Starting phenix.real_space_refine on Sun Feb 18 07:41:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/02_2024/6pc6_20297_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/02_2024/6pc6_20297.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/02_2024/6pc6_20297_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/6pc6_20297/02_2024/6pc6_20297_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/02_2024/6pc6_20297_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/02_2024/6pc6_20297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/02_2024/6pc6_20297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/02_2024/6pc6_20297_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/02_2024/6pc6_20297_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= -0.021 sd= 0.839 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 33503 2.51 5 N 13318 2.21 5 O 22268 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 35": "OE1" <-> "OE2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L 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 GLU 127": "OE1" <-> "OE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ASP 168": "OD1" <-> "OD2" 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 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 131": "OD1" <-> "OD2" 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 GLU 43": "OE1" <-> "OE2" 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: 72127 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': 6, 'rna2p_pur': 280, 'rna2p_pyr': 152, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1060} Link IDs: {'rna2p': 438, 'rna3p': 2458} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2076 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, '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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'O7S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.89, per 1000 atoms: 0.40 Number of scatterers: 72127 At special positions: 0 Unit cell: (227.947, 222.145, 190.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 3015 15.00 F 1 9.00 O 22268 8.00 N 13318 7.00 C 33503 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: 35.21 Conformation dependent library (CDL) restraints added in 1.6 seconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 13 sheets defined 18.2% alpha, 13.8% beta 926 base pairs and 1642 stacking pairs defined. Time for finding SS restraints: 40.31 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 85 removed outlier: 4.503A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) 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 Processing helix chain 'M' and resid 98 through 114 Processing helix chain 'M' and resid 131 through 140 Processing helix chain 'M' and resid 155 through 160 removed outlier: 3.501A pdb=" N LEU M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) 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 removed outlier: 3.789A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 121 through 124 No H-bonds generated for 'chain 'N' and resid 121 through 124' Processing helix chain 'O' and resid 25 through 37 removed outlier: 4.209A 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: 4.541A pdb=" N ARG O 69 " --> pdb=" O GLY O 66 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP O 71 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 108 Proline residue: O 97 - end of helix removed outlier: 4.318A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY O 107 " --> pdb=" O ILE O 103 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 121 removed outlier: 4.350A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.819A 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: 3.675A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.865A 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: 6.796A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.902A 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: 6.526A 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: 6.687A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (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: 6.307A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 169 through 172 removed outlier: 4.728A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP N 181 " --> pdb=" O LEU N 186 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LYS N 190 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL N 177 " --> pdb=" O LYS N 190 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 80 through 83 removed outlier: 6.387A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.483A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.233A 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 76 139 hydrogen bonds defined for protein. 