Starting phenix.real_space_refine on Sat Mar 16 11:11:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/03_2024/6pc5_20296_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/03_2024/6pc5_20296.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/03_2024/6pc5_20296_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/03_2024/6pc5_20296_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/03_2024/6pc5_20296_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/03_2024/6pc5_20296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/03_2024/6pc5_20296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/03_2024/6pc5_20296_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/03_2024/6pc5_20296_neut_updated.pdb" } resolution = 2.7 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= -0.010 sd= 0.917 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 3015 5.49 5 S 22 5.16 5 C 33559 2.51 5 N 13328 2.21 5 O 22281 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 35": "OE1" <-> "OE2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 121": "OD1" <-> "OD2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K GLU 185": "OE1" <-> "OE2" Residue "K ARG 189": "NH1" <-> "NH2" Residue "K ARG 203": "NH1" <-> "NH2" Residue "K ARG 212": "NH1" <-> "NH2" Residue "K ARG 221": "NH1" <-> "NH2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ARG 170": "NH1" <-> "NH2" Residue "M ASP 171": "OD1" <-> "OD2" Residue "M ASP 184": "OD1" <-> "OD2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "O ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 72206 Number of models: 1 Model: "" Number of chains: 9 Chain: "I" Number of atoms: 62206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62206 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 152, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1060} Link IDs: {'rna2p': 438, 'rna3p': 2458} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1542 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Chain: "O" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 60 Classifications: {'peptide': 7} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'MHV:plan-2': 1, 'DBB:plan-1': 1, '004:plan-2': 1, 'MEA:plan-2': 1, 'MHW:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'O7V': 1} Classifications: {'undetermined': 1} Time building chain proxies: 33.54, per 1000 atoms: 0.46 Number of scatterers: 72206 At special positions: 0 Unit cell: (228.776, 222.145, 190.647, 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 22 16.00 P 3015 15.00 F 1 9.00 O 22281 8.00 N 13328 7.00 C 33559 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 36.29 Conformation dependent library (CDL) restraints added in 1.6 seconds 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB MHW C 1 " pdb=" CB DBB C 3 " Number of C-beta restraints generated: 1716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 13 sheets defined 18.4% alpha, 14.2% beta 912 base pairs and 1655 stacking pairs defined. Time for finding SS restraints: 39.79 Creating SS restraints... Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'K' and resid 209 through 213 removed outlier: 3.508A pdb=" N TRP K 213 " --> pdb=" O GLY K 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 209 through 213' Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 79 through 84 removed outlier: 4.481A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.672A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 92 through 98' Processing helix chain 'L' and resid 129 through 138 Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 39 Processing helix chain 'M' and resid 98 through 114 removed outlier: 3.551A pdb=" N GLU M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 140 Processing helix chain 'M' and resid 155 through 160 Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 removed outlier: 3.581A pdb=" N GLN M 195 " --> pdb=" O ASP M 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 71 removed outlier: 3.974A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 101 Processing helix chain 'N' and resid 121 through 124 No H-bonds generated for 'chain 'N' and resid 121 through 124' Processing helix chain 'O' and resid 25 through 37 removed outlier: 4.108A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 68 through 71 No H-bonds generated for 'chain 'O' and resid 68 through 71' Processing helix chain 'O' and resid 89 through 107 Proline residue: O 97 - end of helix removed outlier: 4.381A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA O 104 " --> pdb=" O VAL O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 removed outlier: 3.960A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 135 No H-bonds generated for 'chain 'O' and resid 133 through 135' Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'K' and resid 101 through 105 removed outlier: 3.598A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 129 through 131 Processing sheet with id= E, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.976A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.300A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'M' and resid 2 through 4 Processing sheet with id= H, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.296A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 