3857 time to fit residues: 484.1357 Evaluate side-chains 267 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 226 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 114 LYS Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 0.0770 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 6.9990 chunk 284 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 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: 4.0146 ------------------------------------------------------------------------------- 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 156 ASN N 36 GLN N 167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 80045 Z= 0.357 Angle : 0.640 14.680 123235 Z= 0.339 Chirality : 0.035 0.271 16157 Planarity : 0.007 0.134 4345 Dihedral : 23.670 177.215 48046 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.21 % Favored : 92.58 % Rotamer: Outliers : 7.46 % Allowed : 28.01 % Favored : 64.53 % 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: -1.75 (0.26), residues: 957 helix: -0.88 (0.39), residues: 172 sheet: -0.81 (0.40), residues: 177 loop : -1.39 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 78 HIS 0.004 0.001 HIS M 29 PHE 0.021 0.002 PHE M 19 TYR 0.011 0.002 TYR O 75 ARG 0.007 0.001 ARG K 214 *********************** 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 295 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 238 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7548 (tt0) cc_final: 0.7206 (tt0) REVERT: M 116 ASP cc_start: 0.8640 (m-30) cc_final: 0.8393 (m-30) REVERT: M 136 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8561 (tp-100) REVERT: M 157 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8568 (pt) REVERT: M 191 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7601 (p0) REVERT: M 198 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8345 (mp0) REVERT: N 13 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.4788 (ptm160) REVERT: N 64 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7200 (pt0) REVERT: N 114 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.8930 (mtmm) REVERT: N 131 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7887 (p0) REVERT: N 174 SER cc_start: 0.9047 (m) cc_final: 0.8496 (p) REVERT: O 1 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6370 (pmt) REVERT: O 27 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.6717 (mmm160) REVERT: O 31 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7899 (mm-30) outliers start: 57 outliers final: 34 residues processed: 269 average time/residue: 1.3767 time to fit residues: 504.7252 Evaluate side-chains 261 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 220 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 77 ARG Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 114 LYS Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 27 ARG Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 131 ASN 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: 3.9990 chunk 75 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 382 optimal weight: 2.9990 chunk 317 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 36 GLN N 42 ASN N 167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 80045 Z= 0.336 Angle : 0.630 14.682 123235 Z= 0.336 Chirality : 0.034 0.265 16157 Planarity : 0.007 0.132 4345 Dihedral : 23.678 177.068 48045 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.31 % Favored : 92.48 % Rotamer: Outliers : 7.07 % Allowed : 29.58 % Favored : 63.35 % 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: -1.64 (0.26), residues: 957 helix: -0.62 (0.39), residues: 176 sheet: -0.65 (0.41), residues: 161 loop : -1.39 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 78 HIS 0.005 0.001 HIS K 25 PHE 0.010 0.002 PHE O 89 TYR 0.014 0.002 TYR O 75 ARG 0.006 0.000 ARG K 214 *********************** 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 278 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 224 time to evaluate : 2.167 Fit side-chains revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7548 (tt0) cc_final: 0.7196 (tt0) REVERT: K 181 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8035 (mmm) REVERT: M 116 ASP cc_start: 0.8634 (m-30) cc_final: 0.8385 (m-30) REVERT: M 157 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8614 (pt) REVERT: M 191 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7534 (p0) REVERT: N 13 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.4856 (ptm160) REVERT: N 64 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7212 (pt0) REVERT: N 77 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8250 (ptt90) REVERT: N 88 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: N 114 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9162 (mtmt) REVERT: N 131 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7888 (p0) REVERT: N 174 SER cc_start: 0.9067 (m) cc_final: 0.8397 (p) REVERT: O 1 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6368 (pmt) REVERT: O 27 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8633 (mmm160) REVERT: O 31 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7865 (mm-30) outliers start: 54 outliers final: 36 residues processed: 253 average time/residue: 1.3514 time to fit residues: 470.0757 Evaluate side-chains 264 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 218 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 77 ARG Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 114 LYS Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 27 ARG Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 7.9990 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: 0.9990 