Starting phenix.real_space_refine on Sun Feb 18 08:12:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/02_2024/6pch_20300_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/02_2024/6pch_20300.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/02_2024/6pch_20300_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/02_2024/6pch_20300_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/02_2024/6pch_20300_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/02_2024/6pch_20300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/02_2024/6pch_20300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/02_2024/6pch_20300_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/02_2024/6pch_20300_neut_updated.pdb" } resolution = 2.9 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= -0.017 sd= 1.289 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: 5 Type Number sf(0) Gaussians P 3015 5.49 5 S 22 5.16 5 C 33508 2.51 5 N 13319 2.21 5 O 22270 1.98 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 ASP 229": "OD1" <-> "OD2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K ASP 264": "OD1" <-> "OD2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ARG 170": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N GLU 86": "OE1" <-> "OE2" 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 ASP 71": "OD1" <-> "OD2" Residue "O TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 120": "NH1" <-> "NH2" Residue "O ASP 141": "OD1" <-> "OD2" 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: 72134 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'O8D': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.74, per 1000 atoms: 0.40 Number of scatterers: 72134 At special positions: 0 Unit cell: (228.611, 221.984, 188.852, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 3015 15.00 O 22270 8.00 N 13319 7.00 C 33508 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: 34.74 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: 27 helices and 13 sheets defined 19.0% alpha, 13.1% beta 793 base pairs and 1610 stacking pairs defined. Time for finding SS restraints: 38.92 Creating SS restraints... Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 132 through 134 No H-bonds generated for 'chain 'K' and resid 132 through 134' Processing helix chain 'K' and resid 198 through 202 removed outlier: 3.718A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 213 removed outlier: 3.560A pdb=" N ARG K 212 " --> pdb=" O ALA K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 229 No H-bonds generated for 'chain 'K' and resid 226 through 229' Processing helix chain 'L' and resid 3 through 5 No H-bonds generated for 'chain 'L' and resid 3 through 5' Processing helix chain 'L' and resid 23 through 25 No H-bonds generated for 'chain 'L' and resid 23 through 25' 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: 4.838A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 97 removed outlier: 3.536A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 92 through 97' Processing helix chain 'L' and resid 129 through 138 removed outlier: 3.531A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 37 Processing helix chain 'M' and resid 98 through 114 removed outlier: 3.536A pdb=" N LYS M 106 " --> pdb=" O ARG M 102 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL M 113 " --> pdb=" O LEU M 109 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 141 removed outlier: 3.834A pdb=" N LYS M 137 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS M 139 " --> pdb=" O ALA M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 160 removed outlier: 3.624A pdb=" N ALA M 160 " --> pdb=" O ASN M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 removed outlier: 3.655A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 68 Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'O' and resid 25 through 37 removed outlier: 4.144A 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: 4.414A pdb=" N ARG O 69 " --> pdb=" O GLY O 66 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP O 71 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 95 removed outlier: 3.590A pdb=" N ALA O 94 " --> pdb=" O GLU O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 106 removed outlier: 3.586A pdb=" N GLU O 102 " --> pdb=" O ARG O 99 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL O 105 " --> pdb=" O GLU O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 121 removed outlier: 3.508A pdb=" N PHE O 119 " --> pdb=" O GLY O 115 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 115 through 121' 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 101 through 105 removed outlier: 3.568A pdb=" N ARG K 102 " --> pdb=" O VAL