Starting phenix.real_space_refine on Sat Mar 16 10:30:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/03_2024/6wyv_21969_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/03_2024/6wyv_21969.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/03_2024/6wyv_21969_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/03_2024/6wyv_21969_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/03_2024/6wyv_21969_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/03_2024/6wyv_21969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/03_2024/6wyv_21969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/03_2024/6wyv_21969_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/03_2024/6wyv_21969_neut_updated.pdb" } resolution = 2.75 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= -0.004 sd= 1.095 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 33551 2.51 5 N 13326 2.21 5 O 22279 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 23": "OE1" <-> "OE2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ASP 66": "OD1" <-> "OD2" Residue "K ARG 80": "NH1" <-> "NH2" 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 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 ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ARG 170": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "O PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 72194 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': 151, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 437, 'rna3p': 2459} 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'O7S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 29.24, per 1000 atoms: 0.41 Number of scatterers: 72194 At special positions: 0 Unit cell: (228.83, 220.569, 190.003, 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 22279 8.00 N 13326 7.00 C 33551 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: 35.39 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 DBB C 3 " Number of C-beta restraints generated: 1718 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 18.8% alpha, 13.2% beta 827 base pairs and 1597 stacking pairs defined. Time for finding SS restraints: 39.36 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 132 through 134 No H-bonds generated for 'chain 'K' and resid 132 through 134' 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 212 No H-bonds generated for 'chain 'K' and resid 209 through 212' 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 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.950A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 3.559A 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 137 removed outlier: 3.695A pdb=" N GLU L 136 " --> pdb=" O ARG L 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 39 removed outlier: 3.568A pdb=" N VAL M 33 " --> pdb=" O HIS M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 114 removed outlier: 3.644A pdb=" N ALA M 104 " --> pdb=" O MET M 100 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU M 105 " --> pdb=" O TYR M 101 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL M 113 " --> pdb=" O LEU M 109 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 141 removed outlier: 3.745A pdb=" N MET M 141 " --> pdb=" O LYS M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 160 Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 removed outlier: 3.732A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 70 Processing helix chain 'N' and resid 98 through 101 Processing helix chain 'N' and resid 121 through 125 Processing helix chain 'O' and resid 25 through 36 removed outlier: 4.399A 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 66 through 71 removed outlier: 4.430A pdb=" N ARG O 69 " --> pdb=" O GLY O 66 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP O 71 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 108 removed outlier: 3.555A pdb=" N ARG O 95 " --> pdb=" O GLU O 91 " (cutoff:3.500A) Proline residue: O 97 - end of helix removed outlier: 4.439A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 removed outlier: 3.578A 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 103 through 105 removed outlier: 3.509A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.290A 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: 3.750A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.782A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.962A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'M' and resid 2 through 4 Processing sheet with id= I, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.380A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR M 150 " --> pdb=" O ARG M 170 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 removed outlier: 7.617A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 186 through 190 removed outlier: 3.661A pdb=" N VAL N 189 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU N 28 " --> pdb=" O LYS N 8 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS N 8 " --> pdb=" O GLU N 28 