Starting phenix.real_space_refine on Thu Feb 22 12:12:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwo_27028/02_2024/8cwo_27028_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwo_27028/02_2024/8cwo_27028.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwo_27028/02_2024/8cwo_27028_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwo_27028/02_2024/8cwo_27028_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwo_27028/02_2024/8cwo_27028_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwo_27028/02_2024/8cwo_27028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwo_27028/02_2024/8cwo_27028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwo_27028/02_2024/8cwo_27028_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwo_27028/02_2024/8cwo_27028_updated.pdb" } resolution = 2.84 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= 0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1044 5.49 5 Mg 66 5.21 5 S 40 5.16 5 C 17375 2.51 5 N 6372 2.21 5 O 9445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 186": "OD1" <-> "OD2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "H ASP 48": "OD1" <-> "OD2" Residue "H ASP 118": "OD1" <-> "OD2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "L ASP 14": "OD1" <-> "OD2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "O GLU 74": "OE1" <-> "OE2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "Q GLU 7": "OE1" <-> "OE2" Residue "Q ASP 22": "OD1" <-> "OD2" Residue "Q ASP 55": "OD1" <-> "OD2" Residue "R ASP 25": "OD1" <-> "OD2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "T ASP 59": "OD1" <-> "OD2" Residue "P GLU 35": "OE1" <-> "OE2" Residue "P ASP 52": "OD1" <-> "OD2" Residue "P GLU 54": "OE1" <-> "OE2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P GLU 111": "OE1" <-> "OE2" Residue "P ASP 113": "OD1" <-> "OD2" Residue "P GLU 114": "OE1" <-> "OE2" Residue "P GLU 125": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34342 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 22250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 22250 Classifications: {'RNA': 1034} Modifications used: {'rna2p': 2, 'rna2p_pur': 83, 'rna2p_pyr': 50, 'rna3p': 8, 'rna3p_pur': 508, 'rna3p_pyr': 383} Link IDs: {'rna2p': 134, 'rna3p': 899} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1632 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 189} Chain: "E" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 827 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 785 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1021 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "K" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 858 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "L" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Chain: "O" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "Q" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 728 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "R" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 527 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "T" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 673 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'TRANS': 86} Chain: "P" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 994 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "X" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 277 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "B" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1836 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "Y" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 211 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 6} Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Unusual residues: {' MG': 66} Classifications: {'undetermined': 66, 'water': 1} Link IDs: {None: 66} Time building chain proxies: 18.13, per 1000 atoms: 0.53 Number of scatterers: 34342 At special positions: 0 Unit cell: (182.628, 181.56, 156.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 1044 15.00 Mg 66 11.99 O 9445 8.00 N 6372 7.00 C 17375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.29 Conformation dependent library (CDL) restraints added in 2.7 seconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2798 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 12 sheets defined 40.9% alpha, 14.3% beta 337 base pairs and 617 stacking pairs defined. Time for finding SS restraints: 18.33 Creating SS restraints... Processing helix chain 'D' and resid 8 through 15 Processing helix chain 'D' and resid 25 through 28 Processing helix chain 'D' and resid 45 through 60 Processing helix chain 'D' and resid 64 through 76 Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 93 through 100 Processing helix chain 'D' and resid 106 through 115 Processing helix chain 'D' and resid 148 through 156 Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 192 through 200 removed outlier: 3.610A pdb=" N SER D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 141 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'E' and resid 184 through 187 No H-bonds generated for 'chain 'E' and resid 184 through 187' Processing helix chain 'E' and resid 190 