K 94 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE K 104 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 129 through 131 removed outlier: 3.788A pdb=" N LEU K 130 " --> pdb=" O ALA K 190 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.575A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.544A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.522A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'M' and resid 2 through 4 Processing sheet with id= H, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.401A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR M 150 " --> pdb=" O ARG M 170 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 169 through 171 removed outlier: 4.780A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP N 181 " --> pdb=" O LEU N 186 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LYS N 190 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL N 177 " --> pdb=" O LYS N 190 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 47 through 50 Processing sheet with id= K, first strand: chain 'N' and resid 117 through 119 removed outlier: 3.546A pdb=" N GLY N 117 " --> pdb=" O MET N 165 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.480A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.323A 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 76 117 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1962 hydrogen bonds 3204 hydrogen bond angles 0 basepair planarities 793 basepair parallelities 1610 stacking parallelities Total time for adding SS restraints: 141.98 Time building geometry restraints manager: 37.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4062 1.28 - 1.41: 27849 1.41 - 1.54: 41988 1.54 - 1.68: 6065 1.68 - 1.81: 42 Bond restraints: 80006 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.411 0.391 2.00e-02 2.50e+03 3.83e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.80e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.366 0.269 2.00e-02 2.50e+03 1.82e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.368 0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C5 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.155 1.349 -0.194 2.00e-02 2.50e+03 9.39e+01 ... (remaining 80001 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.96: 17923 106.96 - 113.96: 51097 113.96 - 120.96: 32327 120.96 - 127.96: 16919 127.96 - 134.97: 4912 Bond angle restraints: 123178 Sorted by residual: angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C8 6MZ I1618 " ideal model delta sigma weight residual 91.39 126.93 -35.54 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C4 6MZ I1618 " ideal model delta sigma weight residual 154.15 125.53 28.62 3.00e+00 1.11e-01 9.10e+01 angle pdb=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C8 1MG I 745 " ideal model delta sigma weight residual 100.16 126.05 -25.89 3.00e+00 1.11e-01 7.45e+01 angle pdb=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C4 1MG I 745 " ideal model delta sigma weight residual 146.15 126.35 19.80 3.00e+00 1.11e-01 4.35e+01 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C4 OMG I2251 " ideal model delta sigma weight residual 108.29 126.73 -18.44 3.00e+00 1.11e-01 3.78e+01 ... (remaining 123173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 44226 35.70 - 71.41: 6544 71.41 - 107.11: 790 107.11 - 142.81: 6 142.81 - 178.52: 7 Dihedral angle restraints: 51573 sinusoidal: 48893 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 36.51 -71.51 1 8.00e+00 1.56e-02 1.02e+02 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 90.64 56.36 1 8.00e+00 1.56e-02 6.69e+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 58.45 173.55 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 51570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 16019 0.086 - 0.171: 107 0.171 - 0.257: 0 0.257 - 0.342: 0 0.342 - 0.428: 2 Chirality restraints: 16128 Sorted by residual: chirality pdb=" CA PRO K 227 " pdb=" N PRO K 227 " pdb=" C PRO K 227 " pdb=" CB PRO K 227 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CB VAL K 228 " pdb=" CA VAL K 228 " pdb=" CG1 VAL K 228 " pdb=" CG2 VAL K 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.37e+00 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 -2.59 -0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 16125 not shown) Planarity restraints: 4343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " -0.045 2.00e-02 2.50e+03 6.03e-01 8.17e+03 pdb=" C4' 1MG I 745 " -0.454 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.709 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.592 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.607 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.203 