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 80 through 83 removed outlier: 3.696A pdb=" N ALA N 47 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.567A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE O 55 " --> pdb=" O VAL O 18 " (cutoff:3.500A) 122 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2034 hydrogen bonds 3336 hydrogen bond angles 0 basepair planarities 827 basepair parallelities 1597 stacking parallelities Total time for adding SS restraints: 130.75 Time building geometry restraints manager: 37.67 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: 9598 1.33 - 1.45: 36921 1.45 - 1.57: 27463 1.57 - 1.69: 6046 1.69 - 1.81: 42 Bond restraints: 80070 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.411 0.391 2.00e-02 2.50e+03 3.82e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.413 0.389 2.00e-02 2.50e+03 3.79e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.366 0.269 2.00e-02 2.50e+03 1.80e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.368 0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C21 O7S I3001 " pdb=" C22 O7S I3001 " ideal model delta sigma weight residual 1.604 1.349 0.255 2.00e-02 2.50e+03 1.63e+02 ... (remaining 80065 not shown) Histogram of bond angle deviations from ideal: 99.95 - 107.04: 17945 107.04 - 114.13: 51523 114.13 - 121.22: 33666 121.22 - 128.30: 15465 128.30 - 135.39: 4666 Bond angle restraints: 123265 Sorted by residual: angle pdb=" C06 O7S I3001 " pdb=" C07 O7S I3001 " pdb=" C08 O7S I3001 " ideal model delta sigma weight residual 68.65 120.18 -51.53 3.00e+00 1.11e-01 2.95e+02 angle pdb=" C07 O7S I3001 " pdb=" C09 O7S I3001 " pdb=" C10 O7S I3001 " ideal model delta sigma weight residual 85.68 128.21 -42.53 3.00e+00 1.11e-01 2.01e+02 angle pdb=" C08 O7S I3001 " pdb=" C07 O7S I3001 " pdb=" C09 O7S I3001 " ideal model delta sigma weight residual 154.34 122.03 32.31 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C06 O7S I3001 " pdb=" C07 O7S I3001 " pdb=" C09 O7S I3001 " ideal model delta sigma weight residual 85.69 117.76 -32.07 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C21 O7S I3001 " pdb=" C22 O7S I3001 " pdb=" C23 O7S I3001 " ideal model delta sigma weight residual 154.32 124.57 29.75 3.00e+00 1.11e-01 9.83e+01 ... (remaining 123260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 44135 35.60 - 71.20: 6621 71.20 - 106.79: 790 106.79 - 142.39: 12 142.39 - 177.99: 10 Dihedral angle restraints: 51568 sinusoidal: 48870 harmonic: 2698 Sorted by residual: dihedral pdb=" C MHW C 1 " pdb=" N MHW C 1 " pdb=" CA MHW C 1 " pdb=" CB MHW C 1 " ideal model delta harmonic sigma weight residual -122.60 -179.31 56.71 0 2.50e+00 1.60e-01 5.15e+02 dihedral pdb=" N MHW C 1 " pdb=" C MHW C 1 " pdb=" CA MHW C 1 " pdb=" CB MHW C 1 " ideal model delta harmonic sigma weight residual 122.80 179.27 -56.47 0 2.50e+00 1.60e-01 5.10e+02 dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual 232.00 54.67 177.33 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 51565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 15974 0.069 - 0.137: 179 0.137 - 0.206: 3 0.206 - 0.275: 3 0.275 - 0.343: 1 Chirality restraints: 16160 Sorted by residual: chirality pdb=" C23 O7S I3001 " pdb=" C22 O7S I3001 " pdb=" C24 O7S I3001 " pdb=" C27 O7S I3001 " both_signs ideal model delta sigma weight residual False -2.78 -2.43 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C12 O7S I3001 " pdb=" C11 O7S I3001 " pdb=" C14 O7S I3001 " pdb=" F13 O7S I3001 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.88e+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 2.22 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 16157 not shown) Planarity restraints: 4347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.027 2.00e-02 2.50e+03 6.05e-01 8.22e+03 pdb=" C4' 2MG I2445 " -0.471 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.803 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.582 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.566 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.245 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.865 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.186 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.960 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I1835 " -0.031 2.00e-02 2.50e+03 5.82e-01 7.63e+03 pdb=" C4' 2MG I1835 " -0.443 2.00e-02 2.50e+03 pdb=" O4' 2MG I1835 " -0.686 2.00e-02 2.50e+03 pdb=" C3' 2MG I1835 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG I1835 " 0.569 2.00e-02 2.50e+03 pdb=" C2' 2MG I1835 " 0.217 2.00e-02 2.50e+03 pdb=" O2' 2MG I1835 " -0.897 2.00e-02 2.50e+03 pdb=" C1' 2MG I1835 " -0.219 2.00e-02 2.50e+03 pdb=" N9 2MG I1835 " 0.899 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.029 2.00e-02 2.50e+03 5.66e-01 7.20e+03 pdb=" C4' OMG I2251 " 0.433 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.628 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.590 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.555 