through 209 Processing helix chain 'F' and resid 18 through 33 removed outlier: 4.950A pdb=" N GLU F 33 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 81 Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 43 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 118 through 124 Processing helix chain 'K' and resid 60 through 63 Processing helix chain 'K' and resid 66 through 82 Processing helix chain 'K' and resid 99 through 109 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 115 through 117 No H-bonds generated for 'chain 'L' and resid 115 through 117' Processing helix chain 'O' and resid 4 through 13 Processing helix chain 'O' and resid 23 through 43 Processing helix chain 'O' and resid 48 through 71 Processing helix chain 'O' and resid 73 through 82 Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'R' and resid 26 through 32 Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'T' and resid 5 through 41 Processing helix chain 'T' and resid 45 through 64 Processing helix chain 'T' and resid 69 through 87 Processing helix chain 'P' and resid 53 through 62 Processing helix chain 'P' and resid 68 through 77 Processing helix chain 'P' and resid 79 through 82 No H-bonds generated for 'chain 'P' and resid 79 through 82' Processing helix chain 'P' and resid 102 through 111 Processing helix chain 'P' and resid 114 through 128 Processing helix chain 'X' and resid 5 through 23 Processing helix chain 'X' and resid 25 through 30 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 45 through 62 Processing helix chain 'B' and resid 74 through 87 removed outlier: 4.798A pdb=" N GLU B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER B 79 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 126 removed outlier: 3.904A pdb=" N ALA B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 208 through 232 removed outlier: 4.317A pdb=" N LEU B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 118 through 120 Processing sheet with id= B, first strand: chain 'E' and resid 108 through 110 removed outlier: 5.660A pdb=" N GLY E 127 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA E 148 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE E 129 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N SER E 150 " --> pdb=" O ILE E 129 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 44 through 47 removed outlier: 3.681A pdb=" N GLY F 44 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASP F 11 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE F 85 " --> pdb=" O ASP F 11 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 36 through 42 removed outlier: 6.581A pdb=" N ASN F 64 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL F 40 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL F 62 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 24 through 28 Processing sheet with id= F, first strand: chain 'H' and resid 114 through 117 removed outlier: 6.657A pdb=" N SER H 110 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL H 130 " --> pdb=" O SER H 110 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 89 through 93 Processing sheet with id= H, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.279A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'Q' and resid 80 through 82 removed outlier: 15.802A pdb=" N VAL Q 14 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) removed outlier: 12.292A pdb=" N ARG Q 35 " --> pdb=" O VAL Q 14 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU Q 16 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU Q 33 " --> pdb=" O GLU Q 16 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR Q 29 " --> pdb=" O VAL Q 20 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'Q' and resid 65 through 67 removed outlier: 6.691A pdb=" N ARG Q 67 " --> pdb=" O ILE Q 85 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE Q 85 " --> pdb=" O ARG Q 67 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'P' and resid 3 through 12 removed outlier: 6.663A pdb=" N VAL P 22 " --> pdb=" O GLU P 36 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLU P 36 " --> pdb=" O VAL P 22 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 67 through 70 removed outlier: 7.061A pdb=" N ALA B 161 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 70 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TRP B 163 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL B 164 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 185 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR B 199 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU B 188 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE B 201 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for sheet with id= L 519 hydrogen bonds defined for protein. 1515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 846 hydrogen bonds 1268 hydrogen bond angles 0 basepair planarities 337 basepair parallelities 617 stacking parallelities Total time for adding SS restraints: 25.40 Time building geometry restraints manager: 19.