169 through 172 removed outlier: 4.588A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL N 189 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP N 181 " --> pdb=" O LEU N 186 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS N 190 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL N 177 " --> pdb=" O LYS N 190 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 80 through 83 removed outlier: 6.179A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 115 through 119 removed outlier: 5.816A pdb=" N MET N 165 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE N 118 " --> pdb=" O GLY N 163 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY N 163 " --> pdb=" O PHE N 118 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.446A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE O 55 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'O' and resid 73 through 76 135 hydrogen bonds defined for protein. 378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2297 hydrogen bonds 3744 hydrogen bond angles 0 basepair planarities 912 basepair parallelities 1655 stacking parallelities Total time for adding SS restraints: 146.32 Time building geometry restraints manager: 38.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9429 1.33 - 1.45: 36928 1.45 - 1.57: 27639 1.57 - 1.69: 6046 1.69 - 1.81: 42 Bond restraints: 80084 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.410 0.392 2.00e-02 2.50e+03 3.84e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.80e+02 bond pdb=" C20 O7V I3001 " pdb=" C21 O7V I3001 " ideal model delta sigma weight residual 1.630 1.349 0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.363 0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.367 0.268 2.00e-02 2.50e+03 1.79e+02 ... (remaining 80079 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.87: 17924 106.87 - 113.89: 50661 113.89 - 120.92: 32429 120.92 - 127.95: 17320 127.95 - 134.97: 4951 Bond angle restraints: 123285 Sorted by residual: angle pdb=" C20 O7V I3001 " pdb=" C21 O7V I3001 " pdb=" C22 O7V I3001 " ideal model delta sigma weight residual 85.78 126.93 -41.15 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C13 O7V I3001 " pdb=" C15 O7V I3001 " pdb=" C16 O7V I3001 " ideal model delta sigma weight residual 85.77 125.40 -39.63 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C19 O7V I3001 " pdb=" C20 O7V I3001 " pdb=" C21 O7V I3001 " ideal model delta sigma weight residual 154.32 121.97 32.35 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C15 O7V I3001 " pdb=" C16 O7V I3001 " pdb=" C17 O7V I3001 " ideal model delta sigma weight residual 154.32 124.54 29.78 3.00e+00 1.11e-01 9.85e+01 angle pdb=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C8 2MA I2503 " ideal model delta sigma weight residual 106.32 126.67 -20.35 3.00e+00 1.11e-01 4.60e+01 ... (remaining 123280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 44159 35.77 - 71.54: 6610 71.54 - 107.30: 782 107.30 - 143.07: 8 143.07 - 178.84: 6 Dihedral angle restraints: 51565 sinusoidal: 48869 harmonic: 2696 Sorted by residual: dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual -128.00 50.71 -178.71 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 46.89 -174.89 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U I1313 " pdb=" C1' U I1313 " pdb=" N1 U I1313 " pdb=" C2 U I1313 " ideal model delta sinusoidal sigma weight residual 200.00 90.37 109.63 1 1.50e+01 4.44e-03 5.70e+01 ... (remaining 51562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 16001 0.071 - 0.142: 152 0.142 - 0.213: 4 0.213 - 0.284: 2 0.284 - 0.355: 2 Chirality restraints: 16161 Sorted by residual: chirality pdb=" CA THR C 2 " pdb=" N THR C 2 " pdb=" C THR C 2 " pdb=" CB THR C 2 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C22 O7V I3001 " pdb=" C21 O7V I3001 " pdb=" C23 O7V I3001 " pdb=" C24 O7V I3001 " both_signs ideal model delta sigma weight residual False -2.78 -2.44 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C54 O7V I3001 " pdb=" C53 O7V I3001 " pdb=" C55 O7V I3001 " pdb=" F19 O7V I3001 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 16158 not shown) Planarity restraints: 4349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.022 2.00e-02 2.50e+03 5.95e-01 7.98e+03 pdb=" C4' 2MG I2445 " -0.461 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.765 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.563 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.236 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.872 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.199 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.937 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.037 2.00e-02 2.50e+03 5.90e-01 7.83e+03 pdb=" C4' OMG I2251 " 0.444 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.683 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.595 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.589 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.208 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.921 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.216 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.909 