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.214 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.896 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.231 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.858 2.00e-02 2.50e+03 ... (remaining 4344 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 480 2.52 - 3.11: 50418 3.11 - 3.71: 142582 3.71 - 4.30: 205666 4.30 - 4.90: 269227 Nonbonded interactions: 668373 Sorted by model distance: nonbonded pdb=" O2' G I1980 " pdb=" OP2 U I1982 " model vdw 1.925 2.440 nonbonded pdb=" O2' A I 415 " pdb=" OP1 A I1866 " model vdw 1.930 2.440 nonbonded pdb=" O2' G I1826 " pdb=" OP2 U I1971 " model vdw 1.952 2.440 nonbonded pdb=" OP2 C I 672 " pdb=" OG SER L 42 " model vdw 1.955 2.440 nonbonded pdb=" O2* PSU I1911 " pdb=" OP1 A I1912 " model vdw 1.958 3.040 ... (remaining 668368 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: 10.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 45.010 Check model and map are aligned: 0.840 Set scattering table: 0.500 Process input model: 278.980 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.150 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:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 348.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 0.391 80070 Z= 0.339 Angle : 0.484 51.531 123265 Z= 0.218 Chirality : 0.024 0.343 16160 Planarity : 0.022 0.605 4347 Dihedral : 23.727 177.991 49850 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.14 % Favored : 92.75 % Rotamer: Outliers : 1.57 % Allowed : 14.68 % Favored : 83.75 % 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: -4.66 (0.21), residues: 952 helix: -4.04 (0.23), residues: 165 sheet: -3.09 (0.35), residues: 164 loop : -2.97 (0.20), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 78 HIS 0.002 0.001 HIS M 165 PHE 0.004 0.001 PHE N 101 TYR 0.010 0.001 TYR L 58 ARG 0.002 0.000 ARG L 21 *********************** 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 243 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 231 time to evaluate : 2.134 Fit side-chains revert: symmetry clash REVERT: K 191 THR cc_start: 0.8605 (m) cc_final: 0.8347 (p) REVERT: M 44 ARG cc_start: 0.8480 (ptm160) cc_final: 0.8257 (ptm160) REVERT: M 72 SER cc_start: 0.8897 (t) cc_final: 0.8691 (t) REVERT: M 139 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7890 (ttpt) REVERT: N 13 ARG cc_start: 0.5194 (ptp-170) cc_final: 0.4814 (ptp-170) REVERT: N 201 LEU cc_start: 0.9053 (pt) cc_final: 0.8849 (pp) REVERT: O 69 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.7729 (ttm-80) outliers start: 12 outliers final: 6 residues processed: 240 average time/residue: 1.6545 time to fit residues: 519.4696 Evaluate side-chains 163 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 73 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 358 optimal weight: 4.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 60 GLN K 143 ASN K 153 GLN K 197 ASN K 226 ASN K 251 GLN L 104 GLN M 41 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 164 GLN O 47 HIS O 86 GLN O 138 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 80070 Z= 0.528 Angle : 0.853 17.187 123265 Z= 0.427 Chirality : 0.045 0.310 16160 Planarity : 0.008 0.150 4347 Dihedral : 23.699 177.885 48054 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 6.55 % Allowed : 23.59 % Favored : 69.86 % 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: -3.41 (0.23), residues: 952 helix: -2.75 (0.29), residues: 177 sheet: -1.93 (0.38), residues: 162 loop : -2.30 (0.22), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 78 HIS 0.007 0.002 HIS O 76 PHE 0.015 0.002 PHE M 19 TYR 0.012 0.002 TYR O 44 ARG 0.009 0.001 ARG K 270 *********************** 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 261 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 211 time to evaluate : 2.242 Fit side-chains REVERT: K 63 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.6672 (mpp80) REVERT: K 71 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7197 (tttt) REVERT: K 72 ASP cc_start: 0.8172 (m-30) cc_final: 0.7796 (m-30) REVERT: K 116 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6610 (pt) REVERT: K 143 ASN cc_start: 0.8538 (t0) cc_final: 0.8247 (t0) REVERT: K 182 ARG cc_start: 0.8650 (ttt90) cc_final: 0.8398 (ttm-80) REVERT: L 39 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8516 (mtpm) REVERT: M 75 SER cc_start: 0.8831 (m) cc_final: 0.8576 (m) REVERT: M 139 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7938 (ttpt) REVERT: N 28 GLU cc_start: 0.7411 (tp30) cc_final: 0.6599 (tp30) REVERT: N 70 LYS cc_start: 0.7791 (tttt) cc_final: 0.7517 (tttp) REVERT: O 106 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8152 (mmtp) REVERT: O 142 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.7002 (mp) outliers start: 50 outliers final: 20 residues processed: 247 average time/residue: 1.5464 time to fit residues: 510.1847 Evaluate side-chains 205 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 266 