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3153 1.30 - 1.43: 16185 1.43 - 1.56: 15622 1.56 - 1.68: 2085 1.68 - 1.81: 75 Bond restraints: 37120 Sorted by residual: bond pdb=" N3 2MG A1503 " pdb=" C4 2MG A1503 " ideal model delta sigma weight residual 1.496 1.331 0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" C2 2MG A1503 " pdb=" N3 2MG A1503 " ideal model delta sigma weight residual 1.465 1.303 0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" C2 5MC A1391 " pdb=" N3 5MC A1391 " ideal model delta sigma weight residual 1.493 1.340 0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C2 5MC A1387 " pdb=" N3 5MC A1387 " ideal model delta sigma weight residual 1.493 1.344 0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C5 5MC A1391 " pdb=" C6 5MC A1391 " ideal model delta sigma weight residual 1.494 1.345 0.149 2.00e-02 2.50e+03 5.52e+01 ... (remaining 37115 not shown) Histogram of bond angle deviations from ideal: 96.68 - 106.10: 5910 106.10 - 115.53: 25455 115.53 - 124.95: 19547 124.95 - 134.37: 4408 134.37 - 143.80: 4 Bond angle restraints: 55324 Sorted by residual: angle pdb=" C1' G7M A 509 " pdb=" N9 G7M A 509 " pdb=" C8 G7M A 509 " ideal model delta sigma weight residual 94.96 124.90 -29.94 3.00e+00 1.11e-01 9.96e+01 angle pdb=" C3' U A 853 " pdb=" O3' U A 853 " pdb=" P U A 854 " ideal model delta sigma weight residual 120.20 107.09 13.11 1.50e+00 4.44e-01 7.63e+01 angle pdb=" C3' A A 810 " pdb=" O3' A A 810 " pdb=" P G A 811 " ideal model delta sigma weight residual 120.20 108.29 11.91 1.50e+00 4.44e-01 6.30e+01 angle pdb=" C3' A A 432 " pdb=" O3' A A 432 " pdb=" P A A 433 " ideal model delta sigma weight residual 120.20 108.32 11.88 1.50e+00 4.44e-01 6.27e+01 angle pdb=" N GLU P 118 " pdb=" CA GLU P 118 " pdb=" C GLU P 118 " ideal model delta sigma weight residual 113.01 103.53 9.48 1.20e+00 6.94e-01 6.25e+01 ... (remaining 55319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 21121 35.95 - 71.91: 2566 71.91 - 107.86: 273 107.86 - 143.81: 7 143.81 - 179.77: 6 Dihedral angle restraints: 23973 sinusoidal: 19641 harmonic: 4332 Sorted by residual: dihedral pdb=" O4' U A 330 " pdb=" C1' U A 330 " pdb=" N1 U A 330 " pdb=" C2 U A 330 " ideal model delta sinusoidal sigma weight residual -160.00 15.99 -175.99 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U A 367 " pdb=" C1' U A 367 " pdb=" N1 U A 367 " pdb=" C2 U A 367 " ideal model delta sinusoidal sigma weight residual 200.00 55.90 144.10 1 1.50e+01 4.44e-03 7.72e+01 dihedral pdb=" O4' C A 736 " pdb=" C1' C A 736 " pdb=" N1 C A 736 " pdb=" C2 C A 736 " ideal model delta sinusoidal sigma weight residual 200.00 72.00 128.00 1 1.50e+01 4.44e-03 6.89e+01 ... (remaining 23970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 6763 0.090 - 0.180: 212 0.180 - 0.269: 21 0.269 - 0.359: 6 0.359 - 0.449: 13 Chirality restraints: 7015 Sorted by residual: chirality pdb=" P U Y 19 " pdb=" OP1 U Y 19 " pdb=" OP2 U Y 19 " pdb=" O5' U Y 19 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" P G A 195 " pdb=" OP1 G A 195 " pdb=" OP2 G A 195 " pdb=" O5' G A 195 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" P U Y 22 " pdb=" OP1 U Y 22 " pdb=" OP2 U Y 22 " pdb=" O5' U Y 22 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 7012 not shown) Planarity restraints: 3122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1503 " 0.063 2.00e-02 2.50e+03 5.99e-01 8.08e+03 pdb=" C4' 2MG A1503 " 0.438 2.00e-02 2.50e+03 pdb=" O4' 2MG A1503 " 0.620 2.00e-02 2.50e+03 pdb=" C3' 2MG A1503 " -0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG A1503 " -0.642 2.00e-02 2.50e+03 pdb=" C2' 2MG A1503 " -0.173 2.00e-02 2.50e+03 pdb=" O2' 2MG A1503 " 0.982 2.00e-02 2.50e+03 pdb=" C1' 2MG A1503 " 0.223 2.00e-02 2.50e+03 pdb=" N9 2MG A1503 " -0.917 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1394 " 0.046 2.00e-02 2.50e+03 5.78e-01 7.52e+03 pdb=" C4' 5MC A1394 " 0.435 2.00e-02 2.50e+03 pdb=" O4' 5MC A1394 " 0.611 2.00e-02 2.50e+03 pdb=" C3' 5MC A1394 " -0.591 2.00e-02 2.50e+03 pdb=" O3' 5MC A1394 " -0.599 2.00e-02 2.50e+03 pdb=" C2' 5MC A1394 " -0.195 2.00e-02 2.50e+03 pdb=" O2' 5MC A1394 " 0.939 2.00e-02 2.50e+03 pdb=" C1' 5MC A1394 " 0.228 2.00e-02 2.50e+03 pdb=" N1 5MC A1394 " -0.874 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1391 " 0.042 2.00e-02 2.50e+03 5.63e-01 7.13e+03 pdb=" C4' 5MC A1391 " 0.428 2.00e-02 2.50e+03 pdb=" O4' 5MC A1391 " 0.579 2.00e-02 2.50e+03 pdb=" C3' 5MC A1391 " -0.590 2.00e-02 2.50e+03 pdb=" O3' 5MC A1391 " -0.573 2.00e-02 2.50e+03 pdb=" C2' 5MC A1391 " -0.203 2.00e-02 2.50e+03 pdb=" O2' 5MC A1391 " 0.922 2.00e-02 2.50e+03 pdb=" C1' 5MC A1391 " 0.235 2.00e-02 2.50e+03 pdb=" N1 5MC A1391 " -0.840 2.00e-02 2.50e+03 ... (remaining 3119 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 227 2.46 - 3.07: 21693 3.07 - 3.68: 65435 3.68 - 4.29: 99707 4.29 - 4.90: 133480 Nonbonded interactions: 320542 Sorted by model distance: nonbonded pdb=" OP2 A A1486 " pdb="MG MG A1635 " model vdw 1.853 2.170 nonbonded pdb=" OP1 G A 651 " pdb="MG MG A1614 " model vdw 1.862 2.170 nonbonded pdb=" N7 G A1419 " pdb="MG MG A1619 " model vdw 1.889 2.250 nonbonded pdb=" OP1 A A 789 " pdb="MG MG A1614 " model vdw 1.896 2.170 nonbonded pdb=" N7 G A 364 " pdb="MG MG A1628 " model vdw 1.899 2.250 ... (remaining 320537 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.020 