Starting phenix.real_space_refine on Sun Feb 18 09:31:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/02_2024/6wyv_21969_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/02_2024/6wyv_21969.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/02_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_21969/02_2024/6wyv_21969_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/02_2024/6wyv_21969_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/02_2024/6wyv_21969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/02_2024/6wyv_21969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/02_2024/6wyv_21969_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/02_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-5238/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: 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'O7S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.07, per 1000 atoms: 0.39 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: 34.42 Conformation dependent library (CDL) restraints added in 1.6 seconds 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 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: 38.44 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: 134.57 Time building geometry restraints manager: 36.69 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=" C05 O7S I3001 " pdb=" C06 O7S I3001 " ideal model delta sigma weight residual 1.606 1.348 0.258 2.00e-02 2.50e+03 1.66e+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 68.57 120.18 -51.61 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C07 O7S I3001 " pdb=" C09 O7S I3001 " pdb=" C10 O7S I3001 " ideal model delta sigma weight residual 85.73 128.21 -42.48 3.00e+00 1.11e-01 2.00e+02 angle pdb=" C04 O7S I3001 " pdb=" C05 O7S I3001 " pdb=" C06 O7S I3001 " ideal model delta sigma weight residual 85.76 124.77 -39.01 3.00e+00 1.11e-01 1.69e+02 angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C8 6MZ I1618 " ideal model delta sigma weight residual 91.39 126.74 -35.35 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C08 O7S I3001 " pdb=" C07 O7S I3001 " pdb=" C09 O7S I3001 " ideal model delta sigma weight residual 154.30 122.03 32.27 3.00e+00 1.11e-01 1.16e+02 ... (remaining 123260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 44116 35.47 - 70.93: 6661 70.93 - 106.40: 796 106.40 - 141.87: 18 141.87 - 177.33: 10 Dihedral angle restraints: 51601 sinusoidal: 48903 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 51598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 15775 0.052 - 0.105: 315 0.105 - 0.157: 38 0.157 - 0.209: 1 0.209 - 0.262: 2 Chirality restraints: 16131 Sorted by residual: 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 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 2.29 0.24 2.00e-01 2.50e+01 1.40e+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 -2.66 0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 16128 not shown) Planarity restraints: 4353 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' 3TD I1915 " -0.925 2.00e-02 2.50e+03 6.02e-01 8.17e+03 pdb=" C4' 3TD I1915 " 0.184 2.00e-02 2.50e+03 pdb=" O4' 3TD I1915 " 0.854 2.00e-02 2.50e+03 pdb=" C3' 3TD I1915 " -0.273 2.00e-02 2.50e+03 pdb=" O3' 3TD I1915 " 0.808 2.00e-02 2.50e+03 pdb=" C2' 3TD I1915 " -0.582 2.00e-02 2.50e+03 pdb=" O2' 3TD I1915 " -0.558 2.00e-02 2.50e+03 pdb=" C1' 3TD I1915 " 0.518 2.00e-02 2.50e+03 pdb=" C5 3TD I1915 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " -0.037 2.00e-02 2.50e+03 5.96e-01 7.99e+03 pdb=" C4' 1MG I 745 " -0.449 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.712 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.588 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.213 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.915 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.209 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.927 2.00e-02 2.50e+03 ... (remaining 4350 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: 12.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 46.580 Check model and map are aligned: 0.760 Set scattering table: 0.510 Process input model: 276.830 Find NCS groups from input model: 0.890 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:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 350.420 ------------------------------------------------------------------------------- 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= 0.343 Angle : 0.508 51.611 123265 Z= 0.226 Chirality : 0.024 0.262 16131 Planarity : 0.031 0.605 4353 Dihedral : 23.794 177.331 49883 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 : 2.099 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: 1.6656 time to fit residues: 521.4550 Evaluate side-chains 163 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 1.998 ------------------------------------------------------------------------------- 