Starting phenix.real_space_refine on Sun Feb 18 10:23:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/02_2024/6pc5_20296_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/02_2024/6pc5_20296.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/02_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_20296/02_2024/6pc5_20296_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/02_2024/6pc5_20296_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/02_2024/6pc5_20296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/02_2024/6pc5_20296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/02_2024/6pc5_20296_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc5_20296/02_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 13 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: 28.87, per 1000 atoms: 0.40 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: 32.81 Conformation dependent library (CDL) restraints added in 1.5 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: 40.75 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: 137.38 Time building geometry restraints manager: 35.20 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=" 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 bond pdb=" C15 O7V I3001 " pdb=" C16 O7V I3001 " ideal model delta sigma weight residual 1.601 1.348 0.253 2.00e-02 2.50e+03 1.60e+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=" N30 O7V I3001 " pdb=" C31 O7V I3001 " pdb=" N40 O7V I3001 " ideal model delta sigma weight residual 50.79 114.57 -63.78 3.00e+00 1.11e-01 4.52e+02 angle pdb=" C13 O7V I3001 " pdb=" C15 O7V I3001 " pdb=" C16 O7V I3001 " ideal model delta sigma weight residual 85.81 125.40 -39.59 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C8 6MZ I1618 " ideal model delta sigma weight residual 91.39 126.47 -35.08 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C32 O7V I3001 " pdb=" C31 O7V I3001 " pdb=" N30 O7V I3001 " ideal model delta sigma weight residual 155.49 122.23 33.26 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C19 O7V I3001 " pdb=" C20 O7V I3001 " pdb=" C21 O7V I3001 " ideal model delta sigma weight residual 154.30 121.97 32.33 3.00e+00 1.11e-01 1.16e+02 ... (remaining 123280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 44166 35.77 - 71.54: 6624 71.54 - 107.30: 790 107.30 - 143.07: 14 143.07 - 178.84: 7 Dihedral angle restraints: 51601 sinusoidal: 48905 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 51598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 15975 0.071 - 0.142: 151 0.142 - 0.213: 3 0.213 - 0.284: 1 0.284 - 0.355: 1 Chirality restraints: 16131 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=" CA 004 C 7 " pdb=" N 004 C 7 " pdb=" C 004 C 7 " pdb=" CB 004 C 7 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA DBB C 3 " pdb=" N DBB C 3 " pdb=" C DBB C 3 " pdb=" CB DBB C 3 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.18 2.00e-01 2.50e+01 8.49e-01 ... (remaining 16128 not shown) Planarity restraints: 4355 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' 1MG I 745 " -0.040 2.00e-02 2.50e+03 5.93e-01 7.92e+03 pdb=" C4' 1MG I 745 " -0.446 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.689 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.596 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.205 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.924 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.214 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.917 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 ... (remaining 4352 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: 6.690 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: 0.050 Extract box with map and model: 28.310 Check model and map are aligned: 0.820 Set scattering table: 0.510 Process input model: 282.440 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 331.180 ------------------------------------------------------------------------------- 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= 0.362 Angle : 0.497 63.779 123285 Z= 0.222 Chirality : 0.024 0.355 16131 Planarity : 0.031 0.595 4355 Dihedral : 23.688 178.841 49885 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 : 2.165 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: 1.6691 time to fit residues: 523.7554 Evaluate side-chains 162 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 2.137 ------------------------------------------------------------------------------- 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 136 ASN N 164 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 80084 Z= 0.482 Angle : 0.790 19.701 123285 Z= 0.416 Chirality : 0.042 0.376 16131 Planarity : 0.009 0.145 4355 Dihedral : 23.711 171.315 48094 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.09 % Favored : 93.70 % Rotamer: Outliers : 5.37 % Allowed : 17.30 % Favored : 77.33 % 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: -2.05 (0.25), residues: 952 helix: -1.04 (0.38), residues: 165 sheet: -1.10 (0.36), residues: 178 loop : -1.58 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 248 HIS 0.006 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 211 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 170 time to evaluate : 2.176 Fit side-chains REVERT: K 135 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8962 (mt) REVERT: L 2 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7246 (mmm-85) REVERT: M 61 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7608 (ptm-80) REVERT: M 65 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7307 (p) REVERT: N 128 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7472 (mpp80) REVERT: O 31 GLU cc_start: 0.8181 (tp30) cc_final: 0.7946 (mm-30) outliers start: 41 outliers final: 22 residues processed: 190 average time/residue: 1.5757 time to fit residues: 398.2700 Evaluate side-chains 178 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 98 optimal weight: 6.9990 chunk 359 optimal weight: 