Extract box with map and model: 9.560 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 113.660 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 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 0.165 37120 Z= 0.332 Angle : 0.633 29.938 55324 Z= 0.347 Chirality : 0.040 0.449 7015 Planarity : 0.020 0.599 3122 Dihedral : 23.029 179.765 21175 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 1.08 % Allowed : 6.01 % Favored : 92.91 % Rotamer: Outliers : 1.76 % Allowed : 0.80 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1482 helix: 1.23 (0.20), residues: 653 sheet: -0.88 (0.34), residues: 209 loop : -1.44 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 80 HIS 0.007 0.001 HIS E 161 PHE 0.011 0.001 PHE K 58 TYR 0.018 0.002 TYR D 4 ARG 0.007 0.000 ARG L 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 431 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 172 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7585 (tptm) REVERT: D 193 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8291 (tp-100) REVERT: E 120 ARG cc_start: 0.8509 (mtm-85) cc_final: 0.7907 (mtm-85) REVERT: E 168 GLN cc_start: 0.8459 (mt0) cc_final: 0.8235 (mt0) REVERT: F 18 GLN cc_start: 0.7585 (pm20) cc_final: 0.7364 (pm20) REVERT: H 5 ASP cc_start: 0.8719 (t0) cc_final: 0.8127 (t0) REVERT: L 47 SER cc_start: 0.9308 (t) cc_final: 0.8906 (t) REVERT: R 33 ILE cc_start: 0.9262 (tt) cc_final: 0.9016 (tt) REVERT: R 36 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.8044 (mtm180) REVERT: P 102 ASP cc_start: 0.8848 (m-30) cc_final: 0.8530 (m-30) REVERT: P 117 ARG cc_start: 0.3874 (OUTLIER) cc_final: 0.3305 (tpp-160) REVERT: B 58 LYS cc_start: 0.6083 (mmpt) cc_final: 0.5471 (ttpp) REVERT: B 137 MET cc_start: 0.6205 (ptt) cc_final: 0.5894 (ptt) outliers start: 22 outliers final: 5 residues processed: 447 average time/residue: 1.6279 time to fit residues: 864.5706 Evaluate side-chains 356 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 349 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 207 ARG Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 117 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 195 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 HIS F 53 GLN H 18 ASN H 19 GLN K 83 HIS ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 GLN T 3 ASN T 7 GLN T 19 GLN P 65 GLN B 24 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 37120 Z= 0.418 Angle : 0.682 15.087 55324 Z= 0.367 Chirality : 0.040 0.309 7015 Planarity : 0.007 0.132 3122 Dihedral : 23.462 179.858 18177 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.07 % Favored : 93.39 % Rotamer: Outliers : 4.87 % Allowed : 18.61 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.22), residues: 1482 helix: 1.42 (0.20), residues: 654 sheet: -0.90 (0.33), residues: 218 loop : -1.45 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 80 HIS 0.022 0.001 HIS K 124 PHE 0.015 0.002 PHE R 32 TYR 0.022 0.002 TYR D 4 ARG 0.009 0.001 ARG L 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 356 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: E 168 GLN cc_start: 0.8579 (mt0) cc_final: 0.8370 (mt0) REVERT: E 197 LYS cc_start: 0.9052 (mppt) cc_final: 0.8289 (mppt) REVERT: F 18 GLN cc_start: 0.7457 (pm20) cc_final: 0.7234 (pm20) REVERT: F 41 ASP cc_start: 0.8412 (t0) cc_final: 0.8119 (t0) REVERT: H 5 ASP cc_start: 0.8732 (t0) cc_final: 0.8151 (t0) REVERT: H 12 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8997 (m) REVERT: K 42 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7189 (p0) REVERT: K 44 SER cc_start: 0.8765 (p) cc_final: 0.8480 (p) REVERT: L 47 SER cc_start: 0.9144 (t) cc_final: 0.8827 (t) REVERT: O 7 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8682 (tttp) REVERT: O 11 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7722 (mt-10) REVERT: Q 18 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8847 (mp) REVERT: Q 47 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8527 (mmmt) REVERT: R 51 ASP cc_start: 0.8427 (m-30) cc_final: 0.8226 (m-30) REVERT: T 15 GLU cc_start: 0.8268 (tp30) cc_final: 0.7847 (tp30) REVERT: P 111 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6895 (tm-30) REVERT: B 58 LYS cc_start: 0.5901 (mmpt) cc_final: 0.5283 (ttpp) REVERT: B 137 MET cc_start: 0.6224 (ptt) cc_final: 0.5915 (ptt) REVERT: B 188 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5533 (mt) outliers start: 61 outliers final: 26 residues processed: 380 average time/residue: 1.5117 time to fit residues: 683.1472 Evaluate side-chains 372 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 339 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 13 ILE Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 111 GLU Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 66 GLN F 53 GLN K 83 HIS O 60 GLN P 39 GLN P 65 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37120 Z= 0.204 Angle : 0.595 13.213 55324 Z= 0.328 Chirality : 0.034 0.293 7015 Planarity : 0.006 0.124 3122 Dihedral : 23.381 179.974 18157 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.53 % Favored : 93.99 % Rotamer: Outliers : 4.15 % Allowed : 21.49 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1482 