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: 0.8388 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 80070 Z= 0.528 Angle : 0.887 27.021 123265 Z= 0.455 Chirality : 0.045 0.315 16131 Planarity : 0.009 0.146 4353 Dihedral : 23.869 178.667 48087 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 6.68 % Allowed : 23.59 % Favored : 69.72 % 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: -3.37 (0.23), residues: 952 helix: -2.70 (0.30), residues: 175 sheet: -1.95 (0.38), residues: 162 loop : -2.27 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 78 HIS 0.007 0.002 HIS K 53 PHE 0.017 0.002 PHE M 19 TYR 0.010 0.002 TYR K 161 ARG 0.008 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 263 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 212 time to evaluate : 2.149 Fit side-chains REVERT: K 18 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7662 (mttm) REVERT: K 63 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.6484 (mpp80) REVERT: K 72 ASP cc_start: 0.8170 (m-30) cc_final: 0.7771 (m-30) REVERT: K 116 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6696 (pt) REVERT: K 143 ASN cc_start: 0.8528 (t0) cc_final: 0.8254 (t0) REVERT: K 182 ARG cc_start: 0.8715 (ttt90) cc_final: 0.8359 (ttm-80) REVERT: L 39 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8556 (mtpm) REVERT: M 75 SER cc_start: 0.8827 (m) cc_final: 0.8577 (m) REVERT: M 139 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7947 (ttpt) REVERT: M 158 PHE cc_start: 0.8673 (t80) cc_final: 0.8373 (t80) REVERT: N 28 GLU cc_start: 0.7417 (tp30) cc_final: 0.6612 (tp30) REVERT: N 70 LYS cc_start: 0.7813 (tttt) cc_final: 0.7540 (tttp) REVERT: O 106 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8147 (mmtp) REVERT: O 142 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.7006 (mp) outliers start: 51 outliers final: 22 residues processed: 249 average time/residue: 1.5924 time to fit residues: 525.5507 Evaluate side-chains 214 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 LYS 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 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 L residue 135 ILE 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 21 THR 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: 1.9990 chunk 388 optimal weight: 6.9990 chunk 320 optimal weight: 1.9990 chunk 356 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 128 ASN K 197 ASN K 200 HIS K 251 GLN M 94 GLN N 136 ASN O 138 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 80070 Z= 0.235 Angle : 0.653 20.959 123265 Z= 0.356 Chirality : 0.032 0.273 16131 Planarity : 0.008 0.133 4353 Dihedral : 23.774 176.601 48084 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.20 % Favored : 93.70 % Rotamer: Outliers : 5.64 % Allowed : 27.26 % Favored : 67.10 % 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: -2.64 (0.24), residues: 952 helix: -1.80 (0.34), residues: 183 sheet: -1.72 (0.39), residues: 158 loop : -1.80 (0.22), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 78 HIS 0.005 0.001 HIS K 142 PHE 0.013 0.002 PHE K 67 TYR 0.009 0.001 TYR M 35 ARG 0.004 0.001 ARG L 59 *********************** 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 238 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 195 time to evaluate : 2.134 Fit side-chains REVERT: K 39 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8363 (mtpt) REVERT: K 63 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.6685 (mpp80) REVERT: L 39 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8547 (mtpm) REVERT: M 139 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7957 (ttpt) REVERT: M 158 PHE cc_start: 0.8609 (t80) cc_final: 0.8322 (t80) REVERT: N 201 LEU cc_start: 0.8954 (pt) cc_final: 0.8742 (pp) REVERT: O 106 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8077 (mmtp) REVERT: O 142 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6789 (mp) outliers start: 43 outliers final: 13 residues processed: 223 average time/residue: 1.5250 time to fit residues: 454.2196 Evaluate side-chains 194 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 2.105 ------------------------------------------------------------------------------- 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 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 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 193 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 21 THR 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: 9.9990 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: 0.7980 chunk 381 optimal weight: 0.7980 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 239 ASN K 251 GLN M 94 GLN O 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 80070 Z= 0.448 Angle : 0.808 21.514 123265 Z= 0.422 Chirality : 0.041 0.304 16131 Planarity : 0.009 0.142 4353 Dihedral : 23.969 177.956 48083 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.77 % Favored : 92.12 % Rotamer: Outliers : 8.78 % Allowed : 25.69 % Favored : 65.53 % 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: -2.46 (0.25), residues: 952 helix: -1.69 (0.34), residues: 183 sheet: -1.47 (0.39), residues: 154 loop : -1.71 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 125 HIS 0.013 0.002 HIS N 134 PHE 0.016 0.002 PHE M 19 TYR 0.017 0.002 TYR K 103 ARG 0.008 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 267 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 200 time to evaluate : 2.057 Fit side-chains REVERT: K 39 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8368 (mtpt) REVERT: K 63 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.6641 (mpp80) REVERT: K 143 ASN cc_start: 0.8696 (t0) cc_final: 0.8437 (t0) REVERT: L 10 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7707 (tp30) REVERT: L 39 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8612 (mtpm) REVERT: M 22 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: M 75 SER cc_start: 0.8826 (m) cc_final: 0.8516 (m) REVERT: M 139 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7944 (ttpt) REVERT: M 158 PHE cc_start: 0.8669 (t80) cc_final: 0.8385 (t80) REVERT: M 162 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8210 (ttt180) REVERT: M 197 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7502 (mt-10) REVERT: O 35 ARG cc_start: 0.8772 (mtt90) cc_final: 0.8448 (mtt-85) REVERT: O 96 ARG cc_start: 0.7562 (ttp-170) cc_final: 0.7316 (ttp-170) REVERT: O 98 GLU cc_start: 0.7820 (mp0) cc_final: 0.7346 (mt-10) REVERT: O 106 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8124 (mmtp) REVERT: O 142 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.6841 (mp) outliers start: 67 outliers final: 35 residues processed: 249 average time/residue: 1.5798 time to fit residues: 518.5656 Evaluate side-chains 218 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 177 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 115 GLN 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 192 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 266 PHE Chi-restraints excluded: chain K residue 268 VAL 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 M residue 4 VAL Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 22 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 162 ARG Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 193 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 26 VAL 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 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: 5.9990 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 7.9990 chunk 284 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 263 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 342 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 ASN K 251 GLN L 104 GLN M 94 GLN ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 80070 Z= 0.468 Angle : 0.809 20.535 123265 Z= 0.424 Chirality : 0.043 0.371 16131 Planarity : 0.009 0.142 4353 Dihedral : 24.076 177.411 48083 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.56 % Favored : 92.23 % Rotamer: Outliers : 9.17 % Allowed : 27.52 % Favored : 63.30 % 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: -2.26 (0.25), residues: 952 helix: -1.45 (0.36), residues: 172 sheet: -1.45 (0.38), residues: 154 loop : -1.57 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP N 125 HIS 0.007 0.002 HIS K 142 PHE 0.015 0.002 PHE K 67 TYR 0.023 0.002 TYR K 103 ARG 0.008 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 263 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 193 time to evaluate : 2.097 Fit side-chains REVERT: K 39 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8372 (mtpt) REVERT: K 63 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.6613 (mpp80) REVERT: L 39 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8652 (mtpm) REVERT: M 75 SER cc_start: 0.8819 (m) cc_final: 0.8559 (m) REVERT: M 106 LYS cc_start: 0.8801 (mttt) cc_final: 0.8482 (mtpt) REVERT: M 111 GLU cc_start: 0.8083 (tp30) cc_final: 0.7828 (tp30) REVERT: M 139 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7924 (ttpt) REVERT: M 158 PHE cc_start: 0.8683 (t80) cc_final: 0.8406 (t80) REVERT: M 197 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7532 (mt-10) REVERT: O 96 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7322 (ttp-170) REVERT: O 98 GLU cc_start: 0.7855 (mp0) cc_final: 0.7397 (mt-10) REVERT: O 106 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8082 (mmtp) REVERT: O 108 MET cc_start: 0.8814 (mtt) cc_final: 0.8415 (mtt) REVERT: O 142 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6800 (mp) outliers start: 70 outliers final: 39 residues processed: 241 average time/residue: 1.5487 time to fit residues: 495.9374 Evaluate side-chains 212 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 168 