2.9990 chunk 388 optimal weight: 0.9990 chunk 320 optimal weight: 2.9990 chunk 356 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8687 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 80084 Z= 0.234 Angle : 0.639 17.555 123285 Z= 0.351 Chirality : 0.032 0.337 16131 Planarity : 0.008 0.131 4355 Dihedral : 23.686 173.959 48088 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.88 % Favored : 94.01 % Rotamer: Outliers : 6.16 % Allowed : 18.87 % Favored : 74.97 % 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: -1.47 (0.26), residues: 952 helix: -0.32 (0.40), residues: 165 sheet: -0.66 (0.35), residues: 203 loop : -1.30 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.003 0.001 HIS N 140 PHE 0.006 0.001 PHE M 124 TYR 0.010 0.001 TYR K 103 ARG 0.004 0.000 ARG L 126 *********************** 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 204 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 157 time to evaluate : 4.098 Fit side-chains REVERT: L 2 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7097 (mmm-85) REVERT: L 110 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7228 (t) REVERT: M 61 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7556 (ptm-80) REVERT: M 184 ASP cc_start: 0.7812 (m-30) cc_final: 0.7519 (m-30) outliers start: 47 outliers final: 24 residues processed: 182 average time/residue: 1.5549 time to fit residues: 379.7023 Evaluate side-chains 182 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL 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 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 110 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 61 ARG 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 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 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: 10.0000 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: 7.9990 chunk 381 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 30 GLN M 136 GLN N 49 GLN N 94 GLN O 58 ASN O 128 ASN O 136 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 80084 Z= 0.538 Angle : 0.796 18.276 123285 Z= 0.417 Chirality : 0.044 0.392 16131 Planarity : 0.009 0.144 4355 Dihedral : 23.831 173.617 48087 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.04 % Favored : 92.75 % Rotamer: Outliers : 7.08 % Allowed : 19.40 % Favored : 73.53 % 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: -1.41 (0.26), residues: 952 helix: -0.68 (0.37), residues: 178 sheet: -0.64 (0.40), residues: 176 loop : -1.11 (0.24), residues: 598 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 0.013 0.002 PHE M 124 TYR 0.013 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 200 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 146 time to evaluate : 2.244 Fit side-chains REVERT: K 135 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8916 (mt) REVERT: K 147 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8916 (mtmt) REVERT: K 180 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: L 2 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7185 (mmm-85) REVERT: M 61 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7617 (ptm-80) REVERT: M 65 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7572 (p) REVERT: M 88 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7620 (mmp80) REVERT: M 184 ASP cc_start: 0.7781 (m-30) cc_final: 0.7488 (m-30) REVERT: N 128 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7458 (mpp80) outliers start: 54 outliers final: 34 residues processed: 173 average time/residue: 1.5372 time to fit residues: 356.1823 Evaluate side-chains 180 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 138 time to evaluate : 2.220 ------------------------------------------------------------------------------- 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 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 L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET 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 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 193 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 28 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 5.9990 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 6.9990 chunk 284 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 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 115 GLN L 93 ASN M 136 GLN N 49 GLN N 94 GLN O 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 80084 Z= 0.404 Angle : 0.726 17.925 123285 Z= 0.391 Chirality : 0.038 0.375 16131 Planarity : 0.008 0.141 4355 Dihedral : 23.853 174.053 48087 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.30 % Favored : 93.49 % Rotamer: Outliers : 6.55 % Allowed : 20.31 % 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: -1.35 (0.26), residues: 952 helix: -0.61 (0.38), residues: 180 sheet: -0.54 (0.41), residues: 174 loop : -1.10 (0.24), residues: 598 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 0.015 0.002 PHE M 124 TYR 0.015 0.002 TYR K 103 ARG 0.008 0.001 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 196 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 2.216 Fit side-chains REVERT: K 147 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8846 (mtmt) REVERT: K 180 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: L 2 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7168 (mmm-85) REVERT: M 61 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7623 (ptm-80) REVERT: M 65 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7552 (p) REVERT: M 88 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7591 (mmp80) REVERT: M 184 ASP cc_start: 0.7769 (m-30) cc_final: 0.7511 (m-30) REVERT: N 128 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7408 (mpp80) outliers start: 50 outliers final: 37 residues processed: 172 average time/residue: 1.4961 time to fit residues: 347.2835 Evaluate side-chains 188 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 2.261 ------------------------------------------------------------------------------- 