Starting phenix.real_space_refine on Sun Feb 18 08:19:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/02_2024/6pc7_20298_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/02_2024/6pc7_20298.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/02_2024/6pc7_20298_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/02_2024/6pc7_20298_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/02_2024/6pc7_20298_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/02_2024/6pc7_20298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/02_2024/6pc7_20298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/02_2024/6pc7_20298_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/02_2024/6pc7_20298_neut_updated.pdb" } resolution = 2.5 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= -0.018 sd= 1.319 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 33516 2.51 5 N 13321 2.21 5 O 22271 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 ARG 52": "NH1" <-> "NH2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" 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 GLU 86": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 102": "NH1" <-> "NH2" 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 ARG 77": "NH1" <-> "NH2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N GLU 168": "OE1" <-> "OE2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "O ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 72146 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 62206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62206 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 7, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 14, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 438, 'rna3p': 2458} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1542 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Chain: "O" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'O7V': 1} Classifications: {'undetermined': 1} Time building chain proxies: 29.38, per 1000 atoms: 0.41 Number of scatterers: 72146 At special positions: 0 Unit cell: (228.611, 221.984, 190.509, 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 22271 8.00 N 13321 7.00 C 33516 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 32.97 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... Number of C-beta restraints generated: 1706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 13 sheets defined 17.6% alpha, 14.3% beta 901 base pairs and 1651 stacking pairs defined. Time for finding SS restraints: 38.91 Creating SS restraints... Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'K' and resid 208 through 213 Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 92 through 95 No H-bonds generated for 'chain 'L' and resid 92 through 95' Processing helix chain 'L' and resid 129 through 137 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 38 removed outlier: 3.611A pdb=" N GLN M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 114 removed outlier: 3.731A pdb=" N SER M 110 " --> pdb=" O LYS M 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 140 Processing helix chain 'M' and resid 155 through 160 Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 Processing helix chain 'N' and resid 62 through 71 Processing helix chain 'N' and resid 98 through 101 Processing helix chain 'N' and resid 121 through 124 No H-bonds generated for 'chain 'N' and resid 121 through 124' Processing helix chain 'O' and resid 25 through 37 removed outlier: 3.994A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 68 through 71 No H-bonds generated for 'chain 'O' and resid 68 through 71' Processing helix chain 'O' and resid 89 through 108 Proline residue: O 97 - end of helix removed outlier: 4.432A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 removed outlier: 3.547A pdb=" N PHE O 119 " --> pdb=" O GLY O 115 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 135 No H-bonds generated for 'chain 'O' and resid 133 through 135' Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'K' and resid 101 through 105 removed outlier: 3.753A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.811A 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 removed outlier: 3.511A pdb=" N LEU K 130 " --> pdb=" O ALA K 190 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.782A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.900A 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: 6.642A 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 121 through 123 removed outlier: 6.568A 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 118 through 121 removed outlier: 6.146A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 169 through 172 removed outlier: 4.921A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE N 15 " --> pdb=" O VAL N 20 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL N 20 " --> pdb=" O PHE N 15 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL N 189 