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 50 THR 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 174 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 K residue 268 VAL 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 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 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 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 38 LYS 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 56 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 65 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 6.9990 chunk 343 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 382 optimal weight: 0.8980 chunk 317 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 ASN K 251 GLN M 41 GLN M 94 GLN N 149 ASN O 138 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 80070 Z= 0.262 Angle : 0.671 18.071 123265 Z= 0.365 Chirality : 0.034 0.286 16131 Planarity : 0.008 0.134 4353 Dihedral : 23.952 179.024 48083 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 9.17 % Allowed : 28.83 % Favored : 61.99 % 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: -1.97 (0.25), residues: 952 helix: -1.17 (0.37), residues: 181 sheet: -1.23 (0.40), residues: 154 loop : -1.40 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 125 HIS 0.007 0.001 HIS K 200 PHE 0.017 0.002 PHE K 67 TYR 0.025 0.002 TYR K 103 ARG 0.005 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: 70 poor density : 182 time to evaluate : 2.249 Fit side-chains REVERT: K 39 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8381 (mtpt) REVERT: K 63 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.6718 (mpp80) REVERT: K 72 ASP cc_start: 0.8339 (m-30) cc_final: 0.8138 (m-30) REVERT: L 39 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8819 (mtpt) REVERT: M 106 LYS cc_start: 0.8740 (mttt) cc_final: 0.8432 (mtpt) REVERT: M 111 GLU cc_start: 0.8019 (tp30) cc_final: 0.7764 (tp30) REVERT: M 139 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7922 (ttpt) REVERT: M 158 PHE cc_start: 0.8635 (t80) cc_final: 0.8268 (t80) REVERT: M 197 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7397 (mt-10) REVERT: O 96 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7244 (ttp-170) REVERT: O 98 GLU cc_start: 0.7796 (mp0) cc_final: 0.7311 (mt-10) REVERT: O 106 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8039 (mttp) REVERT: O 108 MET cc_start: 0.8736 (mtt) cc_final: 0.8376 (mtt) REVERT: O 142 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6802 (mp) outliers start: 70 outliers final: 33 residues processed: 229 average time/residue: 1.5832 time to fit residues: 484.7523 Evaluate side-chains 198 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 115 GLN 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 6 LEU 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 M residue 4 VAL Chi-restraints excluded: chain M residue 5 LEU 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 M residue 199 MET 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 174 SER Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 193 VAL 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 65 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 7.9990 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: 4.9990 chunk 213 optimal weight: 40.0000 chunk 380 optimal weight: 4.9990 chunk 238 optimal weight: 8.9990 chunk 232 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 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 143 ASN K 197 ASN M 94 GLN N 49 GLN ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 GLN O 138 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 80070 Z= 0.525 Angle : 0.859 18.173 123265 Z= 0.445 Chirality : 0.045 0.448 16131 Planarity : 0.009 0.145 4353 Dihedral : 24.124 178.397 48082 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.14 % Favored : 90.76 % Rotamer: Outliers : 9.04 % Allowed : 29.75 % Favored : 61.21 % 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: -2.19 (0.25), residues: 952 helix: -1.34 (0.36), residues: 179 sheet: -1.31 (0.38), residues: 164 loop : -1.57 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 125 HIS 0.006 0.002 HIS O 76 PHE 0.019 0.003 PHE K 67 TYR 0.038 0.003 TYR K 103 ARG 0.005 0.001 ARG K 182 *********************** 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 248 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 179 time to evaluate : 2.097 Fit side-chains REVERT: K 39 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8389 (mtpt) REVERT: K 63 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.6647 (mpp80) REVERT: K 71 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7358 (tttt) REVERT: K 72 ASP cc_start: 0.8386 (m-30) cc_final: 0.8173 (m-30) REVERT: K 143 ASN cc_start: 0.8789 (t0) cc_final: 0.8514 (t0) REVERT: K 146 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7401 (mtm) REVERT: L 39 