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.929 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.209 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.944 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.033 2.00e-02 2.50e+03 6.01e-01 8.13e+03 pdb=" C4' 2MG I2445 " -0.461 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.751 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.584 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.224 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.897 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.199 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.944 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 5.84e-01 7.67e+03 pdb=" C4' OMG I2251 " 0.443 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.685 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.594 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.574 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.216 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.904 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.218 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.899 2.00e-02 2.50e+03 ... (remaining 4340 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 182 2.34 - 2.98: 32732 2.98 - 3.62: 124124 3.62 - 4.26: 221679 4.26 - 4.90: 289588 Nonbonded interactions: 668305 Sorted by model distance: nonbonded pdb=" O MET K 225 " pdb=" O ASN K 226 " model vdw 1.702 3.040 nonbonded pdb=" O2' G I2576 " pdb=" OP2 C I2579 " model vdw 1.913 2.440 nonbonded pdb=" O2' 2MA I2503 " pdb=" OP2 G I2505 " model vdw 1.951 3.040 nonbonded pdb=" O2' G I1715 " pdb=" O6 G I1743 " model vdw 1.963 2.440 nonbonded pdb=" O2' A I1084 " pdb=" O2' U I1105 " model vdw 1.972 2.440 ... (remaining 668300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 44.510 Check model and map are aligned: 0.810 Set scattering table: 0.520 Process input model: 291.150 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 360.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 0.005 0.391 80006 Z= 0.309 Angle : 0.395 35.545 123178 Z= 0.195 Chirality : 0.023 0.428 16128 Planarity : 0.031 0.603 4343 Dihedral : 23.641 178.519 49867 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.88 % Favored : 92.02 % Rotamer: Outliers : 2.23 % Allowed : 13.80 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.23), residues: 952 helix: -4.18 (0.22), residues: 162 sheet: -2.43 (0.37), residues: 167 loop : -2.66 (0.21), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 78 HIS 0.003 0.001 HIS K 142 PHE 0.006 0.001 PHE O 119 TYR 0.006 0.001 TYR L 58 ARG 0.001 0.000 ARG O 120 *********************** 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 248 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 231 time to evaluate : 2.246 Fit side-chains revert: symmetry clash REVERT: K 135 ILE cc_start: 0.7951 (mm) cc_final: 0.7700 (tp) REVERT: K 187 ASP cc_start: 0.7238 (m-30) cc_final: 0.6944 (m-30) REVERT: M 111 GLU cc_start: 0.5771 (mm-30) cc_final: 0.5394 (tp30) REVERT: M 144 GLU cc_start: 0.3749 (OUTLIER) cc_final: 0.2680 (tp30) REVERT: M 145 ASP cc_start: 0.7419 (t0) cc_final: 0.7045 (t0) REVERT: N 13 ARG cc_start: 0.4933 (ptp-170) cc_final: 0.4293 (pmt170) REVERT: N 21 SER cc_start: 0.8432 (m) cc_final: 0.8163 (p) REVERT: N 40 LEU cc_start: 0.8223 (mp) cc_final: 0.7804 (tt) REVERT: N 105 LYS cc_start: 0.7795 (ttmm) cc_final: 0.7116 (mmmt) REVERT: N 137 SER cc_start: 0.8704 (m) cc_final: 0.8390 (t) REVERT: O 111 LYS cc_start: 0.6971 (mptt) cc_final: 0.6749 (mptt) outliers start: 17 outliers final: 9 residues processed: 241 average time/residue: 1.7449 time to fit residues: 540.6686 Evaluate side-chains 165 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 73 VAL 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: 10.0000 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 309 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 358 optimal weight: 6.9990 overall best weight: 7.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 46 ASN K 86 ASN K 115 GLN K 200 HIS K 239 ASN L 4 ASN L 99 ASN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN N 49 GLN N 67 HIS N 94 GLN N 126 ASN O 86 GLN O 130 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 80006 Z= 0.446 Angle : 0.848 16.856 123178 Z= 0.439 Chirality : 0.042 0.271 16128 Planarity : 0.009 0.136 4343 Dihedral : 23.747 176.137 48082 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.40 % Favored : 91.49 % Rotamer: Outliers : 7.49 % Allowed : 21.42 % Favored : 71.09 % 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: -3.13 (0.24), residues: 952 helix: -2.90 (0.31), residues: 175 sheet: -1.65 (0.41), residues: 144 loop : -2.02 