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I1835 " -0.040 2.00e-02 2.50e+03 5.77e-01 7.49e+03 pdb=" C4' 2MG I1835 " -0.437 2.00e-02 2.50e+03 pdb=" O4' 2MG I1835 " -0.642 2.00e-02 2.50e+03 pdb=" C3' 2MG I1835 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG I1835 " 0.578 2.00e-02 2.50e+03 pdb=" C2' 2MG I1835 " 0.206 2.00e-02 2.50e+03 pdb=" O2' 2MG I1835 " -0.914 2.00e-02 2.50e+03 pdb=" C1' 2MG I1835 " -0.226 2.00e-02 2.50e+03 pdb=" N9 2MG I1835 " 0.879 2.00e-02 2.50e+03 ... (remaining 4346 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 474 2.55 - 3.14: 51669 3.14 - 3.73: 145755 3.73 - 4.31: 210014 4.31 - 4.90: 268493 Nonbonded interactions: 676405 Sorted by model distance: nonbonded pdb=" OP1 C I 885 " pdb=" O2' C I 893 " model vdw 1.965 2.440 nonbonded pdb=" O2* PSU I1911 " pdb=" OP1 A I1912 " model vdw 1.986 3.040 nonbonded pdb=" O2' A I1508 " pdb=" O4' A I1509 " model vdw 1.995 2.440 nonbonded pdb=" O2' A I1378 " pdb=" OP2 G I1380 " model vdw 1.998 2.440 nonbonded pdb=" O2' G I1826 " pdb=" OP2 U I1971 " model vdw 2.000 2.440 ... (remaining 676400 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: 6.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 27.770 Check model and map are aligned: 0.830 Set scattering table: 0.540 Process input model: 303.140 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 350.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 0.392 80084 Z= 0.363 Angle : 0.438 41.146 123285 Z= 0.206 Chirality : 0.024 0.355 16161 Planarity : 0.023 0.595 4349 Dihedral : 23.603 178.841 49849 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.09 % Favored : 93.80 % Rotamer: Outliers : 1.57 % Allowed : 10.62 % Favored : 87.81 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.23), residues: 952 helix: -2.86 (0.28), residues: 153 sheet: -1.62 (0.35), residues: 180 loop : -2.51 (0.21), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 78 HIS 0.004 0.001 HIS K 200 PHE 0.003 0.001 PHE N 101 TYR 0.008 0.001 TYR L 58 ARG 0.002 0.000 ARG M 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 233 time to evaluate : 2.349 Fit side-chains REVERT: M 194 LYS cc_start: 0.8360 (mptp) cc_final: 0.8151 (mppt) outliers start: 12 outliers final: 6 residues processed: 240 average time/residue: 1.6574 time to fit residues: 518.6443 Evaluate side-chains 162 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 253 LYS Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 358 optimal weight: 0.0870 overall best weight: 7.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 134 ASN L 93 ASN M 41 GLN M 115 GLN N 32 ASN N 36 GLN N 136 ASN N 164 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 80084 Z= 0.484 Angle : 0.743 14.757 123285 Z= 0.383 Chirality : 0.042 0.361 16161 Planarity : 0.008 0.139 4349 Dihedral : 23.545 171.962 48058 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.99 % Favored : 93.80 % Rotamer: Outliers : 5.50 % Allowed : 17.30 % Favored : 77.20 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.25), residues: 952 helix: -0.97 (0.38), residues: 165 sheet: -1.08 (0.35), residues: 186 loop : -1.69 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 248 HIS 0.005 0.002 HIS N 140 PHE 0.010 0.002 PHE M 183 TYR 0.016 0.002 TYR K 83 ARG 0.006 0.001 ARG O 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 2.195 Fit side-chains REVERT: K 135 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8948 (mt) REVERT: L 2 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7212 (mmm160) REVERT: M 61 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7619 (ptm-80) REVERT: M 65 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7230 (p) REVERT: N 128 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7526 (mpp80) outliers start: 42 outliers final: 24 residues processed: 192 average time/residue: 1.5369 time to fit residues: 391.5443 Evaluate side-chains 178 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 2 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 298 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 359 optimal weight: 2.9990 chunk 388 optimal weight: 4.9990 chunk 320 optimal weight: 0.9980 chunk 356 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN N 36 GLN N 49 GLN N 94 GLN O 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 80084 Z= 0.185 Angle : 0.611 14.035 123285 Z= 0.327 Chirality : 0.031 0.346 16161 Planarity : 0.007 0.134 4349 Dihedral : 23.653 172.813 48052 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.99 % Favored : 93.91 % Rotamer: Outliers : 5.90 % Allowed : 18.87 % Favored : 75.23 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.63 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.25), residues: 952 helix: -0.61 (0.39), residues: 165 sheet: -0.80 (0.37), residues: 176 loop : -1.34 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS K 200 PHE 0.012 0.001 PHE M 124 TYR 0.011 0.002 TYR K 83 ARG 0.005 0.001 ARG N 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 2.249 Fit side-chains REVERT: L 2 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7173 (mmm-85) REVERT: M 61 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7548 (ptm-80) REVERT: M 65 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7093 (p) REVERT: N 184 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8107 (mtt180) REVERT: O 31 GLU cc_start: 0.8029 (tp30) cc_final: 0.7813 (mm-30) outliers start: 45 outliers final: 28 residues processed: 176 average time/residue: 1.5466 time to fit residues: 362.7584 Evaluate side-chains 187 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 2 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 7 LYS Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 7.9990 chunk 270 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 381 optimal weight: 0.0770 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 overall best weight: 6.