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: 5.5990 ------------------------------------------------------------------------------- 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 36 GLN N 42 ASN N 167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 80045 Z= 0.488 Angle : 0.722 14.766 123235 Z= 0.375 Chirality : 0.040 0.309 16157 Planarity : 0.007 0.138 4345 Dihedral : 23.731 177.229 48045 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.46 % Favored : 91.33 % Rotamer: Outliers : 7.98 % Allowed : 29.58 % Favored : 62.43 % 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: -1.73 (0.26), residues: 957 helix: -0.65 (0.39), residues: 175 sheet: -0.76 (0.40), residues: 163 loop : -1.46 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 78 HIS 0.006 0.001 HIS M 29 PHE 0.018 0.002 PHE M 19 TYR 0.017 0.002 TYR O 16 ARG 0.007 0.001 ARG K 214 *********************** 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 288 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 227 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 181 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7950 (mmm) REVERT: L 128 THR cc_start: 0.9303 (p) cc_final: 0.9050 (p) REVERT: M 116 ASP cc_start: 0.8648 (m-30) cc_final: 0.8396 (m-30) REVERT: M 191 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7551 (p0) REVERT: N 13 ARG cc_start: 0.6089 (OUTLIER) cc_final: 0.4960 (ptm160) REVERT: N 64 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7246 (pt0) REVERT: N 88 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: N 114 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9007 (mtmm) REVERT: N 131 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7913 (p0) REVERT: N 174 SER cc_start: 0.9088 (m) cc_final: 0.8554 (p) REVERT: O 1 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6381 (pmt) REVERT: O 31 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7864 (mm-30) outliers start: 61 outliers final: 37 residues processed: 254 average time/residue: 1.3343 time to fit residues: 468.8173 Evaluate side-chains 266 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 222 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 77 ARG Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 114 LYS Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 131 ASN 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: 5.9990 chunk 242 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 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 M 136 GLN M 156 ASN M 195 GLN N 36 GLN N 167 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 80045 Z= 0.441 Angle : 0.699 14.831 123235 Z= 0.366 Chirality : 0.038 0.297 16157 Planarity : 0.007 0.137 4345 Dihedral : 23.739 177.404 48043 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.84 % Favored : 91.95 % Rotamer: Outliers : 6.54 % Allowed : 31.28 % Favored : 62.17 % 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: -1.70 (0.26), residues: 957 helix: -0.59 (0.39), residues: 175 sheet: -0.77 (0.40), residues: 163 loop : -1.44 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 78 HIS 0.007 0.001 HIS K 25 PHE 0.021 0.002 PHE O 119 TYR 0.016 0.002 TYR O 75 ARG 0.006 0.000 ARG K 214 *********************** 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 275 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 225 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 181 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7978 (mmm) REVERT: L 128 THR cc_start: 0.9302 (p) cc_final: 0.9057 (p) REVERT: M 116 ASP cc_start: 0.8645 (m-30) cc_final: 0.8393 (m-30) REVERT: M 156 ASN cc_start: 0.8428 (m-40) cc_final: 0.8173 (t0) REVERT: M 191 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7536 (p0) REVERT: M 197 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: N 13 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.4907 (ptm160) REVERT: N 64 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7237 (pt0) REVERT: N 88 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: N 114 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.8990 (mtmm) REVERT: N 131 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7910 (p0) REVERT: N 174 SER cc_start: 0.9108 (m) cc_final: 0.8557 (p) REVERT: O 1 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6373 (pmt) REVERT: O 31 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7850 (mm-30) outliers start: 50 outliers final: 36 residues processed: 251 average time/residue: 1.2947 time to fit residues: 451.4222 Evaluate side-chains 265 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 221 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain M residue 197 GLU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 77 ARG Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 114 LYS Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.9990 chunk 364 optimal weight: 6.9990 chunk 332 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 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: 0.9990 chunk 335 optimal weight: 2.9990 chunk 353 optimal weight: 0.