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP K 248 HIS 0.006 0.002 HIS K 230 PHE 0.014 0.002 PHE L 66 TYR 0.011 0.002 TYR K 161 ARG 0.010 0.001 ARG O 69 *********************** 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 239 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 182 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 145 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7038 (mt-10) REVERT: K 187 ASP cc_start: 0.7782 (m-30) cc_final: 0.7430 (m-30) REVERT: K 270 ARG cc_start: 0.6588 (ptm160) cc_final: 0.6015 (ttm110) REVERT: L 66 PHE cc_start: 0.8737 (p90) cc_final: 0.8482 (p90) REVERT: M 94 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8554 (mt0) REVERT: M 111 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6497 (tm-30) REVERT: M 144 GLU cc_start: 0.4276 (OUTLIER) cc_final: 0.3471 (tp30) REVERT: N 13 ARG cc_start: 0.5171 (ptp-170) cc_final: 0.4585 (pmt170) REVERT: N 40 LEU cc_start: 0.8440 (mp) cc_final: 0.7682 (tt) REVERT: N 62 LYS cc_start: 0.8457 (ptpt) cc_final: 0.8235 (ptmm) REVERT: N 105 LYS cc_start: 0.7835 (ttmm) cc_final: 0.7109 (mmmt) REVERT: N 160 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8693 (mtmm) REVERT: N 190 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7868 (tmmt) REVERT: O 111 LYS cc_start: 0.7039 (mptt) cc_final: 0.6398 (mttp) outliers start: 57 outliers final: 27 residues processed: 213 average time/residue: 1.6317 time to fit residues: 456.2949 Evaluate side-chains 179 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 134 ASN Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 64 VAL 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: 8.9990 chunk 111 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 359 optimal weight: 0.9990 chunk 388 optimal weight: 4.9990 chunk 320 optimal weight: 2.9990 chunk 356 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 94 GLN ** N 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 80006 Z= 0.192 Angle : 0.635 17.191 123178 Z= 0.348 Chirality : 0.031 0.253 16128 Planarity : 0.008 0.127 4343 Dihedral : 23.645 175.261 48077 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.09 % Favored : 93.80 % Rotamer: Outliers : 6.96 % Allowed : 26.28 % Favored : 66.75 % 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: -2.56 (0.25), residues: 952 helix: -2.24 (0.34), residues: 180 sheet: -1.45 (0.41), residues: 148 loop : -1.64 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 248 HIS 0.006 0.001 HIS K 15 PHE 0.009 0.002 PHE O 119 TYR 0.011 0.001 TYR O 44 ARG 0.006 0.001 ARG K 14 *********************** 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 242 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 189 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.4788 (ttpt) REVERT: K 125 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7724 (ttpt) REVERT: K 145 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: M 94 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8585 (mt0) REVERT: M 111 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6344 (tm-30) REVERT: M 144 GLU cc_start: 0.4263 (OUTLIER) cc_final: 0.3639 (tp30) REVERT: M 171 ASP cc_start: 0.7570 (m-30) cc_final: 0.6934 (t70) REVERT: N 13 ARG cc_start: 0.5062 (ptp-170) cc_final: 0.4594 (pmt170) REVERT: N 40 LEU cc_start: 0.8313 (mp) cc_final: 0.7657 (tt) REVERT: N 62 LYS cc_start: 0.8442 (ptpt) cc_final: 0.8221 (ptmm) REVERT: N 105 LYS cc_start: 0.7779 (ttmm) cc_final: 0.7312 (mmmt) REVERT: N 190 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7779 (tmmm) REVERT: O 142 ILE cc_start: 0.6128 (OUTLIER) cc_final: 0.5759 (mp) outliers start: 53 outliers final: 22 residues processed: 218 average time/residue: 1.5727 time to fit residues: 453.6980 Evaluate side-chains 189 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain O residue 5 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 381 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 overall best weight: 5.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 GLN N 49 GLN N 94 GLN O 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 80006 Z= 0.366 Angle : 0.778 16.803 123178 Z= 0.409 Chirality : 0.038 0.271 16128 Planarity : 0.009 0.134 4343 Dihedral : 23.834 170.939 48076 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.98 % Favored : 91.91 % Rotamer: Outliers : 7.88 % Allowed : 28.52 % Favored : 63.60 % 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: -2.34 (0.25), residues: 952 helix: -2.17 (0.35), residues: 173 sheet: -1.14 (0.41), residues: 140 loop : -1.52 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.020 0.002 PHE L 66 TYR 0.014 0.002 TYR O 44 ARG 0.007 0.001 ARG K 14 *********************** 