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP N 181 " --> pdb=" O LEU N 186 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS N 190 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL N 177 " --> pdb=" O LYS N 190 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 80 through 83 removed outlier: 6.205A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 115 through 119 removed outlier: 6.090A pdb=" N MET N 165 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE N 118 " --> pdb=" O GLY N 163 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY N 163 " --> pdb=" O PHE N 118 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.699A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE O 55 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'O' and resid 73 through 76 removed outlier: 3.515A pdb=" N HIS O 76 " --> pdb=" O LYS O 85 " (cutoff:3.500A) 131 hydrogen bonds defined for protein. 372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2259 hydrogen bonds 3678 hydrogen bond angles 0 basepair planarities 901 basepair parallelities 1651 stacking parallelities Total time for adding SS restraints: 136.12 Time building geometry restraints manager: 35.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5153 1.31 - 1.43: 40218 1.43 - 1.56: 28559 1.56 - 1.68: 6048 1.68 - 1.81: 42 Bond restraints: 80020 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.409 0.393 2.00e-02 2.50e+03 3.87e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.410 0.392 2.00e-02 2.50e+03 3.83e+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 1.81e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.367 0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C15 O7V I3001 " pdb=" C16 O7V I3001 " ideal model delta sigma weight residual 1.601 1.348 0.253 2.00e-02 2.50e+03 1.60e+02 ... (remaining 80015 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.93: 17925 106.93 - 113.90: 50587 113.90 - 120.88: 32158 120.88 - 127.85: 17425 127.85 - 134.82: 5103 Bond angle restraints: 123198 Sorted by residual: angle pdb=" N30 O7V I3001 " pdb=" C31 O7V I3001 " pdb=" N40 O7V I3001 " ideal model delta sigma weight residual 50.79 114.46 -63.67 3.00e+00 1.11e-01 4.50e+02 angle pdb=" C13 O7V I3001 " pdb=" C15 O7V I3001 " pdb=" C16 O7V I3001 " ideal model delta sigma weight residual 85.81 125.34 -39.53 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C8 6MZ I1618 " ideal model delta sigma weight residual 91.39 126.51 -35.12 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C32 O7V I3001 " pdb=" C31 O7V I3001 " pdb=" N30 O7V I3001 " ideal model delta sigma weight residual 155.49 122.51 32.98 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C19 O7V I3001 " pdb=" C20 O7V I3001 " pdb=" C21 O7V I3001 " ideal model delta sigma weight residual 154.30 124.62 29.68 3.00e+00 1.11e-01 9.78e+01 ... (remaining 123193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 44160 35.72 - 71.43: 6591 71.43 - 107.15: 804 107.15 - 142.86: 13 142.86 - 178.58: 7 Dihedral angle restraints: 51575 sinusoidal: 48895 harmonic: 2680 Sorted by residual: dihedral pdb=" C4* PSU I1911 " pdb=" C3* PSU I1911 " pdb=" C2* PSU I1911 " pdb=" C1* PSU I1911 " ideal model delta sinusoidal sigma weight residual -35.00 34.45 -69.45 1 8.00e+00 1.56e-02 9.73e+01 dihedral pdb=" C5* PSU I1911 " pdb=" C4* PSU I1911 " pdb=" C3* PSU I1911 " pdb=" O3* PSU I1911 " ideal model delta sinusoidal sigma weight residual 147.00 77.72 69.28 1 8.00e+00 1.56e-02 9.69e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual 232.00 59.53 172.47 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 51572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 16084 0.107 - 0.213: 36 0.213 - 0.320: 2 0.320 - 0.427: 1 0.427 - 0.534: 1 Chirality restraints: 16124 Sorted by residual: chirality pdb=" CA MET K 225 " pdb=" N MET K 225 " pdb=" C MET K 225 " pdb=" CB MET K 225 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.12e+00 chirality pdb=" CA ASP K 229 " pdb=" N ASP K 229 " pdb=" C ASP K 229 " pdb=" CB ASP K 229 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C3* PSU I1911 " pdb=" C4* PSU I1911 " pdb=" O3* PSU I1911 " pdb=" C2* PSU I1911 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 16121 not shown) Planarity restraints: 4344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " -0.044 2.00e-02 2.50e+03 5.92e-01 7.88e+03 pdb=" C4' 1MG I 745 " -0.445 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.672 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.600 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.201 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.931 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.217 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.913 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 6MZ I1618 " -0.876 2.00e-02 2.50e+03 5.88e-01 7.79e+03 pdb=" C4' 6MZ I1618 " 0.220 2.00e-02 2.50e+03 pdb=" O4' 6MZ I1618 " 0.690 2.00e-02 2.50e+03 pdb=" C3' 6MZ I1618 " -0.206 2.00e-02 