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 1 MET 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 157 LYS 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: 7.9990 chunk 343 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 382 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 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: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN L 93 ASN M 136 GLN N 49 GLN N 94 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 80084 Z= 0.375 Angle : 0.709 17.540 123285 Z= 0.382 Chirality : 0.038 0.363 16131 Planarity : 0.008 0.139 4355 Dihedral : 23.825 174.243 48087 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.20 % Favored : 93.59 % Rotamer: Outliers : 6.95 % Allowed : 20.71 % Favored : 72.35 % 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: -1.23 (0.26), residues: 952 helix: -0.50 (0.38), residues: 179 sheet: -0.50 (0.41), residues: 174 loop : -1.02 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.006 0.001 HIS K 200 PHE 0.011 0.001 PHE M 124 TYR 0.016 0.002 TYR K 103 ARG 0.006 0.001 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 198 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 145 time to evaluate : 2.235 Fit side-chains REVERT: K 39 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8277 (mttt) REVERT: K 147 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8837 (mtmt) REVERT: K 180 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: L 2 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7080 (mmm160) REVERT: M 61 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7566 (ptm-80) REVERT: M 65 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7563 (p) REVERT: M 88 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7607 (mmp80) REVERT: M 184 ASP cc_start: 0.7750 (m-30) cc_final: 0.7475 (m-30) REVERT: N 128 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7400 (mpp80) outliers start: 53 outliers final: 36 residues processed: 175 average time/residue: 1.4863 time to fit residues: 350.7968 Evaluate side-chains 187 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 143 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 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 1 MET 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 157 LYS 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 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: 10.0000 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: 3.9990 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: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN M 41 GLN M 136 GLN N 49 GLN N 94 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 80084 Z= 0.555 Angle : 0.818 18.159 123285 Z= 0.428 Chirality : 0.045 0.403 16131 Planarity : 0.009 0.143 4355 Dihedral : 23.977 173.714 48087 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.25 % Favored : 92.54 % Rotamer: Outliers : 6.68 % Allowed : 22.15 % Favored : 71.17 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.63 % Twisted General : 0.22 % 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: -0.63 (0.38), residues: 178 sheet: -0.59 (0.40), residues: 181 loop : -0.98 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 248 HIS 0.005 0.001 HIS O 76 PHE 0.016 0.002 PHE M 124 TYR 0.017 0.002 TYR K 103 ARG 0.008 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 186 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 135 time to evaluate : 2.243 Fit side-chains REVERT: K 39 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8376 (mttt) REVERT: K 147 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8518 (mtmt) REVERT: K 180 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: L 2 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7123 (mmm160) REVERT: M 61 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7644 (ptm-80) REVERT: M 88 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7635 (mmp80) REVERT: M 184 ASP cc_start: 0.7765 (m-30) cc_final: 0.7449 (m-30) REVERT: N 128 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7554 (mpp80) outliers start: 51 outliers final: 37 residues processed: 166 average time/residue: 1.5532 time to fit residues: 343.3244 Evaluate side-chains 178 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 134 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1 MET 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 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 62 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 227 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 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 251 GLN L 93 ASN M 136 GLN N 49 GLN N 94 GLN N 173 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 80084 Z= 0.346 Angle : 0.689 17.548 123285 Z= 0.374 Chirality : 0.037 0.355 16131 Planarity : 0.008 0.135 4355 Dihedral : 23.868 174.600 48087 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.09 % Favored : 93.70 % Rotamer: Outliers : 6.55 % Allowed : 22.15 % Favored : 71.30 % 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: -1.16 (0.26), residues: 952 helix: -0.46 (0.38), residues: 180 sheet: -0.42 (0.41), residues: 173 loop : -0.97 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.004 0.001 HIS K 200 PHE 0.008 0.001 PHE M 124 TYR 0.016 0.002 TYR K 103 ARG 0.003 0.000 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 192 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 142 time to evaluate : 2.656 Fit side-chains REVERT: K 147 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8811 (mtmt) REVERT: L 2 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.6992 (mmm160) REVERT: L 14 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8398 (mttm) REVERT: M 61 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7568 (ptm-80) REVERT: M 65 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7627 (p) REVERT: M 184 ASP cc_start: 0.7738 (m-30) cc_final: 0.7427 (m-30) REVERT: M 195 GLN