helix: 1.70 (0.20), residues: 651 sheet: -0.69 (0.33), residues: 228 loop : -1.41 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 135 HIS 0.015 0.001 HIS K 124 PHE 0.007 0.001 PHE P 105 TYR 0.017 0.001 TYR D 4 ARG 0.006 0.000 ARG Q 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 367 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: E 171 GLU cc_start: 0.7770 (tp30) cc_final: 0.7441 (tt0) REVERT: E 198 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8458 (mm-30) REVERT: F 18 GLN cc_start: 0.7457 (pm20) cc_final: 0.7232 (pm20) REVERT: F 41 ASP cc_start: 0.8354 (t0) cc_final: 0.8111 (t0) REVERT: H 5 ASP cc_start: 0.8674 (t0) cc_final: 0.8105 (t0) REVERT: K 42 ASP cc_start: 0.7766 (t0) cc_final: 0.7189 (p0) REVERT: K 82 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: L 47 SER cc_start: 0.9011 (t) cc_final: 0.8634 (t) REVERT: L 94 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7847 (mtp85) REVERT: O 7 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8711 (ttpp) REVERT: O 11 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7611 (mt-10) REVERT: Q 47 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8585 (mmmt) REVERT: Q 64 ASP cc_start: 0.8159 (m-30) cc_final: 0.7932 (m-30) REVERT: R 64 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7738 (mt-10) REVERT: T 15 GLU cc_start: 0.8300 (tp30) cc_final: 0.7860 (tp30) REVERT: P 62 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9191 (p) REVERT: B 58 LYS cc_start: 0.6027 (mmpt) cc_final: 0.5359 (ttpp) REVERT: B 188 LEU cc_start: 0.6184 (pt) cc_final: 0.5756 (OUTLIER) outliers start: 52 outliers final: 23 residues processed: 383 average time/residue: 1.5666 time to fit residues: 711.0993 Evaluate side-chains 382 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 355 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain B residue 182 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 240 optimal weight: 0.0570 chunk 118 optimal weight: 5.9990 chunk 215 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 overall best weight: 1.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN E 168 GLN F 53 GLN H 18 ASN H 19 GLN K 83 HIS L 75 GLN O 60 GLN P 65 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 37120 Z= 0.197 Angle : 0.584 13.055 55324 Z= 0.321 Chirality : 0.033 0.280 7015 Planarity : 0.006 0.123 3122 Dihedral : 23.326 179.951 18156 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.80 % Favored : 93.72 % Rotamer: Outliers : 5.11 % Allowed : 22.84 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1482 helix: 1.89 (0.20), residues: 643 sheet: -0.54 (0.34), residues: 221 loop : -1.31 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 59 HIS 0.012 0.001 HIS K 124 PHE 0.012 0.001 PHE K 58 TYR 0.016 0.001 TYR D 4 ARG 0.006 0.000 ARG R 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 372 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 171 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: E 201 GLU cc_start: 0.8603 (pp20) cc_final: 0.8387 (mp0) REVERT: F 18 GLN cc_start: 0.7407 (pm20) cc_final: 0.7197 (pm20) REVERT: F 41 ASP cc_start: 0.8295 (t0) cc_final: 0.8053 (t0) REVERT: H 5 ASP cc_start: 0.8677 (t0) cc_final: 0.8120 (t0) REVERT: K 42 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7225 (p0) REVERT: K 82 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8366 (pm20) REVERT: L 47 SER cc_start: 0.8997 (t) cc_final: 0.8630 (t) REVERT: L 56 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7812 (ttm-80) REVERT: O 7 LYS cc_start: 0.9050 (ttpp) cc_final: 0.8607 (tttp) REVERT: O 11 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7481 (mt-10) REVERT: Q 47 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8552 (mmmt) REVERT: R 64 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7814 (mt-10) REVERT: T 15 GLU cc_start: 0.8319 (tp30) cc_final: 0.7921 (tp30) REVERT: P 62 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9204 (p) REVERT: B 188 LEU cc_start: 0.6265 (pt) cc_final: 0.5858 (OUTLIER) outliers start: 64 outliers final: 33 residues processed: 393 average time/residue: 1.4842 time to fit residues: 695.3113 Evaluate side-chains 391 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 354 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 182 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 179 optimal weight: 0.0170 chunk 99 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 166 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN E 168 GLN F 53 GLN K 83 HIS L 75 GLN P 65 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 37120 Z= 0.162 Angle : 0.576 12.857 55324 Z= 0.316 Chirality : 0.032 0.272 7015 Planarity : 0.006 0.122 3122 Dihedral : 23.316 179.508 18156 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.87 % Favored : 93.72 % Rotamer: Outliers : 4.55 % Allowed : 23.96 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1482 helix: 1.86 (0.20), residues: 647 sheet: -0.54 (0.34), residues: 227 loop : -1.30 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 135 HIS 0.009 0.001 HIS K 124 PHE 0.008 0.001 PHE B 56 TYR 0.015 0.001 TYR D 4 ARG 0.009 0.000 ARG E 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 