2.50e+03 pdb=" O3' 6MZ I1618 " 0.915 2.00e-02 2.50e+03 pdb=" C2' 6MZ I1618 " -0.614 2.00e-02 2.50e+03 pdb=" O2' 6MZ I1618 " -0.605 2.00e-02 2.50e+03 pdb=" C1' 6MZ I1618 " 0.447 2.00e-02 2.50e+03 pdb=" N9 6MZ I1618 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.023 2.00e-02 2.50e+03 5.82e-01 7.62e+03 pdb=" C4' 2MG I2445 " -0.449 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.704 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.561 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.225 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.885 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.215 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.901 2.00e-02 2.50e+03 ... (remaining 4341 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 451 2.54 - 3.13: 51323 3.13 - 3.72: 144541 3.72 - 4.31: 209130 4.31 - 4.90: 268753 Nonbonded interactions: 674198 Sorted by model distance: nonbonded pdb=" O2' A I2052 " pdb=" O GLN N 148 " model vdw 1.954 2.440 nonbonded pdb=" O2' A I1084 " pdb=" O2' U I1105 " model vdw 1.955 2.440 nonbonded pdb=" OP1 A I 730 " pdb=" O2' U I1775 " model vdw 1.968 2.440 nonbonded pdb=" O2' G I1715 " pdb=" O6 G I1743 " model vdw 1.984 2.440 nonbonded pdb=" O2' G I1826 " pdb=" OP2 U I1971 " model vdw 1.992 2.440 ... (remaining 674193 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: 19.770 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: 0.000 Extract box with map and model: 52.730 Check model and map are aligned: 0.000 Set scattering table: 0.170 Process input model: 279.540 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 365.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 0.393 80020 Z= 0.330 Angle : 0.507 63.667 123198 Z= 0.229 Chirality : 0.025 0.534 16124 Planarity : 0.030 0.592 4344 Dihedral : 23.763 178.581 49869 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.20 % Favored : 93.70 % Rotamer: Outliers : 2.23 % Allowed : 12.35 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.93 (0.22), residues: 952 helix: -3.43 (0.24), residues: 176 sheet: -1.86 (0.35), residues: 197 loop : -2.71 (0.21), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 78 HIS 0.009 0.001 HIS K 230 PHE 0.004 0.001 PHE O 89 TYR 0.006 0.001 TYR K 103 ARG 0.003 0.000 ARG L 47 *********************** 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 212 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 2.120 Fit side-chains revert: symmetry clash REVERT: K 82 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7587 (mt-10) REVERT: K 103 TYR cc_start: 0.8949 (m-80) cc_final: 0.8343 (m-80) REVERT: K 212 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8834 (mmm-85) REVERT: M 194 LYS cc_start: 0.7867 (mptp) cc_final: 0.7613 (mtpm) outliers start: 17 outliers final: 5 residues processed: 211 average time/residue: 1.7574 time to fit residues: 477.1877 Evaluate side-chains 147 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 212 ARG Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 88 THR 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: 8.9990 chunk 159 optimal weight: 8.9990 chunk 309 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 358 optimal weight: 0.0470 overall best weight: 6.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 143 ASN K 200 HIS K 239 ASN L 93 ASN M 41 GLN M 156 ASN N 32 ASN N 126 ASN N 167 ASN O 80 HIS O 135 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 80020 Z= 0.495 Angle : 0.828 25.443 123198 Z= 0.427 Chirality : 0.042 0.311 16124 Planarity : 0.009 0.139 4344 Dihedral : 23.736 179.788 48080 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.72 % Favored : 93.07 % Rotamer: Outliers : 6.31 % Allowed : 19.58 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.40 (0.24), residues: 952 helix: -1.61 (0.33), residues: 174 sheet: -1.23 (0.36), residues: 188 loop : -1.75 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.012 0.002 PHE O 89 TYR 0.014 0.002 TYR K 171 ARG 0.008 0.001 ARG O 37 *********************** 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 206 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 2.180 Fit side-chains revert: symmetry clash REVERT: K 82 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7775 (mt-10) REVERT: K 103 TYR cc_start: 0.8976 (m-80) cc_final: 0.8280 (m-80) REVERT: K 163 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: L 92 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8249 (mp) REVERT: M 100 MET cc_start: 0.8364 (mtp) cc_final: 0.8148 (mtm) REVERT: M 194 LYS cc_start: 0.8065 (mptp) cc_final: 0.7679 (mtpm) REVERT: N 89 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: N 128 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7549 (mtp180) REVERT: O 91 GLU cc_start: 0.7655 (mm-30) cc_final: 0.6959 (mt-10) REVERT: O 95 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7211 (mpt-90) REVERT: O 99 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.8103 (mmm-85) outliers start: 48 outliers final: 18 