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 chunk 244 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 359 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 320 optimal weight: 1.9990 chunk 356 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 197 ASN K 251 GLN N 134 HIS N 136 ASN O 128 ASN O 138 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 80070 Z= 0.213 Angle : 0.593 13.860 123265 Z= 0.316 Chirality : 0.031 0.267 16160 Planarity : 0.007 0.130 4347 Dihedral : 23.645 176.101 48051 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.50 % Allowed : 27.65 % Favored : 66.84 % 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: -2.53 (0.24), residues: 952 helix: -1.67 (0.35), residues: 183 sheet: -1.54 (0.38), residues: 169 loop : -1.77 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 78 HIS 0.010 0.001 HIS K 142 PHE 0.015 0.002 PHE K 240 TYR 0.011 0.001 TYR K 103 ARG 0.005 0.000 ARG O 37 *********************** 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 243 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 201 time to evaluate : 2.275 Fit side-chains REVERT: K 39 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8350 (mtpt) REVERT: K 63 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.6632 (mpp80) REVERT: K 103 TYR cc_start: 0.7938 (m-10) cc_final: 0.7728 (m-80) REVERT: M 139 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7911 (ttpt) REVERT: M 158 PHE cc_start: 0.8570 (t80) cc_final: 0.8286 (t80) REVERT: N 70 LYS cc_start: 0.7835 (tttt) cc_final: 0.7635 (tttp) REVERT: N 201 LEU cc_start: 0.8945 (pt) cc_final: 0.8739 (pp) REVERT: O 106 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8075 (mmtp) REVERT: O 142 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6790 (mp) outliers start: 42 outliers final: 14 residues processed: 226 average time/residue: 1.5470 time to fit residues: 466.4612 Evaluate side-chains 188 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 266 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain N residue 200 ASP Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 142 ILE 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: 20.0000 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: 10.0000 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** K 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 GLN M 46 GLN M 94 GLN ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.071 80070 Z= 0.704 Angle : 0.982 16.893 123265 Z= 0.485 Chirality : 0.054 0.464 16160 Planarity : 0.009 0.161 4347 Dihedral : 23.953 179.424 48050 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.93 % Favored : 90.86 % Rotamer: Outliers : 10.22 % Allowed : 25.16 % Favored : 64.61 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % 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: -2.60 (0.24), residues: 952 helix: -1.84 (0.34), residues: 178 sheet: -1.60 (0.37), residues: 161 loop : -1.78 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 125 HIS 0.008 0.002 HIS K 142 PHE 0.018 0.003 PHE M 19 TYR 0.013 0.002 TYR O 74 ARG 0.009 0.001 ARG K 69 *********************** 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 265 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 187 time to evaluate : 2.235 Fit side-chains REVERT: K 18 LYS cc_start: 0.8194 (mtpp) cc_final: 0.7931 (mttm) REVERT: K 39 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8286 (mtpt) REVERT: K 63 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.6557 (mpp80) REVERT: K 116 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7512 (pt) REVERT: K 143 ASN cc_start: 0.8739 (t0) cc_final: 0.8502 (t0) REVERT: L 39 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8655 (mtpm) REVERT: L 103 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8483 (tp) REVERT: M 3 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7132 (mm) REVERT: M 75 SER cc_start: 0.8861 (m) cc_final: 0.8604 (m) REVERT: M 106 LYS cc_start: 0.8777 (mttp) cc_final: 0.8462 (mtpt) REVERT: M 139 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7923 (ttpt) REVERT: M 158 PHE cc_start: 0.8729 (t80) cc_final: 0.8472 (t80) REVERT: O 35 ARG cc_start: 0.8802 (mtt90) cc_final: 0.8461 (mtt-85) REVERT: O 96 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7363 (ttp-170) REVERT: O 98 GLU cc_start: 0.7828 (mp0) cc_final: 0.7443 (mt-10) REVERT: O 106 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8168 (mmtp) REVERT: O 142 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.6668 (tp) outliers start: 78 outliers final: 42 residues processed: 242 average time/residue: 1.6056 time to fit residues: 514.2742 Evaluate side-chains 223 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 174 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 63 ARG Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 266 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 193 VAL Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain N residue 200 ASP Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 39 