384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2336 hydrogen bonds 3782 hydrogen bond angles 0 basepair planarities 926 basepair parallelities 1642 stacking parallelities Total time for adding SS restraints: 134.64 Time building geometry restraints manager: 37.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.55: 73903 1.55 - 1.88: 6094 1.88 - 2.21: 0 2.21 - 2.55: 0 2.55 - 2.88: 1 Bond restraints: 79998 Sorted by residual: bond pdb=" C ASN K 226 " pdb=" N VAL K 228 " ideal model delta sigma weight residual 1.332 2.883 -1.551 1.36e-02 5.41e+03 1.30e+04 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 3.86e+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 3.85e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.364 0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.367 0.268 2.00e-02 2.50e+03 1.79e+02 ... (remaining 79993 not shown) Histogram of bond angle deviations from ideal: 51.92 - 72.30: 1 72.30 - 92.68: 0 92.68 - 113.07: 63518 113.07 - 133.45: 59628 133.45 - 153.83: 19 Bond angle restraints: 123166 Sorted by residual: angle pdb=" O ASN K 226 " pdb=" C ASN K 226 " pdb=" N VAL K 228 " ideal model delta sigma weight residual 122.59 51.92 70.67 1.33e+00 5.65e-01 2.82e+03 angle pdb=" CA ASN K 226 " pdb=" C ASN K 226 " pdb=" N VAL K 228 " ideal model delta sigma weight residual 116.84 153.83 -36.99 1.71e+00 3.42e-01 4.68e+02 angle pdb=" C06 O7S I3001 " pdb=" C07 O7S I3001 " pdb=" C08 O7S I3001 " ideal model delta sigma weight residual 68.57 120.15 -51.58 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 85.73 128.50 -42.77 3.00e+00 1.11e-01 2.03e+02 angle pdb=" C04 O7S I3001 " pdb=" C05 O7S I3001 " pdb=" C06 O7S I3001 " ideal model delta sigma weight residual 85.76 124.50 -38.74 3.00e+00 1.11e-01 1.67e+02 ... (remaining 123161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 44040 35.67 - 71.34: 6696 71.34 - 107.01: 805 107.01 - 142.68: 14 142.68 - 178.35: 12 Dihedral angle restraints: 51567 sinusoidal: 48890 harmonic: 2677 Sorted by residual: dihedral pdb=" CA ASN K 226 " pdb=" C ASN K 226 " pdb=" N VAL K 228 " pdb=" CA VAL K 228 " ideal model delta harmonic sigma weight residual 180.00 62.45 117.55 0 5.00e+00 4.00e-02 5.53e+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 53.65 178.35 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 42.89 -170.89 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 51564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 12081 0.030 - 0.059: 3783 0.059 - 0.089: 163 0.089 - 0.119: 89 0.119 - 0.148: 7 Chirality restraints: 16123 Sorted by residual: chirality pdb=" C3' G I 271 " pdb=" C4' G I 271 " pdb=" O3' G I 271 " pdb=" C2' G I 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" C1' A I1395 " pdb=" O4' A I1395 " pdb=" C2' A I1395 " pdb=" N9 A I1395 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE K 135 " pdb=" N ILE K 135 " pdb=" C ILE K 135 " pdb=" CB ILE K 135 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 16120 not shown) Planarity restraints: 4340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " -0.040 2.00e-02 2.50e+03 5.94e-01 7.94e+03 pdb=" C4' 1MG I 745 " -0.447 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.692 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.595 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.206 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.924 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.213 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.921 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.033 2.00e-02 2.50e+03 5.91e-01 7.86e+03 pdb=" C4' OMG I2251 " 0.446 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.706 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.594 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.579 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.216 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.908 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.212 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.916 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.020 2.00e-02 2.50e+03 5.87e-01 7.75e+03 pdb=" C4' 2MG I2445 " -0.454 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.731 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.560 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.231 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.878 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.207 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.914 2.00e-02 2.50e+03 ... (remaining 4337 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 436 2.52 - 3.12: 49800 3.12 - 3.71: 