residues processed: 185 average time/residue: 1.8416 time to fit residues: 437.7232 Evaluate side-chains 169 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 270 ARG Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 56 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 95 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 359 optimal weight: 2.9990 chunk 388 optimal weight: 0.8980 chunk 320 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN M 94 GLN M 156 ASN N 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 80020 Z= 0.248 Angle : 0.648 19.837 123198 Z= 0.354 Chirality : 0.033 0.285 16124 Planarity : 0.008 0.131 4344 Dihedral : 23.682 178.047 48074 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.88 % Favored : 93.91 % Rotamer: Outliers : 4.99 % Allowed : 21.42 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.69 (0.25), residues: 952 helix: -0.91 (0.36), residues: 177 sheet: -0.74 (0.36), residues: 191 loop : -1.34 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 78 HIS 0.005 0.001 HIS K 200 PHE 0.007 0.001 PHE O 89 TYR 0.008 0.001 TYR K 103 ARG 0.005 0.000 ARG M 88 *********************** 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 198 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 2.161 Fit side-chains revert: symmetry clash REVERT: K 163 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6347 (tm-30) REVERT: L 92 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8238 (mp) REVERT: M 100 MET cc_start: 0.8320 (mtp) cc_final: 0.8119 (mtm) REVERT: M 194 LYS cc_start: 0.8087 (mptp) cc_final: 0.7728 (mtpm) REVERT: N 28 GLU cc_start: 0.7904 (tt0) cc_final: 0.7624 (tt0) REVERT: N 56 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7809 (ptpp) REVERT: N 89 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: N 128 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7443 (mtp180) REVERT: N 183 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: O 23 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8030 (ttmm) REVERT: O 91 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6941 (mt-10) REVERT: O 95 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7074 (mpt-90) REVERT: O 96 ARG cc_start: 0.8360 (pmt170) cc_final: 0.8137 (pmm150) REVERT: O 99 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.8148 (mmm-85) outliers start: 38 outliers final: 14 residues processed: 177 average time/residue: 1.7631 time to fit residues: 403.6261 Evaluate side-chains 177 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 270 ARG Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 56 LYS Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 95 ARG 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: 8.9990 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 8.9990 chunk 360 optimal weight: 3.9990 chunk 381 optimal weight: 0.4980 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 overall best weight: 4.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN M 94 GLN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 80020 Z= 0.365 Angle : 0.717 17.702 123198 Z= 0.385 Chirality : 0.038 0.298 16124 Planarity : 0.008 0.136 4344 Dihedral : 23.759 179.954 48072 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.25 % Favored : 92.54 % Rotamer: Outliers : 6.31 % Allowed : 22.34 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.48 (0.25), residues: 952 helix: -0.82 (0.37), residues: 177 sheet: -0.49 (0.36), residues: 182 loop : -1.20 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.008 0.002 PHE M 183 TYR 0.012 0.002 TYR K 83 ARG 0.005 0.001 ARG M 88 *********************** 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 211 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 163 time to evaluate : 2.197 Fit side-chains revert: symmetry clash REVERT: K 35 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: K 100 GLU cc_start: 0.7845 (tt0) cc_final: 0.7531 (tt0) REVERT: K 163 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6403 (tm-30) REVERT: L 76 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8030 (pt0) REVERT: L 92 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8278 (mp) REVERT: M 100 MET cc_start: 0.8373 (mtp) cc_final: 0.8163 (mtm) REVERT: N 89 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: N 128 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7518 (mtp180) REVERT: N 183 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: O 23 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8010 (ttmm) REVERT: O 91 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7020 (mt-10) REVERT: O 95 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7134 (mpt-90) REVERT: O 96 ARG cc_start: 0.8391 (pmt170) cc_final: 0.8178 (pmm150) REVERT: O 99 ARG cc_start: 0.8579 (mmm-85) cc_final: 0.8164 (mmm-85) outliers start: 48 outliers final: 23 residues processed: 189 average time/residue: 1.6966 time to fit residues: 417.1493 Evaluate side-chains 179 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 