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN N 49 GLN N 94 GLN O 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 80084 Z= 0.452 Angle : 0.711 14.412 123285 Z= 0.370 Chirality : 0.040 0.379 16161 Planarity : 0.007 0.140 4349 Dihedral : 23.678 173.779 48052 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.38 % Rotamer: Outliers : 7.21 % Allowed : 18.74 % Favored : 74.05 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.63 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.26), residues: 952 helix: -0.70 (0.37), residues: 178 sheet: -0.58 (0.40), residues: 171 loop : -1.14 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 248 HIS 0.006 0.001 HIS M 165 PHE 0.011 0.002 PHE M 124 TYR 0.012 0.002 TYR K 96 ARG 0.007 0.001 ARG O 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 159 time to evaluate : 2.233 Fit side-chains REVERT: K 135 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8925 (mt) REVERT: K 147 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8454 (mtmt) REVERT: K 180 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: L 2 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7148 (mmm-85) REVERT: M 61 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7620 (ptm-80) REVERT: M 65 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7404 (p) REVERT: N 128 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7499 (mpp80) REVERT: O 31 GLU cc_start: 0.8177 (tp30) cc_final: 0.7963 (mm-30) outliers start: 55 outliers final: 30 residues processed: 187 average time/residue: 1.4755 time to fit residues: 370.6985 Evaluate side-chains 187 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 2 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 3.9990 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 7.9990 chunk 284 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 0.9990 chunk 263 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 342 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 93 ASN M 136 GLN N 49 GLN N 94 GLN O 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 80084 Z= 0.397 Angle : 0.673 14.153 123285 Z= 0.356 Chirality : 0.038 0.372 16161 Planarity : 0.007 0.138 4349 Dihedral : 23.684 174.118 48052 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.20 % Favored : 93.59 % Rotamer: Outliers : 6.16 % Allowed : 20.71 % Favored : 73.13 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.63 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 952 helix: -0.59 (0.37), residues: 178 sheet: -0.54 (0.41), residues: 169 loop : -1.07 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.006 0.001 HIS M 165 PHE 0.011 0.001 PHE M 124 TYR 0.014 0.002 TYR K 103 ARG 0.004 0.000 ARG O 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 148 time to evaluate : 2.266 Fit side-chains REVERT: K 147 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8810 (mtmt) REVERT: K 180 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: L 2 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7147 (mmm-85) REVERT: M 61 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7579 (ptm-80) REVERT: M 65 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7457 (p) REVERT: M 88 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7621 (mmp80) REVERT: N 128 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7475 (mpp80) REVERT: O 31 GLU cc_start: 0.8182 (tp30) cc_final: 0.7959 (mm-30) outliers start: 47 outliers final: 36 residues processed: 174 average time/residue: 1.4742 time to fit residues: 344.9199 Evaluate side-chains 192 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 149 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 2 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 88 ARG Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain N residue 7 LYS Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 8.9990 chunk 343 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 382 optimal weight: 4.9990 chunk 317 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 93 ASN M 136 GLN N 49 GLN N 94 GLN O 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 80084 Z= 0.346 Angle : 0.655 14.068 123285 Z= 0.348 Chirality : 0.037 0.365 16161 Planarity : 0.007 0.138 4349 Dihedral : 23.694 174.168 48052 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.38 % Rotamer: Outliers : 6.29 % Allowed : 21.76 % Favored : 71.95 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.63 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 952 helix: -0.53 (0.37), residues: 179 sheet: -0.53 (0.41), residues: 169 loop : -1.01 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS M 165 