145264 3.71 - 4.31: 210862 4.31 - 4.90: 270771 Nonbonded interactions: 677133 Sorted by model distance: nonbonded pdb=" O2' G I1475 " pdb=" O6 G I1514 " model vdw 1.930 2.440 nonbonded pdb=" O2' A I1084 " pdb=" O2' U I1105 " model vdw 1.943 2.440 nonbonded pdb=" O2* PSU I1911 " pdb=" OP1 A I1912 " model vdw 1.951 3.040 nonbonded pdb=" O2' G I1715 " pdb=" O6 G I1743 " model vdw 1.972 2.440 nonbonded pdb=" O2' A I1508 " pdb=" O4' A I1509 " model vdw 2.003 2.440 ... (remaining 677128 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: 18.780 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: 44.900 Check model and map are aligned: 0.890 Set scattering table: 0.520 Process input model: 284.560 Find NCS groups from input model: 0.930 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 363.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.008 1.551 79998 Z= 0.495 Angle : 0.562 70.672 123166 Z= 0.281 Chirality : 0.025 0.148 16123 Planarity : 0.031 0.594 4340 Dihedral : 23.840 178.353 49863 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.11 % Allowed : 10.13 % Favored : 87.76 % 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: -3.58 (0.22), residues: 949 helix: -2.95 (0.27), residues: 176 sheet: -1.72 (0.40), residues: 134 loop : -2.49 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.005 0.001 PHE K 240 TYR 0.007 0.001 TYR L 58 ARG 0.003 0.000 ARG K 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 2.189 Fit side-chains revert: symmetry clash REVERT: K 132 MET cc_start: 0.8526 (mtm) cc_final: 0.8226 (mtm) REVERT: L 118 THR cc_start: 0.8736 (t) cc_final: 0.8496 (p) REVERT: M 127 GLU cc_start: 0.7861 (pm20) cc_final: 0.7637 (pm20) REVERT: O 12 LYS cc_start: 0.8211 (mmmt) cc_final: 0.8007 (mmtp) outliers start: 16 outliers final: 8 residues processed: 212 average time/residue: 1.8111 time to fit residues: 491.0789 Evaluate side-chains 153 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 123 LYS Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain O residue 81 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 0.6980 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 201 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 309 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 358 optimal weight: 4.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 60 GLN K 163 GLN M 30 GLN M 41 GLN M 90 GLN M 115 GLN M 195 GLN N 32 ASN N 130 GLN O 128 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 79998 Z= 0.346 Angle : 0.701 17.784 123166 Z= 0.379 Chirality : 0.036 0.304 16123 Planarity : 0.008 0.132 4340 Dihedral : 23.807 179.305 48080 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.68 % Favored : 94.01 % Rotamer: Outliers : 3.95 % Allowed : 16.84 % Favored : 79.21 % 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: -1.97 (0.25), residues: 951 helix: -0.88 (0.34), residues: 170 sheet: -0.90 (0.40), residues: 156 loop : -1.61 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 78 HIS 0.004 0.001 HIS O 76 PHE 0.010 0.001 PHE M 85 TYR 0.011 0.002 TYR K 62 ARG 0.003 0.001 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 2.203 Fit side-chains REVERT: K 269 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7440 (mmm-85) REVERT: L 118 THR cc_start: 0.8829 (t) cc_final: 0.8590 (p) REVERT: M 136 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7837 (tp-100) REVERT: M 156 ASN cc_start: 0.8671 (m-40) cc_final: 0.8417 (m-40) outliers start: 30 outliers final: 15 residues processed: 172 average time/residue: 1.7005 time to fit residues: 380.7958 Evaluate side-chains 157 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN 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: 6.9990 chunk 111 optimal weight: 8.9990 chunk 298 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 359 optimal weight: 0.8980 chunk 388 optimal weight: 6.9990 chunk 320 optimal weight: 0.9990 chunk 356 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 60 GLN K 163 GLN M 90 GLN M 115 GLN N 130 GLN N 167 ASN O 58 ASN O 128 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 79998 Z= 0.359 Angle : 0.686 17.015 123166 Z= 0.372 Chirality : 0.036 0.279 16123 Planarity : 0.008 0.137 4340 Dihedral : 23.841 177.490 48075 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.10 % Favored : 93.69 % Rotamer: Outliers : 3.95 % Allowed : 18.68 % Favored : 77.37 % 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: 951 helix: -0.14 (0.38), residues: 168 sheet: -0.69 (0.37), residues: 172 loop : -1.26 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 248 HIS 0.003 0.001 HIS N 140 PHE 0.010 0.002 PHE K 240 TYR 0.012 0.002 TYR K 161 ARG 0.003 0.000 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 