95 ARG 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: 0.9980 chunk 216 optimal weight: 50.0000 chunk 5 optimal weight: 7.9990 chunk 284 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 0.8980 chunk 263 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 342 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN O 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 80020 Z= 0.315 Angle : 0.695 17.324 123198 Z= 0.375 Chirality : 0.036 0.271 16124 Planarity : 0.008 0.134 4344 Dihedral : 23.754 179.490 48072 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.83 % Favored : 92.96 % Rotamer: Outliers : 6.57 % Allowed : 23.13 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.34 (0.25), residues: 952 helix: -0.71 (0.37), residues: 177 sheet: -0.37 (0.37), residues: 173 loop : -1.11 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 78 HIS 0.003 0.001 HIS K 53 PHE 0.010 0.002 PHE O 89 TYR 0.010 0.002 TYR K 103 ARG 0.007 0.001 ARG M 88 *********************** 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 197 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 147 time to evaluate : 2.203 Fit side-chains REVERT: K 163 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6409 (tm-30) REVERT: L 76 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8018 (pt0) REVERT: L 92 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8270 (mp) REVERT: M 100 MET cc_start: 0.8383 (mtp) cc_final: 0.8183 (mtm) REVERT: N 28 GLU cc_start: 0.7994 (tt0) cc_final: 0.7760 (tt0) REVERT: N 89 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: N 128 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7518 (mtp180) REVERT: N 183 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: O 23 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8071 (ttmm) REVERT: O 91 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6976 (mt-10) REVERT: O 95 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7100 (mpt-90) REVERT: O 96 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8205 (pmm150) REVERT: O 99 ARG cc_start: 0.8593 (mmm-85) cc_final: 0.8216 (mmm-85) outliers start: 50 outliers final: 29 residues processed: 177 average time/residue: 1.6475 time to fit residues: 383.1916 Evaluate side-chains 182 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 134 ASN Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 122 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 95 ARG 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: 8.9990 chunk 343 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 382 optimal weight: 2.9990 chunk 317 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 80020 Z= 0.350 Angle : 0.705 16.100 123198 Z= 0.379 Chirality : 0.037 0.278 16124 Planarity : 0.008 0.135 4344 Dihedral : 23.792 176.881 48072 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.14 % Favored : 92.65 % Rotamer: Outliers : 6.70 % Allowed : 23.78 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.21 (0.26), residues: 952 helix: -0.74 (0.37), residues: 183 sheet: -0.39 (0.38), residues: 165 loop : -0.94 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.007 0.001 PHE N 90 TYR 0.011 0.002 TYR K 83 ARG 0.006 0.001 ARG M 88 *********************** 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 194 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 143 time to evaluate : 2.210 Fit side-chains revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7967 (tt0) cc_final: 0.7738 (tt0) REVERT: K 163 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6384 (tm-30) REVERT: L 13 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8087 (mmtp) REVERT: L 76 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8044 (pt0) REVERT: L 92 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8265 (mp) REVERT: M 100 MET cc_start: 0.8393 (mtp) cc_final: 0.8191 (mtm) REVERT: M 194 LYS cc_start: 0.8168 (mptp) cc_final: 0.7806 (mtpm) REVERT: N 89 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: N 128 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7508 (mtp180) REVERT: N 183 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7845 (pm20) REVERT: O 23 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8065 (ttmm) REVERT: O 91 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6973 (mt-10) REVERT: O 95 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7132 (mpt-90) REVERT: O 96 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8166 (pmm150) REVERT: O 99 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8209 (mmm-85) outliers start: 51 outliers final: 31 residues processed: 176 average time/residue: 1.6264 time to fit residues: 377.0320 Evaluate side-chains 175 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 134 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 134 ASN Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 30 GLU Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 95 ARG 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: 