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8676 (mtpm) REVERT: M 75 SER cc_start: 0.8842 (m) cc_final: 0.8627 (m) REVERT: M 139 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7928 (ttpt) REVERT: O 35 ARG cc_start: 0.8741 (mtt90) cc_final: 0.8342 (mtt180) REVERT: O 98 GLU cc_start: 0.7830 (mp0) cc_final: 0.7406 (mt-10) REVERT: O 106 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8099 (mmtp) REVERT: O 142 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.6826 (mp) outliers start: 69 outliers final: 36 residues processed: 224 average time/residue: 1.6164 time to fit residues: 477.9913 Evaluate side-chains 211 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 50 THR 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 114 ASP Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 174 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 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 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 M residue 199 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 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: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** K 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 197 ASN M 94 GLN N 49 GLN N 149 ASN O 136 GLN O 138 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 80070 Z= 0.330 Angle : 0.707 16.906 123265 Z= 0.381 Chirality : 0.037 0.307 16131 Planarity : 0.009 0.137 4353 Dihedral : 24.013 176.658 48081 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.35 % Favored : 92.54 % Rotamer: Outliers : 7.73 % Allowed : 31.85 % Favored : 60.42 % 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: -2.04 (0.25), residues: 952 helix: -1.15 (0.36), residues: 181 sheet: -1.32 (0.38), residues: 165 loop : -1.45 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 125 HIS 0.005 0.001 HIS K 142 PHE 0.021 0.002 PHE K 67 TYR 0.037 0.002 TYR K 103 ARG 0.004 0.001 ARG O 96 *********************** 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 242 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 183 time to evaluate : 2.201 Fit side-chains REVERT: K 39 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8400 (mtpt) REVERT: K 63 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.6667 (mpp80) REVERT: K 143 ASN cc_start: 0.8685 (t0) cc_final: 0.8434 (t0) REVERT: L 39 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8855 (mtpt) REVERT: M 106 LYS cc_start: 0.8821 (mttt) cc_final: 0.8470 (mtpt) REVERT: M 139 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7914 (ttpt) REVERT: M 158 PHE cc_start: 0.8654 (t80) cc_final: 0.8261 (t80) REVERT: M 197 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7389 (mt-10) REVERT: O 96 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6851 (ttm110) REVERT: O 98 GLU cc_start: 0.7889 (mp0) cc_final: 0.7376 (mt-10) REVERT: O 106 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8063 (mmtp) REVERT: O 142 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6788 (mp) outliers start: 59 outliers final: 35 residues processed: 222 average time/residue: 1.5039 time to fit residues: 447.1070 Evaluate side-chains 204 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 164 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 114 ASP 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 219 THR 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 68 SER 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 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 199 MET 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.9980 chunk 364 optimal weight: 0.8980 chunk 332 optimal weight: 0.0270 chunk 354 optimal weight: 9.9990 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: 5.9990 chunk 335 optimal weight: 4.9990 chunk 353 optimal weight: 6.9990 overall best weight: 2.5842 ------------------------------------------------------------------------------- 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 M 94 GLN N 149 ASN O 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 80070 Z= 0.208 Angle : 0.664 16.971 123265 Z= 0.365 Chirality : 0.032 0.300 16131 Planarity : 0.008 0.133 4353 Dihedral : 24.067 176.037 48081 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.25 % Favored : 92.65 % Rotamer: Outliers : 6.03 % Allowed : 34.73 % 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: -1.91 (0.26), residues: 952 helix: -1.04 (0.37), residues: 181 sheet: -1.35 (0.37), residues: 172 loop : -1.32 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 125 HIS 0.005 0.001 HIS K 15 PHE 0.029 0.002 PHE K 240 TYR 0.040 0.002 TYR K 103 ARG 0.006 0.000 ARG O 37 *********************** 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 222 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 176 time to evaluate : 2.089 Fit side-chains REVERT: K 39 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8392 (mtpt) REVERT: L 39 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8806 (mtpt) REVERT: M 106 LYS cc_start: 0.8770 (mttt) cc_final: 0.8429 (mtpt) REVERT: M 139 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7903 (ttpt) REVERT: M 158 PHE cc_start: 0.8628 (t80) cc_final: 0.8274 (t80) REVERT: O 96 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6817 (ttm110) REVERT: O 98 GLU cc_start: 0.7879 (mp0) cc_final: 0.7359 (mt-10) REVERT: O 106 LYS cc_start: 0.8511 (mmtt) cc_final: 0.8024 (mmtp) REVERT: O 142 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6725 (mp) outliers start: 46 outliers final: 26 residues processed: 207 average time/residue: 1.5569 time to fit residues: 428.3164 Evaluate side-chains 209 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 114 ASP 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 6 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 51 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 7 ASP 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 208 LYS Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 17 VAL 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 128 ASN 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: 0.9990 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 260 optimal weight: 7.9990 chunk 393 optimal weight: 0.9980 chunk 362 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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 M 94 GLN N 149 ASN O 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 80070 Z= 0.389 Angle : 0.745 16.797 123265 Z= 0.397 Chirality : 0.039 0.340 16131 Planarity : 0.009 0.141 4353 Dihedral : 24.025 177.768 48081 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.88 % Favored : 92.02 % Rotamer: Outliers : 5.50 % Allowed : 35.26 % 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: -1.97 (0.26), residues: 952 helix: -1.15 (0.36), residues: 181 sheet: -1.37 (0.37), residues: 171 loop : -1.35 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 125 HIS 0.005 0.001 HIS O 76 PHE 0.033 0.002 PHE N 90 TYR 0.038 0.002 TYR K 103 ARG 0.006 0.001 ARG N 59 ********************** 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 223 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 2.322 Fit side-chains REVERT: K 39 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8404 (mtpt) REVERT: K 143 ASN cc_start: 0.8679 (t0) cc_final: 0.8458 (t0) REVERT: L 39 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8666 (mtpm) REVERT: M 106 LYS cc_start: 0.8810 (mttt) cc_final: 0.8451 (mtpt) REVERT: M 139 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7946 (ttpt) REVERT: M 158 PHE cc_start: 0.8659 (t80) cc_final: 0.8301 (t80) REVERT: M 197 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7401 (mt-10) REVERT: O 96 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6696 (ttm110) REVERT: O 98 GLU cc_start: 0.7914 (mp0) cc_final: 0.7448 (mt-10) REVERT: O 106 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8059 (mmtp) REVERT: O 142 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6860 (mp) outliers start: 42 outliers final: 28 residues processed: 210 average time/residue: 1.5140 time to fit residues: 424.9613 Evaluate side-chains 191 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 39 LYS 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 168 ASP Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 219 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 80 SER 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 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 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 197 THR 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 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: 0.9990 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: 9.9990 chunk 131 optimal weight: 6.9990 chunk 322 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 153 GLN K 197 ASN M 94 GLN N 149 ASN O 136 GLN O 138 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.121873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.092564 restraints weight = 155310.935| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 0.61 r_work: 0.3202 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 80070 Z= 0.268 Angle : 0.694 16.800 123265 Z= 0.377 Chirality : 0.034 0.308 16131 Planarity : 0.008 0.136 4353 Dihedral : 24.068 176.986 48081 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.56 % Favored : 92.33 % Rotamer: Outliers : 5.11 % Allowed : 35.78 % 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: -1.92 (0.26), residues: 952 helix: -1.08 (0.37), residues: 181 sheet: -1.41 (0.37), residues: 171 loop : -1.30 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 125 HIS 0.005 0.001 HIS K 15 PHE 0.037 0.002 PHE N 90 TYR 0.042 0.002 TYR K 103 ARG 0.006 0.001 ARG N 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13092.50 seconds wall clock time: 233 minutes 37.23 seconds (14017.23 seconds total)