PHE 0.012 0.001 PHE M 124 TYR 0.012 0.001 TYR K 103 ARG 0.004 0.000 ARG O 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 151 time to evaluate : 2.267 Fit side-chains REVERT: K 39 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8393 (mttt) REVERT: K 135 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8919 (mt) REVERT: K 147 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8809 (mtmt) REVERT: K 180 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: L 2 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7138 (mmm-85) REVERT: M 61 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7576 (ptm-80) REVERT: M 65 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7460 (p) REVERT: M 88 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7607 (mmp80) REVERT: N 128 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7474 (mpp80) REVERT: N 184 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7662 (mtp180) REVERT: O 31 GLU cc_start: 0.8176 (tp30) cc_final: 0.7956 (mm-30) outliers start: 48 outliers final: 34 residues processed: 177 average time/residue: 1.5259 time to fit residues: 363.4386 Evaluate side-chains 194 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 2 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 88 ARG Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain N residue 7 LYS Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 40.0000 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 40.0000 chunk 321 optimal weight: 4.9990 chunk 213 optimal weight: 40.0000 chunk 380 optimal weight: 7.9990 chunk 238 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 251 GLN L 93 ASN M 41 GLN M 136 GLN N 36 GLN N 49 GLN N 94 GLN O 136 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 80084 Z= 0.443 Angle : 0.701 15.097 123285 Z= 0.368 Chirality : 0.040 0.361 16161 Planarity : 0.007 0.139 4349 Dihedral : 23.803 174.085 48052 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.72 % Favored : 93.07 % Rotamer: Outliers : 6.68 % Allowed : 21.76 % Favored : 71.56 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.63 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.26), residues: 952 helix: -0.68 (0.37), residues: 181 sheet: -0.65 (0.41), residues: 171 loop : -0.96 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 248 HIS 0.004 0.001 HIS O 76 PHE 0.009 0.002 PHE M 124 TYR 0.012 0.002 TYR K 103 ARG 0.006 0.001 ARG O 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 150 time to evaluate : 2.677 Fit side-chains REVERT: K 39 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8350 (mttt) REVERT: K 147 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8840 (mtmt) REVERT: K 180 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: L 2 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.6939 (mmm160) REVERT: M 61 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7612 (ptm-80) REVERT: M 65 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7696 (p) REVERT: M 88 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7600 (mmp80) REVERT: N 128 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7464 (mpp80) outliers start: 51 outliers final: 32 residues processed: 177 average time/residue: 1.5007 time to fit residues: 356.5717 Evaluate side-chains 188 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain L residue 2 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 88 ARG Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 227 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN M 136 GLN N 49 GLN N 94 GLN O 58 ASN O 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 80084 Z= 0.486 Angle : 0.719 14.736 123285 Z= 0.375 Chirality : 0.042 0.416 16161 Planarity : 0.008 0.143 4349 Dihedral : 23.796 174.152 48052 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.62 % Favored : 93.17 % Rotamer: Outliers : 6.42 % Allowed : 21.63 % Favored : 71.95 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.63 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.26), residues: 952 helix: -0.71 (0.37), residues: 180 sheet: -0.64 (0.40), residues: 176 loop : -1.00 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 248 HIS 0.006 0.001 HIS M 165 PHE 0.012 0.002 PHE M 124 TYR 0.014 0.002 TYR K 103 ARG 0.006 0.001 ARG O 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 150 time to evaluate : 2.202 Fit side-chains REVERT: K 39 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8337 (mttt) REVERT: K 135 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8972 (mt) REVERT: K 147 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8811 (mtmt) REVERT: L 2 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7047 (mmm160) REVERT: M 61 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7611 (ptm-80) REVERT: M 65 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7742 (p) REVERT: M 88 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7638 (mmp80) REVERT: M 195 GLN cc_start: 0.8017 (mt0) cc_final: 0.7613 (tp40) REVERT: N 128 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7460 (mpp80) outliers start: 49 outliers final: 34 residues processed: 178 average time/residue: 1.4676 time to fit residues: 352.6190 Evaluate side-chains 187 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 