LYS Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 9.9990 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 2.9990 chunk 284 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 0.9990 chunk 263 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 342 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN K 197 ASN ** K 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN K 251 GLN L 104 GLN M 24 ASN M 41 GLN M 94 GLN M 165 HIS N 149 ASN O 138 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 80070 Z= 0.226 Angle : 0.609 14.032 123265 Z= 0.325 Chirality : 0.033 0.283 16160 Planarity : 0.007 0.132 4347 Dihedral : 23.782 175.759 48050 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.20 % Favored : 93.70 % Rotamer: Outliers : 8.26 % Allowed : 28.83 % Favored : 62.91 % 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: -2.07 (0.25), residues: 952 helix: -1.32 (0.36), residues: 182 sheet: -1.38 (0.38), residues: 166 loop : -1.41 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 213 HIS 0.005 0.001 HIS K 142 PHE 0.016 0.001 PHE K 67 TYR 0.014 0.001 TYR K 103 ARG 0.006 0.001 ARG K 182 *********************** 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 250 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 187 time to evaluate : 2.278 Fit side-chains REVERT: K 63 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.6631 (mpp80) REVERT: K 116 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7215 (pt) REVERT: L 39 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8622 (mtpm) REVERT: M 106 LYS cc_start: 0.8691 (mttp) cc_final: 0.8379 (mtpt) REVERT: M 139 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7969 (ttpt) REVERT: M 158 PHE cc_start: 0.8594 (t80) cc_final: 0.8266 (t80) REVERT: M 197 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7340 (mt-10) REVERT: N 70 LYS cc_start: 0.7961 (tttt) cc_final: 0.7610 (tttp) REVERT: O 106 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8016 (mttp) REVERT: O 108 MET cc_start: 0.8743 (mtt) cc_final: 0.8352 (mtt) REVERT: O 142 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6546 (tp) outliers start: 63 outliers final: 29 residues processed: 229 average time/residue: 1.5018 time to fit residues: 463.5092 Evaluate side-chains 195 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 266 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 38 LYS Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 142 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: 6.9990 chunk 75 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 382 optimal weight: 1.9990 chunk 317 optimal weight: 20.0000 chunk 176 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 143 ASN K 197 ASN ** K 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 GLN N 149 ASN O 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 80070 Z= 0.409 Angle : 0.738 13.995 123265 Z= 0.383 Chirality : 0.040 0.349 16160 Planarity : 0.008 0.140 4347 Dihedral : 23.895 177.208 48050 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.77 % Favored : 92.12 % Rotamer: Outliers : 9.70 % Allowed : 29.10 % Favored : 61.21 % 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: -2.00 (0.25), residues: 952 helix: -1.17 (0.37), residues: 174 sheet: -1.29 (0.38), residues: 160 loop : -1.42 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 125 HIS 0.006 0.002 HIS K 142 PHE 0.017 0.002 PHE K 67 TYR 0.016 0.002 TYR K 103 ARG 0.007 0.001 ARG K 182 *********************** 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 252 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 178 time to evaluate : 2.304 Fit side-chains REVERT: K 63 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.6574 (mpp80) REVERT: K 116 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7407 (pt) REVERT: K 143 ASN cc_start: 0.8716 (t0) cc_final: 0.8390 (t0) REVERT: L 36 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7999 (mttt) REVERT: L 39 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8666 (mtpm) REVERT: M 75 SER cc_start: 0.8818 (m) cc_final: 0.8575 (m) REVERT: M 139 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7946 (ttpt) REVERT: M 158 PHE cc_start: 0.8663 (t80) cc_final: 0.8305 (t80) REVERT: M 197 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7467 (mt-10) REVERT: O 35 ARG cc_start: 0.8731 (mtt90) cc_final: 0.8409 (mtt180) REVERT: O 98 GLU cc_start: 0.7867 (mp0) cc_final: 0.7489 (mt-10) REVERT: O 106 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8059 (mmtp) REVERT: O 142 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.6629 (tp) outliers start: 74 outliers final: 42 residues processed: 231 average time/residue: 1.6213 time to fit residues: 493.8090 Evaluate side-chains 200 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 153 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 266 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain N residue 200 ASP Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 30.0000 chunk 279 optimal weight: 20.0000 