2.316 Fit side-chains REVERT: M 144 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: M 156 ASN cc_start: 0.8754 (m-40) cc_final: 0.8501 (m-40) REVERT: N 13 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.5997 (ptp-170) REVERT: N 88 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6721 (mt-10) REVERT: N 184 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7940 (mtp180) REVERT: N 185 ASN cc_start: 0.8131 (m-40) cc_final: 0.7908 (m110) outliers start: 30 outliers final: 17 residues processed: 171 average time/residue: 1.7742 time to fit residues: 391.5244 Evaluate side-chains 160 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 131 ASN 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: 6.9990 chunk 270 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 360 optimal weight: 7.9990 chunk 381 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 60 GLN K 115 GLN M 90 GLN M 115 GLN N 130 GLN N 167 ASN O 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 79998 Z= 0.525 Angle : 0.783 17.011 123166 Z= 0.414 Chirality : 0.043 0.326 16123 Planarity : 0.009 0.142 4340 Dihedral : 23.938 178.087 48075 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.62 % Favored : 93.17 % Rotamer: Outliers : 5.53 % Allowed : 17.89 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.22 (0.26), residues: 951 helix: 0.02 (0.39), residues: 165 sheet: -0.62 (0.37), residues: 176 loop : -1.12 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 248 HIS 0.004 0.001 HIS N 140 PHE 0.011 0.002 PHE K 240 TYR 0.013 0.003 TYR O 53 ARG 0.005 0.001 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 149 time to evaluate : 2.178 Fit side-chains REVERT: K 20 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.9070 (m) REVERT: K 133 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7696 (tpp-160) REVERT: M 144 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: N 13 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.5987 (ptp-170) REVERT: N 88 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6860 (mt-10) REVERT: N 184 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7957 (mtp180) REVERT: N 185 ASN cc_start: 0.8216 (m-40) cc_final: 0.7935 (m110) outliers start: 42 outliers final: 25 residues processed: 177 average time/residue: 1.7609 time to fit residues: 403.9406 Evaluate side-chains 178 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 133 ARG Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 131 ASN 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: 2.9990 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 0.8980 chunk 263 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 60 GLN K 115 GLN M 90 GLN M 115 GLN N 130 GLN O 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 79998 Z= 0.352 Angle : 0.707 16.675 123166 Z= 0.384 Chirality : 0.037 0.293 16123 Planarity : 0.008 0.137 4340 Dihedral : 23.981 178.782 48075 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.31 % Favored : 93.48 % Rotamer: Outliers : 5.39 % Allowed : 18.68 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.14 (0.26), residues: 951 helix: 0.11 (0.40), residues: 167 sheet: -0.56 (0.37), residues: 176 loop : -1.08 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.003 0.001 HIS N 140 PHE 0.009 0.001 PHE L 66 TYR 0.012 0.002 TYR M 35 ARG 0.003 0.000 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 150 time to evaluate : 2.376 Fit side-chains REVERT: K 133 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8455 (tpp-160) REVERT: M 144 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: N 13 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.5972 (ptp-170) REVERT: N 59 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7995 (ttt180) REVERT: N 184 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7946 (mtp180) REVERT: N 185 ASN cc_start: 0.8144 (m-40) cc_final: 0.7905 (m110) outliers start: 41 outliers final: 27 residues processed: 178 average time/residue: 1.6830 time to fit residues: 388.8320 Evaluate side-chains 181 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 133 ARG Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 131 ASN 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: 3.9990 chunk 75 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 382 optimal weight: 10.0000 chunk 317 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 90 GLN M 115 GLN N 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 79998 Z= 0.379 Angle : 0.707 16.496 123166 Z= 0.383 Chirality : 0.038 0.291 16123 Planarity : 0.008 0.137 4340 Dihedral : 23.939 179.975 48075 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.38 % Rotamer: Outliers : 5.13 % Allowed : 19.08 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.02 (0.26), residues: 951 helix: 0.22 (0.40), residues: 167 sheet: -0.51 (0.37), residues: 176 loop : -1.00 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 60 HIS 0.003 0.001 HIS N 140 PHE 0.008 0.001 PHE K 240 TYR 0.011 0.002 TYR M 35 ARG 0.003 0.000 ARG N 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 146 time to evaluate : 2.243 Fit side-chains REVERT: K 98 ASP cc_start: 0.8350 (p0) cc_final: 0.8108 (p0) REVERT: K 133 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8103 (ttp-170) REVERT: K 269 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7469 (tmm-80) REVERT: M 144 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: N 13 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.5971 (ptp-170) REVERT: N 59 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7939 (ttt180) REVERT: N 88 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6671 (mt-10) REVERT: N 184 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7934 (mtp180) REVERT: N 185 ASN cc_start: 0.8136 (m-40) cc_final: 0.7906 (m110) outliers start: 39 outliers final: 25 residues processed: 174 average time/residue: 1.7152 time to fit residues: 387.4833 Evaluate side-chains 178 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 133 ARG Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 131 ASN 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: 40.0000 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 40.0000 chunk 321 optimal weight: 2.9990 chunk 213 optimal weight: 40.0000 chunk 380 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 90 GLN M 115 GLN N 130 GLN O 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 79998 Z= 0.472 Angle : 0.754 16.699 123166 Z= 0.403 Chirality : 0.041 0.317 16123 Planarity : 0.009 0.141 4340 Dihedral : 23.989 177.045 48075 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.83 % Favored : 92.95 % Rotamer: Outliers : 5.92 % Allowed : 19.08 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.95 (0.26), residues: 951 helix: 0.21 (0.40), residues: 165 sheet: -0.57 (0.37), residues: 176 loop : -0.88 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 60 HIS 0.004 0.001 HIS N 140 PHE 0.011 0.002 PHE K 240 TYR 0.012 0.002 TYR M 35 ARG 0.004 0.001 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 148 time to evaluate : 2.220 Fit side-chains REVERT: K 98 ASP cc_start: 0.8428 (p0) cc_final: 0.8155 (p0) REVERT: M 144 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: N 13 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.5986 (ptp-170) REVERT: N 59 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7994 (ttt180) REVERT: N 184 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7963 (mtp180) REVERT: N 185 ASN cc_start: 0.8183 (m-40) cc_final: 0.7904 (m110) REVERT: O 12 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7905 (mmtp) outliers start: 45 outliers final: 27 residues processed: 181 average time/residue: 1.7315 time to fit residues: 407.8034 Evaluate side-chains 178 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 93 ILE 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: 5.9990 chunk 114 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 41 GLN M 90 GLN M 115 GLN N 130 GLN O 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 79998 Z= 0.489 Angle : 0.759 16.570 123166 Z= 0.404 Chirality : 0.042 0.317 16123 Planarity : 0.009 0.141 4340 Dihedral : 23.980 177.425 48075 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.26 % Favored : 92.53 % Rotamer: Outliers : 4.87 % Allowed : 19.87 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.94 (0.26), residues: 951 helix: 0.23 (0.40), residues: 165 sheet: -0.59 (0.37), residues: 176 loop : -0.87 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 60 HIS 0.005 0.001 HIS K 230 PHE 0.010 0.002 PHE K 240 TYR 0.019 0.002 TYR O 53 ARG 0.004 0.001 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 2.203 Fit side-chains REVERT: K 98 ASP cc_start: 0.8439 (p0) cc_final: 0.8194 (p0) REVERT: M 144 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7404 (pm20) REVERT: N 13 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.5974 (ptp-170) REVERT: N 59 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8008 (ttt180) REVERT: N 88 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: N 184 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7934 (mtp180) REVERT: N 185 ASN cc_start: 0.8148 (m-40) cc_final: 0.7832 (m110) outliers start: 37 outliers final: 27 residues processed: 174 average time/residue: 1.6954 time to fit residues: 384.2087 Evaluate side-chains 179 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain N residue 