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 238 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 178 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 145 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: K 185 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7138 (tm-30) REVERT: K 187 ASP cc_start: 0.7884 (m-30) cc_final: 0.7671 (m-30) REVERT: K 189 ARG cc_start: 0.7866 (mtt-85) cc_final: 0.7427 (mtp85) REVERT: K 270 ARG cc_start: 0.6540 (ptm160) cc_final: 0.5849 (ttm110) REVERT: M 94 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8671 (mt0) REVERT: M 111 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6025 (tm-30) REVERT: M 115 GLN cc_start: 0.6921 (mp10) cc_final: 0.6495 (mp10) REVERT: M 144 GLU cc_start: 0.4426 (OUTLIER) cc_final: 0.3944 (tp30) REVERT: M 157 LEU cc_start: 0.8732 (pt) cc_final: 0.8203 (tp) REVERT: N 13 ARG cc_start: 0.5204 (ptp-170) cc_final: 0.4608 (pmt170) REVERT: N 40 LEU cc_start: 0.8366 (mp) cc_final: 0.7726 (tt) REVERT: N 62 LYS cc_start: 0.8441 (ptpt) cc_final: 0.8221 (ptmm) REVERT: N 105 LYS cc_start: 0.7734 (ttmm) cc_final: 0.7281 (mmmt) REVERT: N 190 LYS cc_start: 0.8399 (ttmt) cc_final: 0.7872 (tmmm) REVERT: O 111 LYS cc_start: 0.6997 (mptt) cc_final: 0.6260 (mttm) outliers start: 60 outliers final: 35 residues processed: 214 average time/residue: 1.6018 time to fit residues: 452.4228 Evaluate side-chains 215 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 53 HIS Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 64 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 5.9990 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 342 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 25 HIS ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 HIS O 86 GLN O 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 80006 Z= 0.455 Angle : 0.852 17.349 123178 Z= 0.442 Chirality : 0.043 0.311 16128 Planarity : 0.009 0.137 4343 Dihedral : 24.149 173.210 48076 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.24 % Favored : 90.65 % Rotamer: Outliers : 10.25 % Allowed : 26.15 % Favored : 63.60 % 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: -2.50 (0.25), residues: 952 helix: -2.33 (0.34), residues: 163 sheet: -1.19 (0.40), residues: 151 loop : -1.66 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP K 248 HIS 0.006 0.002 HIS K 230 PHE 0.022 0.002 PHE L 66 TYR 0.015 0.002 TYR O 44 ARG 0.005 0.001 ARG K 80 *********************** 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 258 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 180 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7652 (tp30) cc_final: 0.7261 (tp30) REVERT: K 125 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8077 (ttpt) REVERT: K 185 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: K 187 ASP cc_start: 0.8130 (m-30) cc_final: 0.7494 (m-30) REVERT: K 270 ARG cc_start: 0.6678 (ptm160) cc_final: 0.5900 (ttm110) REVERT: M 88 ARG cc_start: 0.8105 (mmp80) cc_final: 0.7897 (mpt180) REVERT: M 94 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8649 (mt0) REVERT: M 111 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6441 (tm-30) REVERT: M 123 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.5878 (ptmt) REVERT: M 157 LEU cc_start: 0.8914 (pt) cc_final: 0.8513 (tp) REVERT: N 13 ARG cc_start: 0.5410 (ptp-170) cc_final: 0.5054 (pmt170) REVERT: N 40 LEU cc_start: 0.8358 (mp) cc_final: 0.7718 (tt) REVERT: N 62 LYS cc_start: 0.8473 (ptpt) cc_final: 0.8240 (ptmm) REVERT: N 74 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: N 105 LYS cc_start: 0.7696 (ttmm) cc_final: 0.7238 (mmmt) REVERT: N 165 MET cc_start: 0.8425 (ttt) cc_final: 0.8211 (ttp) REVERT: O 111 LYS cc_start: 0.7105 (mptt) cc_final: 0.6466 (mttp) REVERT: O 142 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6344 (mp) outliers start: 78 outliers final: 42 residues processed: 231 average time/residue: 1.5906 time to fit residues: 484.0399 Evaluate side-chains 204 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 156 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 53 HIS Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 123 LYS Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 30 THR 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 131 ASN Chi-restraints excluded: chain O residue 141 ASP 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: 10.0000 chunk 343 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 224 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 382 optimal weight: 0.3980 chunk 317 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 overall best weight: 6.