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: 7.9990 chunk 232 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 197 ASN ** K 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 80070 Z= 0.545 Angle : 0.853 14.059 123265 Z= 0.434 Chirality : 0.047 0.535 16160 Planarity : 0.008 0.146 4347 Dihedral : 24.093 177.976 48050 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.93 % Favored : 90.97 % Rotamer: Outliers : 9.83 % Allowed : 29.23 % Favored : 60.94 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % 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: -2.21 (0.25), residues: 952 helix: -1.27 (0.36), residues: 173 sheet: -1.49 (0.37), residues: 173 loop : -1.55 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP N 125 HIS 0.006 0.002 HIS O 76 PHE 0.022 0.003 PHE M 19 TYR 0.026 0.003 TYR K 103 ARG 0.008 0.001 ARG O 37 *********************** 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 246 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 171 time to evaluate : 2.626 Fit side-chains REVERT: K 63 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.6671 (mpp80) REVERT: L 39 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8670 (mtpm) REVERT: M 75 SER cc_start: 0.8855 (m) cc_final: 0.8649 (m) REVERT: M 111 GLU cc_start: 0.8155 (tp30) cc_final: 0.7951 (tp30) REVERT: M 139 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7903 (ttpt) REVERT: M 197 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7435 (mt-10) REVERT: O 96 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6656 (ttm110) REVERT: O 106 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8128 (mmtp) REVERT: O 142 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.6826 (mp) outliers start: 75 outliers final: 39 residues processed: 227 average time/residue: 1.5730 time to fit residues: 480.2325 Evaluate side-chains 201 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 158 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 266 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 107 PHE Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 142 ILE 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: 9.9990 chunk 227 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 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: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 ASN ** K 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 GLN O 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 80070 Z= 0.302 Angle : 0.650 13.898 123265 Z= 0.345 Chirality : 0.035 0.311 16160 Planarity : 0.007 0.136 4347 Dihedral : 23.887 176.146 48050 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.67 % Favored : 92.23 % Rotamer: Outliers : 7.73 % Allowed : 32.11 % Favored : 60.16 % 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: -1.99 (0.25), residues: 952 helix: -1.20 (0.36), residues: 180 sheet: -1.33 (0.37), residues: 180 loop : -1.37 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 125 HIS 0.005 0.001 HIS O 76 PHE 0.020 0.002 PHE K 67 TYR 0.028 0.002 TYR K 103 ARG 0.008 0.001 ARG O 37 *********************** 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 229 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 170 time to evaluate : 2.230 Fit side-chains REVERT: K 63 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.6680 (mpp80) REVERT: K 72 ASP cc_start: 0.8391 (m-30) cc_final: 0.8161 (m-30) REVERT: K 116 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7429 (pt) REVERT: L 39 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8668 (mtpm) REVERT: M 106 LYS cc_start: 0.8796 (mttp) cc_final: 0.8353 (mmmm) REVERT: M 111 GLU cc_start: 0.7996 (tp30) cc_final: 0.7768 (tp30) REVERT: M 139 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7927 (ttpt) REVERT: M 158 PHE cc_start: 0.8648 (t80) cc_final: 0.8316 (t80) REVERT: M 197 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7379 (mt-10) REVERT: O 96 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6671 (ttm110) REVERT: O 106 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8029 (mmtp) REVERT: O 142 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6801 (mp) outliers start: 59 outliers final: 28 residues processed: 211 average time/residue: 1.5164 time to fit residues: 430.2362 Evaluate side-chains 193 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 200 ASP Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.9990 chunk 364 optimal weight: 10.0000 chunk 332 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 chunk 213 optimal weight: 30.0000 chunk 154 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 40.0000 chunk 320 optimal weight: 5.9990 chunk 335 optimal weight: 4.9990 chunk 353 optimal weight: 6.9990 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN ** K 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 HIS M 94 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 80070 Z= 0.354 Angle : 0.699 13.871 123265 Z= 0.366 Chirality : 0.038 0.297 16160 Planarity : 0.007 0.139 4347 Dihedral : 23.927 176.799 