6.9990 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 30.0000 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 50.0000 chunk 321 optimal weight: 3.9990 chunk 213 optimal weight: 40.0000 chunk 380 optimal weight: 0.7980 chunk 238 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 80020 Z= 0.432 Angle : 0.761 16.108 123198 Z= 0.403 Chirality : 0.040 0.298 16124 Planarity : 0.009 0.138 4344 Dihedral : 23.865 176.607 48072 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.46 % Favored : 92.33 % Rotamer: Outliers : 7.23 % Allowed : 23.26 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.26 (0.26), residues: 952 helix: -0.81 (0.37), residues: 181 sheet: -0.42 (0.38), residues: 165 loop : -0.95 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.010 0.002 PHE O 89 TYR 0.010 0.002 TYR O 75 ARG 0.006 0.001 ARG M 88 *********************** 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 192 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 137 time to evaluate : 2.188 Fit side-chains REVERT: K 100 GLU cc_start: 0.7886 (tt0) cc_final: 0.7600 (tt0) REVERT: K 163 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6364 (tm-30) REVERT: L 76 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8021 (pt0) REVERT: L 92 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8256 (mp) REVERT: M 194 LYS cc_start: 0.8228 (mptp) cc_final: 0.7861 (mtpm) REVERT: N 28 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: N 89 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: N 128 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7575 (mtp180) REVERT: N 183 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: O 23 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8069 (ttmm) REVERT: O 91 GLU cc_start: 0.7534 (mm-30) cc_final: 0.6943 (mt-10) REVERT: O 95 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7124 (mpt-90) REVERT: O 96 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8236 (pmm150) REVERT: O 99 ARG cc_start: 0.8734 (mmm-85) cc_final: 0.8262 (mmm-85) outliers start: 55 outliers final: 31 residues processed: 174 average time/residue: 1.6636 time to fit residues: 378.8894 Evaluate side-chains 180 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 122 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 95 ARG 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: 10.0000 chunk 227 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 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 243 HIS ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.100 80020 Z= 0.509 Angle : 0.817 15.971 123198 Z= 0.426 Chirality : 0.044 0.318 16124 Planarity : 0.009 0.142 4344 Dihedral : 23.944 175.852 48072 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.77 % Favored : 92.02 % Rotamer: Outliers : 6.96 % Allowed : 24.18 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.39 (0.26), residues: 952 helix: -0.82 (0.38), residues: 175 sheet: -0.69 (0.36), residues: 185 loop : -1.02 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.006 0.001 HIS K 230 PHE 0.012 0.002 PHE O 89 TYR 0.017 0.002 TYR K 103 ARG 0.007 0.001 ARG K 133 *********************** 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 186 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 133 time to evaluate : 2.270 Fit side-chains REVERT: K 163 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6429 (tm-30) REVERT: L 76 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8056 (pt0) REVERT: L 92 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8245 (mp) REVERT: M 194 LYS cc_start: 0.8251 (mptp) cc_final: 0.7871 (mtpm) REVERT: N 89 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: N 128 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7575 (mtp180) REVERT: N 183 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: O 91 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6927 (mt-10) REVERT: O 95 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7166 (mpt-90) REVERT: O 96 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8272 (pmm150) REVERT: O 99 ARG cc_start: 0.8794 (mmm-85) cc_final: 0.8343 (mmm-85) outliers start: 53 outliers final: 35 residues processed: 169 average time/residue: 1.6739 time to fit residues: 371.7778 Evaluate side-chains 173 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 130 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 122 GLU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 95 ARG 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: 0.9990 chunk 364 optimal weight: 1.9990 chunk 332 optimal weight: 0.8980 chunk 354 optimal weight: 0.9980 chunk 213 optimal weight: 40.0000 chunk 154 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 3.9990 chunk 335 optimal weight: 0.6980 chunk 353 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN L 99 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN O 136 GLN O 138 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 80020 Z= 0.132 Angle : 0.670 16.145 123198 