145 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 2 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 88 ARG Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.8980 chunk 364 optimal weight: 0.9990 chunk 332 optimal weight: 1.9990 chunk 354 optimal weight: 4.9990 chunk 213 optimal weight: 40.0000 chunk 154 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 40.0000 chunk 320 optimal weight: 2.9990 chunk 335 optimal weight: 0.0040 chunk 353 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN N 49 GLN N 94 GLN N 173 GLN ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 80084 Z= 0.132 Angle : 0.617 14.189 123285 Z= 0.331 Chirality : 0.032 0.388 16161 Planarity : 0.006 0.127 4349 Dihedral : 23.906 175.115 48052 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.30 % Favored : 93.49 % Rotamer: Outliers : 4.19 % Allowed : 25.03 % Favored : 70.77 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.63 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.26), residues: 952 helix: -0.50 (0.37), residues: 180 sheet: -0.39 (0.43), residues: 158 loop : -0.89 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 248 HIS 0.004 0.001 HIS K 15 PHE 0.012 0.002 PHE M 124 TYR 0.010 0.001 TYR K 103 ARG 0.004 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 2.629 Fit side-chains REVERT: K 39 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8330 (mttt) REVERT: K 135 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8952 (mt) REVERT: M 61 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7450 (ptm-80) REVERT: M 65 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7496 (p) REVERT: M 88 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7565 (mmp80) REVERT: M 195 GLN cc_start: 0.7983 (mt0) cc_final: 0.7604 (tp40) REVERT: N 128 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7418 (mpp80) REVERT: N 184 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7767 (mtp180) outliers start: 32 outliers final: 18 residues processed: 171 average time/residue: 1.5467 time to fit residues: 356.6697 Evaluate side-chains 178 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 88 ARG Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 10.0000 chunk 375 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 chunk 393 optimal weight: 10.0000 chunk 362 optimal weight: 0.9980 chunk 313 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 GLN M 165 HIS N 49 GLN N 94 GLN N 173 GLN ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 80084 Z= 0.397 Angle : 0.669 14.093 123285 Z= 0.353 Chirality : 0.038 0.413 16161 Planarity : 0.007 0.139 4349 Dihedral : 23.756 174.335 48052 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.38 % Rotamer: Outliers : 3.93 % Allowed : 25.95 % Favored : 70.12 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.63 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.26), residues: 952 helix: -0.55 (0.38), residues: 180 sheet: -0.48 (0.41), residues: 168 loop : -0.88 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.011 0.001 PHE M 124 TYR 0.014 0.002 TYR K 103 ARG 0.005 0.001 ARG O 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 3.035 Fit side-chains REVERT: K 39 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8347 (mttt) REVERT: K 135 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8930 (mt) REVERT: M 61 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7566 (ptm-80) REVERT: M 65 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7613 (p) REVERT: M 88 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7618 (mmp80) REVERT: M 195 GLN cc_start: 0.8022 (mt0) cc_final: 0.7609 (tp40) REVERT: N 128 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7466 (mpp80) REVERT: N 184 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7394 (mtp180) outliers start: 30 outliers final: 21 residues processed: 159 average time/residue: 1.5162 time to fit residues: 324.9042 Evaluate side-chains 168 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 88 ARG Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 7.9990 chunk 333 optimal weight: 0.5980 chunk 95 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 322 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 165 HIS N 49 GLN N 94 GLN ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.080978 restraints weight = 138574.012| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 0.46 r_work: 0.2946 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 80084 Z= 0.266 Angle : 0.628 13.997 123285 Z= 0.337 Chirality : 0.034 0.403 16161 Planarity : 0.007 0.136 4349 Dihedral : 23.788 174.519 48052 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.09 % Favored : 93.70 % Rotamer: Outliers : 4.46 % Allowed : 25.29 % Favored : 70.25 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.63 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.26), residues: 952 helix: -0.51 (0.38), residues: 180 sheet: -0.48 (0.41), residues: 168 loop : -0.84 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.003 0.001 HIS K 200 PHE 0.010 0.001 PHE M 124 TYR 0.015 0.002 TYR K 103 ARG 0.007 0.000 ARG L 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10214.51 seconds wall clock time: 184 minutes 23.23 seconds (11063.23 seconds total)