364 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 171 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: F 18 GLN cc_start: 0.7490 (pm20) cc_final: 0.7283 (pm20) REVERT: F 41 ASP cc_start: 0.8284 (t0) cc_final: 0.7984 (t0) REVERT: F 54 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8808 (mmtp) REVERT: F 57 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: H 5 ASP cc_start: 0.8669 (t0) cc_final: 0.8114 (t0) REVERT: K 42 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7137 (p0) REVERT: K 82 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8428 (pm20) REVERT: L 47 SER cc_start: 0.9003 (t) cc_final: 0.8640 (t) REVERT: L 94 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7829 (mtp85) REVERT: O 7 LYS cc_start: 0.9056 (ttpp) cc_final: 0.8698 (tttp) REVERT: O 11 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7515 (mt-10) REVERT: R 64 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7819 (mt-10) REVERT: T 15 GLU cc_start: 0.8301 (tp30) cc_final: 0.7936 (tp30) REVERT: P 62 VAL cc_start: 0.9423 (OUTLIER) cc_final: 0.9189 (p) REVERT: B 50 ILE cc_start: 0.7485 (mp) cc_final: 0.7154 (pt) REVERT: B 188 LEU cc_start: 0.6457 (pt) cc_final: 0.5983 (OUTLIER) outliers start: 57 outliers final: 30 residues processed: 383 average time/residue: 1.5056 time to fit residues: 686.6938 Evaluate side-chains 384 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 348 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 125 ASN Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 182 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 240 optimal weight: 30.0000 chunk 199 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 83 HIS L 46 ASN P 65 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 37120 Z= 0.339 Angle : 0.636 13.214 55324 Z= 0.346 Chirality : 0.036 0.277 7015 Planarity : 0.006 0.127 3122 Dihedral : 23.277 179.640 18156 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.48 % Favored : 93.18 % Rotamer: Outliers : 5.19 % Allowed : 25.00 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1482 helix: 1.68 (0.20), residues: 651 sheet: -0.35 (0.36), residues: 207 loop : -1.32 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 80 HIS 0.012 0.001 HIS K 124 PHE 0.012 0.002 PHE R 32 TYR 0.028 0.002 TYR D 4 ARG 0.009 0.000 ARG E 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 368 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: D 87 GLN cc_start: 0.8897 (tt0) cc_final: 0.8697 (tt0) REVERT: D 191 ASN cc_start: 0.8758 (t0) cc_final: 0.8554 (t0) REVERT: E 171 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: F 18 GLN cc_start: 0.7591 (pm20) cc_final: 0.7391 (pm20) REVERT: F 41 ASP cc_start: 0.8365 (t0) cc_final: 0.8058 (t0) REVERT: F 54 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8791 (mmtp) REVERT: F 57 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: H 5 ASP cc_start: 0.8674 (t0) cc_final: 0.8117 (t0) REVERT: K 42 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7326 (p0) REVERT: K 82 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8477 (pm20) REVERT: L 47 SER cc_start: 0.8927 (t) cc_final: 0.8596 (t) REVERT: L 56 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7878 (ttm-80) REVERT: L 94 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7946 (mtp85) REVERT: O 7 LYS cc_start: 0.9063 (ttpp) cc_final: 0.8604 (tttp) REVERT: O 11 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7555 (mt-10) REVERT: O 62 ARG cc_start: 0.8980 (tpp-160) cc_final: 0.8525 (tpp-160) REVERT: Q 1 MET cc_start: 0.4425 (OUTLIER) cc_final: 0.3298 (ptp) REVERT: Q 47 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8478 (mmmt) REVERT: T 15 GLU cc_start: 0.8311 (tp30) cc_final: 0.7853 (tp30) REVERT: B 188 LEU cc_start: 0.6537 (pt) cc_final: 0.6053 (mm) outliers start: 65 outliers final: 42 residues processed: 393 average time/residue: 1.5004 time to fit residues: 704.2074 Evaluate side-chains 410 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 359 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 125 ASN Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 182 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 40.0000 chunk 27 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 19 GLN K 83 HIS L 75 GLN P 65 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37120 Z= 0.177 Angle : 0.606 13.066 55324 Z= 0.332 Chirality : 0.033 0.282 7015 Planarity : 0.006 0.124 3122 Dihedral : 23.368 179.747 18156 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.21 % Favored : 93.39 % Rotamer: Outliers : 4.79 % Allowed : 25.64 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1482 helix: 1.71 (0.20), residues: 644 sheet: -0.42 (0.35), residues: 219 loop : -1.39 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 59 HIS 0.007 0.001 HIS K 124 PHE 0.015 0.001 PHE P 105 TYR 0.030 0.002 TYR D 4 ARG 0.010 0.000 ARG E 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 366 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 ASN cc_start: 0.8687 (t0) cc_final: 0.8454 (t0) REVERT: E 171 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: F 18 GLN cc_start: 0.7581 (pm20) cc_final: 0.7380 (pm20) REVERT: F 41 ASP cc_start: 