cc_start: 0.8014 (mt0) cc_final: 0.7606 (tp40) REVERT: N 128 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7387 (mpp80) outliers start: 50 outliers final: 36 residues processed: 172 average time/residue: 1.5598 time to fit residues: 357.8118 Evaluate side-chains 183 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 141 time to evaluate : 2.164 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain L residue 2 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 14 LYS 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 1 MET 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 96 VAL 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 193 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.9980 chunk 364 optimal weight: 5.9990 chunk 332 optimal weight: 0.9990 chunk 354 optimal weight: 7.9990 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: 8.9990 chunk 335 optimal weight: 0.0270 chunk 353 optimal weight: 0.0010 overall best weight: 1.6048 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 80084 Z= 0.147 Angle : 0.651 17.790 123285 Z= 0.357 Chirality : 0.030 0.338 16131 Planarity : 0.008 0.130 4355 Dihedral : 23.948 174.984 48087 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.20 % Favored : 93.59 % Rotamer: Outliers : 4.98 % Allowed : 23.59 % Favored : 71.43 % 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: -1.00 (0.26), residues: 952 helix: -0.26 (0.39), residues: 177 sheet: -0.30 (0.43), residues: 163 loop : -0.88 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.003 0.001 HIS K 200 PHE 0.009 0.001 PHE M 124 TYR 0.013 0.001 TYR K 103 ARG 0.004 0.000 ARG N 59 *********************** 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 184 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 2.224 Fit side-chains REVERT: K 269 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7130 (mmm160) REVERT: L 2 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.6997 (mmm-85) REVERT: M 61 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7460 (ptm-80) REVERT: M 65 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7560 (p) REVERT: M 184 ASP cc_start: 0.7727 (m-30) cc_final: 0.7500 (m-30) REVERT: M 195 GLN cc_start: 0.7976 (mt0) cc_final: 0.7592 (tp40) REVERT: N 128 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7365 (mpp80) outliers start: 38 outliers final: 29 residues processed: 168 average time/residue: 1.5334 time to fit residues: 345.3504 Evaluate side-chains 177 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 88 SER 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 K residue 269 ARG 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 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 75 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 96 VAL 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 M residue 199 MET 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 O residue 21 THR 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: 7.9990 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 chunk 393 optimal weight: 2.9990 chunk 362 optimal weight: 0.7980 chunk 313 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 80084 Z= 0.355 Angle : 0.691 17.560 123285 Z= 0.375 Chirality : 0.037 0.345 16131 Planarity : 0.008 0.137 4355 Dihedral : 23.848 174.341 48087 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.09 % Favored : 93.70 % Rotamer: Outliers : 4.59 % Allowed : 24.51 % Favored : 70.90 % 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: -1.02 (0.26), residues: 952 helix: -0.40 (0.38), residues: 179 sheet: -0.35 (0.41), residues: 173 loop : -0.84 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.004 0.001 HIS K 200 PHE 0.009 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 179 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 2.292 Fit side-chains REVERT: L 14 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8416 (mttm) REVERT: M 61 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7567 (ptm-80) REVERT: M 65 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7629 (p) REVERT: M 184 ASP cc_start: 0.7749 (m-30) cc_final: 0.7497 (m-30) REVERT: M 195 GLN cc_start: 0.7989 (mt0) cc_final: 0.7592 (tp40) REVERT: N 128 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7384 (mpp80) outliers start: 35 outliers final: 30 residues processed: 164 average time/residue: 1.5441 time to fit residues: 339.5560 Evaluate side-chains 177 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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 88 SER 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 7 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 116 VAL 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 75 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 96 VAL 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 M residue 199 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 7.9990 chunk 333 optimal weight: 0.9980 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: 4.9990 chunk 131 optimal weight: 8.9990 chunk 322 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.080603 restraints weight = 138363.158| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 0.55 r_work: 0.2944 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 80084 Z= 0.360 Angle : 0.692 17.551 123285 Z= 0.375 Chirality : 0.037 0.337 16131 Planarity : 0.008 0.136 4355 Dihedral : 23.839 174.394 48087 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.30 % Favored : 93.49 % Rotamer: Outliers : 4.59 % Allowed : 24.77 % Favored : 70.64 % 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: -1.02 (0.26), residues: 952 helix: -0.42 (0.38), residues: 177 sheet: -0.35 (0.41), residues: 173 loop : -0.84 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.005 0.001 HIS M 165 PHE 0.010 0.001 PHE M 124 TYR 0.017 0.002 TYR K 103 ARG 0.005 0.001 ARG O 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10202.58 seconds wall clock time: 184 minutes 37.42 seconds (11077.42 seconds total)