Z= 0.366 Chirality : 0.033 0.262 16124 Planarity : 0.008 0.126 4344 Dihedral : 23.985 174.058 48072 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.67 % Favored : 94.12 % Rotamer: Outliers : 4.34 % Allowed : 26.81 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.12 (0.26), residues: 952 helix: -0.57 (0.38), residues: 182 sheet: -0.50 (0.38), residues: 172 loop : -0.85 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.011 0.002 PHE O 89 TYR 0.011 0.001 TYR K 83 ARG 0.007 0.001 ARG M 88 *********************** 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 172 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 2.191 Fit side-chains REVERT: K 163 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6304 (tm-30) REVERT: L 99 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7567 (m110) REVERT: M 194 LYS cc_start: 0.8192 (mptp) cc_final: 0.7925 (mtpm) REVERT: N 89 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: N 183 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: O 23 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8179 (ttmm) REVERT: O 91 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6844 (mt-10) REVERT: O 95 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7077 (mpt-90) REVERT: O 96 ARG cc_start: 0.8269 (pmt170) cc_final: 0.8025 (pmm150) REVERT: O 99 ARG cc_start: 0.8680 (mmm-85) cc_final: 0.8316 (mmm-85) outliers start: 33 outliers final: 17 residues processed: 158 average time/residue: 1.6569 time to fit residues: 343.6059 Evaluate side-chains 152 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 122 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 95 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: 8.9990 chunk 375 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 260 optimal weight: 8.9990 chunk 393 optimal weight: 1.9990 chunk 362 optimal weight: 3.9990 chunk 313 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 GLN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN O 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 80020 Z= 0.243 Angle : 0.704 59.197 123198 Z= 0.393 Chirality : 0.036 0.264 16124 Planarity : 0.008 0.126 4344 Dihedral : 23.981 174.083 48072 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.99 % Favored : 93.80 % Rotamer: Outliers : 3.29 % Allowed : 27.86 % Favored : 68.86 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.16 (0.26), residues: 952 helix: -0.60 (0.38), residues: 183 sheet: -0.57 (0.36), residues: 192 loop : -0.86 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.011 0.001 PHE O 89 TYR 0.011 0.001 TYR K 83 ARG 0.005 0.000 ARG M 88 ********************** 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 153 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 2.246 Fit side-chains REVERT: K 163 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6314 (tm-30) REVERT: L 92 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8223 (mp) REVERT: M 194 LYS cc_start: 0.8192 (mptp) cc_final: 0.7920 (mtpm) REVERT: N 89 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: N 183 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: O 23 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8142 (ttmm) REVERT: O 91 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6861 (mt-10) REVERT: O 95 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7083 (mpt-90) REVERT: O 99 ARG cc_start: 0.8686 (mmm-85) cc_final: 0.8327 (mmm-85) outliers start: 25 outliers final: 18 residues processed: 144 average time/residue: 1.7166 time to fit residues: 322.9316 Evaluate side-chains 146 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 122 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 42 ASN Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 95 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: 10.0000 chunk 333 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 chunk 322 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 GLN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN O 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.128369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102121 restraints weight = 123385.938| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 0.54 r_work: 0.3262 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 80020 Z= 0.243 Angle : 0.704 59.197 123198 Z= 0.393 Chirality : 0.036 0.264 16124 Planarity : 0.008 0.126 4344 Dihedral : 23.981 174.083 48072 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.99 % Favored : 93.80 % Rotamer: Outliers : 3.15 % Allowed : 28.12 % Favored : 68.73 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.16 (0.26), residues: 952 helix: -0.60 (0.38), residues: 183 sheet: -0.57 (0.36), residues: 192 loop : -0.86 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.011 0.001 PHE O 89 TYR 0.011 0.001 TYR K 83 ARG 0.005 0.000 ARG M 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11498.75 seconds wall clock time: 208 minutes 23.19 seconds (12503.19 seconds total)