0.8299 (t0) cc_final: 0.7988 (t0) REVERT: F 57 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: H 5 ASP cc_start: 0.8656 (t0) cc_final: 0.8119 (t0) REVERT: K 42 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7333 (p0) REVERT: K 82 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8519 (pm20) REVERT: L 47 SER cc_start: 0.8840 (t) cc_final: 0.8493 (t) REVERT: L 94 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7851 (mtp85) REVERT: O 7 LYS cc_start: 0.9019 (ttpp) cc_final: 0.8515 (tttp) REVERT: O 11 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7472 (mt-10) REVERT: O 62 ARG cc_start: 0.8965 (tpp-160) cc_final: 0.8538 (tpp-160) REVERT: Q 1 MET cc_start: 0.4429 (OUTLIER) cc_final: 0.3338 (ptp) REVERT: Q 47 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8505 (mmmt) REVERT: T 15 GLU cc_start: 0.8289 (tp30) cc_final: 0.7849 (tp30) REVERT: B 89 MET cc_start: 0.3810 (tpp) cc_final: 0.3449 (tpt) REVERT: B 188 LEU cc_start: 0.6593 (pt) cc_final: 0.6136 (mm) outliers start: 60 outliers final: 40 residues processed: 386 average time/residue: 1.5055 time to fit residues: 691.1722 Evaluate side-chains 405 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 358 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 125 ASN Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 182 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 152 optimal weight: 0.5980 chunk 163 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS L 46 ASN L 75 GLN P 65 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 37120 Z= 0.445 Angle : 0.688 13.156 55324 Z= 0.370 Chirality : 0.040 0.288 7015 Planarity : 0.007 0.129 3122 Dihedral : 23.300 178.888 18156 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.82 % Favored : 92.85 % Rotamer: Outliers : 4.95 % Allowed : 26.44 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1482 helix: 1.47 (0.20), residues: 649 sheet: -0.44 (0.36), residues: 213 loop : -1.40 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 80 HIS 0.011 0.001 HIS K 124 PHE 0.018 0.002 PHE R 32 TYR 0.026 0.002 TYR D 4 ARG 0.014 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 355 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 18 ASP cc_start: 0.8377 (t0) cc_final: 0.7876 (t0) REVERT: D 191 ASN cc_start: 0.8884 (t0) cc_final: 0.8638 (t0) REVERT: E 171 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7513 (tt0) REVERT: F 18 GLN cc_start: 0.7648 (pm20) cc_final: 0.7271 (pm20) REVERT: F 41 ASP cc_start: 0.8338 (t0) cc_final: 0.8068 (t0) REVERT: F 54 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8898 (mmtp) REVERT: F 57 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: F 84 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8507 (tttp) REVERT: H 5 ASP cc_start: 0.8673 (t0) cc_final: 0.8127 (t0) REVERT: K 82 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: L 47 SER cc_start: 0.8936 (t) cc_final: 0.8634 (t) REVERT: L 56 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7865 (ttm-80) REVERT: L 94 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7943 (mtp85) REVERT: O 11 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7669 (mt-10) REVERT: Q 47 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8513 (mmmt) REVERT: T 15 GLU cc_start: 0.8316 (tp30) cc_final: 0.7956 (tp30) REVERT: B 28 LYS cc_start: 0.3542 (OUTLIER) cc_final: 0.3234 (ttmm) REVERT: B 188 LEU cc_start: 0.6553 (pt) cc_final: 0.6154 (mm) outliers start: 62 outliers final: 41 residues processed: 375 average time/residue: 1.5499 time to fit residues: 689.7295 Evaluate side-chains 400 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 351 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 125 ASN Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 182 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 66 GLN F 53 GLN H 19 GLN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 GLN O 60 GLN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37120 Z= 0.159 Angle : 0.600 12.607 55324 Z= 0.329 Chirality : 0.032 0.274 7015 Planarity : 0.006 0.121 3122 Dihedral : 23.331 179.762 18156 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.87 % Favored : 93.79 % Rotamer: Outliers : 3.51 % Allowed : 28.35 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1482 helix: 1.77 (0.20), residues: 645 sheet: -0.35 (0.35), residues: 223 loop : -1.41 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 59 HIS 0.005 0.001 HIS K 124 PHE 0.008 0.001 PHE B 56 TYR 0.020 0.001 TYR D 4 ARG 0.013 0.000 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 367 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 ASN cc_start: 0.8751 (t0) cc_final: 0.8522 (t0) REVERT: E 171 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: E 201 GLU cc_start: 0.8566 (pp20) cc_final: 0.8342 (mp0) REVERT: F 16 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8173 (mm-30) REVERT: F 18 GLN cc_start: 0.7612 (pm20) cc_final: 0.7256 (pm20) REVERT: F 41 ASP cc_start: 0.8329 (t0) cc_final: 0.8091 (t0) REVERT: H 5 ASP cc_start: 0.8661 (t0) cc_final: 0.8189 (t0) REVERT: K 81 MET cc_start: 0.8047 (mtt) cc_final: 0.7842 (mtt) REVERT: L 47 SER cc_start: 0.8939 (t) cc_final: 0.8593 (t) REVERT: L 94 