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- 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 N 36 GLN N 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 80045 Z= 0.209 Angle : 0.608 14.974 123235 Z= 0.328 Chirality : 0.032 0.254 16157 Planarity : 0.007 0.128 4345 Dihedral : 23.824 177.628 48043 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.84 % Favored : 92.06 % Rotamer: Outliers : 5.24 % Allowed : 32.85 % Favored : 61.91 % 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: -1.53 (0.26), residues: 957 helix: -0.41 (0.39), residues: 175 sheet: -0.69 (0.40), residues: 164 loop : -1.32 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 78 HIS 0.008 0.001 HIS K 25 PHE 0.020 0.002 PHE N 127 TYR 0.019 0.002 TYR O 75 ARG 0.006 0.000 ARG K 214 *********************** 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 269 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 229 time to evaluate : 2.118 Fit side-chains revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7515 (tt0) cc_final: 0.7262 (tt0) REVERT: K 153 GLN cc_start: 0.8632 (mt0) cc_final: 0.8414 (mt0) REVERT: K 163 GLN cc_start: 0.7997 (pt0) cc_final: 0.7767 (pm20) REVERT: K 181 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8038 (mmm) REVERT: L 128 THR cc_start: 0.9280 (p) cc_final: 0.9035 (p) REVERT: M 116 ASP cc_start: 0.8615 (m-30) cc_final: 0.8367 (m-30) REVERT: M 156 ASN cc_start: 0.8409 (m-40) cc_final: 0.8115 (t0) REVERT: M 191 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7522 (p0) REVERT: M 197 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: N 13 ARG cc_start: 0.6064 (OUTLIER) cc_final: 0.4892 (ptm160) REVERT: N 64 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7192 (pt0) REVERT: N 77 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8278 (ptt90) REVERT: N 88 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: N 114 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9151 (mtmt) REVERT: N 131 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7892 (p0) REVERT: N 174 SER cc_start: 0.9089 (m) cc_final: 0.8393 (p) REVERT: O 1 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6280 (pmt) outliers start: 40 outliers final: 24 residues processed: 247 average time/residue: 1.3455 time to fit residues: 456.1379 Evaluate side-chains 256 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 223 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain M residue 197 GLU Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 77 ARG Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 114 LYS Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 131 ASN 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: 7.9990 chunk 228 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 393 optimal weight: 4.9990 chunk 362 optimal weight: 6.9990 chunk 313 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 242 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 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 25 HIS K 60 GLN M 62 GLN M 136 GLN N 36 GLN N 49 GLN N 167 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 80045 Z= 0.488 Angle : 0.717 14.839 123235 Z= 0.372 Chirality : 0.040 0.304 16157 Planarity : 0.007 0.138 4345 Dihedral : 23.734 177.281 48043 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.15 % Favored : 91.64 % Rotamer: Outliers : 4.32 % Allowed : 34.42 % Favored : 61.26 % 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: -1.67 (0.26), residues: 957 helix: -0.52 (0.39), residues: 175 sheet: -0.82 (0.40), residues: 164 loop : -1.41 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP M 78 HIS 0.006 0.001 HIS K 25 PHE 0.020 0.002 PHE N 127 TYR 0.018 0.002 TYR O 75 ARG 0.011 0.001 ARG K 203 ********************** 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 259 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 226 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 181 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7965 (mmm) REVERT: L 128 THR cc_start: 0.9282 (p) cc_final: 0.9055 (p) REVERT: M 116 ASP cc_start: 0.8648 (m-30) cc_final: 0.8400 (m-30) REVERT: M 191 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7548 (p0) REVERT: N 13 ARG cc_start: 0.6061 (OUTLIER) cc_final: 0.4929 (ptm160) REVERT: N 64 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7248 (pt0) REVERT: N 88 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: N 114 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9018 (mtmm) REVERT: N 131 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7915 (p0) REVERT: N 174 SER cc_start: 0.9106 (m) cc_final: 0.8508 (p) REVERT: O 1 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6379 (pmt) outliers start: 33 outliers final: 26 residues processed: 243 average time/residue: 1.3629 time to fit residues: 456.8244 Evaluate side-chains 252 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 219 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 77 ARG Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 114 LYS Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 5.9990 chunk 333 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 288 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 322 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 167 ASN O 80 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.104658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.080838 restraints weight = 153493.581| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 0.65 r_work: 0.2896 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 80045 Z= 0.278 Angle : 0.634 14.986 123235 Z= 0.339 Chirality : 0.033 0.271 16157 Planarity : 0.007 0.133 4345 Dihedral : 23.801 177.763 48043 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.63 % Favored : 92.16 % Rotamer: Outliers : 4.71 % Allowed : 34.55 % Favored : 60.73 % 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: -1.57 (0.26), residues: 957 helix: -0.41 (0.39), residues: 175 sheet: -0.82 (0.40), residues: 164 loop : -1.33 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP M 78 HIS 0.018 0.002 HIS M 165 PHE 0.023 0.002 PHE N 127 TYR 0.018 0.002 TYR O 75 ARG 0.010 0.000 ARG K 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11278.79 seconds wall clock time: 202 minutes 36.73 seconds (12156.73 seconds total)