48049 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.09 % Favored : 91.81 % Rotamer: Outliers : 6.42 % Allowed : 34.34 % Favored : 59.24 % 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: -1.95 (0.26), residues: 952 helix: -1.14 (0.36), residues: 177 sheet: -1.31 (0.37), residues: 173 loop : -1.35 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 125 HIS 0.005 0.001 HIS K 15 PHE 0.021 0.002 PHE K 67 TYR 0.025 0.002 TYR K 103 ARG 0.006 0.001 ARG K 214 *********************** 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 215 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 166 time to evaluate : 2.251 Fit side-chains revert: symmetry clash REVERT: K 63 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.6682 (mpp80) REVERT: K 72 ASP cc_start: 0.8416 (m-30) cc_final: 0.8191 (m-30) REVERT: L 39 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8653 (mtpm) REVERT: L 104 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: M 139 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7932 (ttpt) REVERT: M 197 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7349 (mt-10) REVERT: O 96 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6732 (ttm110) REVERT: O 106 LYS cc_start: 0.8535 (mmtt) cc_final: 0.8053 (mmtp) REVERT: O 142 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6872 (mp) outliers start: 49 outliers final: 35 residues processed: 201 average time/residue: 1.5624 time to fit residues: 418.5487 Evaluate side-chains 198 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 158 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 38 LYS Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 200 ASP Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 142 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: 3.9990 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 260 optimal weight: 5.9990 chunk 393 optimal weight: 0.9990 chunk 362 optimal weight: 10.0000 chunk 313 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 80070 Z= 0.374 Angle : 0.705 13.853 123265 Z= 0.368 Chirality : 0.038 0.302 16160 Planarity : 0.008 0.139 4347 Dihedral : 23.956 176.952 48048 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.61 % Favored : 91.28 % Rotamer: Outliers : 6.16 % Allowed : 34.73 % Favored : 59.11 % 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: -1.93 (0.26), residues: 952 helix: -1.12 (0.37), residues: 177 sheet: -1.36 (0.37), residues: 172 loop : -1.32 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP N 125 HIS 0.005 0.001 HIS O 76 PHE 0.022 0.002 PHE K 67 TYR 0.033 0.002 TYR K 103 ARG 0.005 0.001 ARG K 214 ********************** 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 215 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 168 time to evaluate : 2.759 Fit side-chains REVERT: K 63 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.6587 (mpp80) REVERT: L 39 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8660 (mtpm) REVERT: L 69 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7679 (ttt180) REVERT: M 106 LYS cc_start: 0.8818 (mmmm) cc_final: 0.8409 (mmmm) REVERT: M 139 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7925 (ttpt) REVERT: M 158 PHE cc_start: 0.8660 (t80) cc_final: 0.8323 (t80) REVERT: O 96 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6753 (ttm110) REVERT: O 106 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8033 (mmtp) REVERT: O 142 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.6874 (mp) outliers start: 47 outliers final: 33 residues processed: 202 average time/residue: 1.5438 time to fit residues: 417.4252 Evaluate side-chains 200 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 162 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 38 LYS Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 200 ASP Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 6.9990 chunk 333 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 322 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 GLN O 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.121107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.091798 restraints weight = 155808.606| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 0.63 r_work: 0.3187 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 80070 Z= 0.279 Angle : 0.665 13.959 123265 Z= 0.353 Chirality : 0.035 0.287 16160 Planarity : 0.007 0.136 4347 Dihedral : 23.981 176.622 48048 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.30 % Favored : 91.60 % Rotamer: Outliers : 6.03 % Allowed : 35.26 % Favored : 58.72 % 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: -1.86 (0.26), residues: 952 helix: -1.09 (0.37), residues: 177 sheet: -1.35 (0.37), residues: 172 loop : -1.25 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 125 HIS 0.004 0.001 HIS K 15 PHE 0.023 0.002 PHE K 67 TYR 0.045 0.002 TYR K 103 ARG 0.005 0.000 ARG K 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12881.17 seconds wall clock time: 230 minutes 3.25 seconds (13803.25 seconds total)