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7832 (mtp85) REVERT: O 7 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8593 (ttpp) REVERT: O 11 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7466 (mt-10) REVERT: O 62 ARG cc_start: 0.8914 (tpp-160) cc_final: 0.8539 (tpp-160) REVERT: Q 47 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8487 (mmmt) REVERT: Q 87 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7621 (mp0) REVERT: R 36 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8080 (mtm180) REVERT: T 15 GLU cc_start: 0.8292 (tp30) cc_final: 0.7873 (tp30) REVERT: B 28 LYS cc_start: 0.3518 (mtmt) cc_final: 0.3242 (ttmm) REVERT: B 50 ILE cc_start: 0.7433 (mp) cc_final: 0.7072 (pt) REVERT: B 169 LYS cc_start: 0.5605 (mmmt) cc_final: 0.5367 (tttp) REVERT: B 188 LEU cc_start: 0.6553 (pt) cc_final: 0.6138 (mm) outliers start: 44 outliers final: 26 residues processed: 381 average time/residue: 1.5460 time to fit residues: 701.2037 Evaluate side-chains 386 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 357 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 125 ASN Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 182 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 228 optimal weight: 0.0770 chunk 197 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 121 optimal weight: 0.0470 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 168 GLN F 53 GLN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 GLN O 60 GLN P 65 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37120 Z= 0.213 Angle : 0.604 12.670 55324 Z= 0.330 Chirality : 0.033 0.267 7015 Planarity : 0.006 0.123 3122 Dihedral : 23.272 179.903 18156 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.41 % Favored : 93.25 % Rotamer: Outliers : 2.88 % Allowed : 29.63 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1482 helix: 1.73 (0.20), residues: 641 sheet: -0.28 (0.36), residues: 221 loop : -1.38 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 59 HIS 0.007 0.001 HIS K 124 PHE 0.015 0.001 PHE K 58 TYR 0.021 0.002 TYR D 4 ARG 0.015 0.000 ARG R 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 356 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 ASN cc_start: 0.8753 (t0) cc_final: 0.8502 (t0) REVERT: E 171 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: E 201 GLU cc_start: 0.8577 (pp20) cc_final: 0.8319 (mp0) REVERT: F 16 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8196 (mm-30) REVERT: F 18 GLN cc_start: 0.7650 (pm20) cc_final: 0.7319 (pm20) REVERT: F 41 ASP cc_start: 0.8362 (t0) cc_final: 0.8149 (t0) REVERT: F 54 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8807 (mmtp) REVERT: H 5 ASP cc_start: 0.8672 (t0) cc_final: 0.8188 (t0) REVERT: L 47 SER cc_start: 0.8957 (t) cc_final: 0.8639 (t) REVERT: L 94 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7853 (mtp85) REVERT: O 7 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8472 (ttpp) REVERT: O 11 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7387 (mt-10) REVERT: Q 47 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8524 (mmmt) REVERT: Q 87 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7577 (mp0) REVERT: R 64 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7763 (mt-10) REVERT: T 15 GLU cc_start: 0.8292 (tp30) cc_final: 0.7895 (tp30) REVERT: T 33 ARG cc_start: 0.8708 (ttp80) cc_final: 0.8467 (ttp-170) REVERT: P 101 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7876 (ttpt) REVERT: B 169 LYS cc_start: 0.5608 (mmmt) cc_final: 0.5371 (tttp) REVERT: B 188 LEU cc_start: 0.6571 (pt) cc_final: 0.6143 (mm) outliers start: 36 outliers final: 28 residues processed: 370 average time/residue: 1.5682 time to fit residues: 688.9429 Evaluate side-chains 382 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 349 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 125 ASN Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 101 LYS Chi-restraints excluded: chain P residue 103 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 182 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 203 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 36 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 83 HIS L 46 ASN L 75 GLN O 60 GLN P 65 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.089201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.063494 restraints weight = 78395.469| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 1.58 r_work: 0.2639 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 37120 Z= 0.381 Angle : 0.667 12.853 55324 Z= 0.361 Chirality : 0.038 0.274 7015 Planarity : 0.007 0.128 3122 Dihedral : 23.259 179.964 18156 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.48 % Favored : 93.18 % Rotamer: Outliers : 3.75 % Allowed : 28.83 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1482 helix: 1.57 (0.20), residues: 641 sheet: -0.31 (0.37), residues: 213 loop : -1.36 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 80 HIS 0.010 0.001 HIS K 124 PHE 0.014 0.002 PHE R 32 TYR 0.028 0.002 TYR D 4 ARG 0.015 0.001 ARG R 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11503.89 seconds wall clock time: 207 minutes 7.01 seconds (12427.01 seconds total)