202 ILE Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.9980 chunk 364 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 354 optimal weight: 4.9990 chunk 213 optimal weight: 50.0000 chunk 154 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 5.9990 chunk 335 optimal weight: 1.9990 chunk 353 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 41 GLN M 90 GLN M 115 GLN N 130 GLN O 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 79998 Z= 0.180 Angle : 0.616 15.928 123166 Z= 0.344 Chirality : 0.031 0.260 16123 Planarity : 0.008 0.126 4340 Dihedral : 23.908 178.536 48073 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.20 % Favored : 93.59 % Rotamer: Outliers : 2.89 % Allowed : 21.97 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.91 (0.26), residues: 951 helix: -0.11 (0.38), residues: 187 sheet: -0.47 (0.37), residues: 174 loop : -0.78 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 60 HIS 0.009 0.001 HIS O 130 PHE 0.005 0.001 PHE N 118 TYR 0.016 0.002 TYR O 53 ARG 0.004 0.000 ARG O 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 2.232 Fit side-chains REVERT: K 98 ASP cc_start: 0.8446 (p0) cc_final: 0.8225 (p0) REVERT: N 13 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.5886 (ptp-170) REVERT: N 59 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7809 (ttt180) REVERT: N 184 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7967 (mtp180) REVERT: N 185 ASN cc_start: 0.7968 (m-40) cc_final: 0.7749 (m110) REVERT: O 12 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7819 (mmtp) outliers start: 22 outliers final: 12 residues processed: 173 average time/residue: 1.7248 time to fit residues: 389.3062 Evaluate side-chains 164 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 81 ILE 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: 7.9990 chunk 375 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 260 optimal weight: 7.9990 chunk 393 optimal weight: 7.9990 chunk 362 optimal weight: 6.9990 chunk 313 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN K 226 ASN M 41 GLN M 90 GLN M 115 GLN N 130 GLN N 167 ASN O 128 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.105 79998 Z= 0.628 Angle : 0.836 16.894 123166 Z= 0.435 Chirality : 0.047 0.344 16123 Planarity : 0.009 0.145 4340 Dihedral : 23.985 177.323 48073 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.73 % Favored : 93.06 % Rotamer: Outliers : 3.55 % Allowed : 21.84 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.86 (0.26), residues: 951 helix: 0.32 (0.40), residues: 165 sheet: -0.52 (0.37), residues: 175 loop : -0.83 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 60 HIS 0.005 0.002 HIS M 165 PHE 0.028 0.002 PHE O 119 TYR 0.022 0.003 TYR O 53 ARG 0.006 0.001 ARG K 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 2.207 Fit side-chains REVERT: K 98 ASP cc_start: 0.8495 (p0) cc_final: 0.8278 (p0) REVERT: M 144 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: N 13 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.5972 (ptp-170) REVERT: N 184 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7951 (mtp180) REVERT: N 185 ASN cc_start: 0.8093 (m-40) cc_final: 0.7892 (m110) outliers start: 27 outliers final: 17 residues processed: 165 average time/residue: 1.6394 time to fit residues: 355.6836 Evaluate side-chains 159 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 226 ASN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE 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: 2.9990 chunk 333 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 322 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN K 226 ASN M 41 GLN M 90 GLN M 115 GLN N 130 GLN O 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.101658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.076737 restraints weight = 143219.427| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 0.58 r_work: 0.2920 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 79998 Z= 0.336 Angle : 0.860 59.187 123166 Z= 0.457 Chirality : 0.038 0.860 16123 Planarity : 0.009 0.144 4340 Dihedral : 23.989 177.224 48073 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.83 % Favored : 92.85 % Rotamer: Outliers : 3.42 % Allowed : 21.58 % Favored : 75.00 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.84 (0.27), residues: 951 helix: 0.40 (0.41), residues: 165 sheet: -0.54 (0.37), residues: 175 loop : -0.83 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 60 HIS 0.005 0.001 HIS N 140 PHE 0.023 0.002 PHE O 119 TYR 0.018 0.002 TYR O 53 ARG 0.004 0.001 ARG N 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11496.15 seconds wall clock time: 207 minutes 59.61 seconds (12479.61 seconds total)