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 251 GLN N 49 GLN O 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 80006 Z= 0.367 Angle : 0.766 17.244 123178 Z= 0.406 Chirality : 0.039 0.267 16128 Planarity : 0.009 0.133 4343 Dihedral : 24.041 176.365 48072 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.24 % Favored : 90.65 % Rotamer: Outliers : 8.94 % Allowed : 29.17 % Favored : 61.89 % 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: -2.33 (0.25), residues: 952 helix: -2.04 (0.36), residues: 167 sheet: -1.02 (0.42), residues: 141 loop : -1.59 (0.23), residues: 644 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 0.008 0.002 PHE M 85 TYR 0.016 0.002 TYR O 44 ARG 0.004 0.001 ARG K 189 *********************** 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 242 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 174 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7545 (tp30) cc_final: 0.7111 (tp30) REVERT: K 125 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8028 (ttpt) REVERT: K 145 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: K 175 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6899 (ptm-80) REVERT: K 185 GLU cc_start: 0.7325 (tm-30) cc_final: 0.7092 (tm-30) REVERT: K 270 ARG cc_start: 0.6513 (ptm160) cc_final: 0.5857 (ttm110) REVERT: M 94 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8661 (mt0) REVERT: M 111 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6219 (tm-30) REVERT: M 123 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.5789 (ptmt) REVERT: M 157 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8455 (tp) REVERT: N 13 ARG cc_start: 0.5376 (ptp-170) cc_final: 0.5045 (pmt170) REVERT: N 40 LEU cc_start: 0.8386 (mp) cc_final: 0.7737 (tt) REVERT: N 62 LYS cc_start: 0.8472 (ptpt) cc_final: 0.8219 (ptmm) REVERT: N 105 LYS cc_start: 0.7712 (ttmm) cc_final: 0.7470 (mtpp) REVERT: N 165 MET cc_start: 0.8434 (ttt) cc_final: 0.8233 (ttp) REVERT: O 7 LYS cc_start: 0.8675 (mptp) cc_final: 0.8328 (mtmt) REVERT: O 99 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7806 (mmm160) outliers start: 68 outliers final: 43 residues processed: 216 average time/residue: 1.6376 time to fit residues: 467.1562 Evaluate side-chains 217 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 167 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 53 HIS Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 123 LYS Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 99 ARG 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: 0.9980 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 30.0000 chunk 279 optimal weight: 20.0000 chunk 216 optimal weight: 40.0000 chunk 321 optimal weight: 1.9990 chunk 213 optimal weight: 30.0000 chunk 380 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 ASN N 49 GLN O 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 80006 Z= 0.334 Angle : 0.742 17.301 123178 Z= 0.395 Chirality : 0.037 0.260 16128 Planarity : 0.009 0.132 4343 Dihedral : 24.019 176.864 48072 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.14 % Favored : 90.76 % Rotamer: Outliers : 8.94 % Allowed : 29.43 % Favored : 61.63 % 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: -2.17 (0.25), residues: 952 helix: -1.62 (0.37), residues: 168 sheet: -0.90 (0.43), residues: 130 loop : -1.58 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.004 0.001 HIS K 142 PHE 0.018 0.002 PHE L 66 TYR 0.015 0.002 TYR O 44 ARG 0.013 0.001 ARG K 14 *********************** 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 236 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 168 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7625 (tp30) cc_final: 0.7213 (tp30) REVERT: K 125 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7966 (ttpt) REVERT: K 145 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6896 (mp0) REVERT: K 270 ARG cc_start: 0.6580 (ptm160) cc_final: 0.5860 (ttm110) REVERT: M 94 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8666 (mt0) REVERT: M 111 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6288 (tm-30) REVERT: M 123 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.5675 (ptmt) REVERT: M 157 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8426 (tp) REVERT: N 13 ARG cc_start: 0.5304 (ptp-170) cc_final: 0.5027 (pmt170) REVERT: N 40 LEU cc_start: 0.8356 (mp) cc_final: 0.7733 (tt) REVERT: N 62 LYS cc_start: 0.8475 (ptpt) cc_final: 0.8197 (ptmm) REVERT: N 105 LYS cc_start: 0.7717 (ttmm) cc_final: 0.7469 (mtpp) REVERT: O 7 LYS cc_start: 0.8664 (mptp) cc_final: 0.8316 (mtmt) REVERT: O 111 LYS cc_start: 0.7079 (mptt) cc_final: 0.6453 (mttp) REVERT: O 142 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.6250 (mp) outliers start: 68 outliers final: 46 residues processed: 207 average time/residue: 1.6057 time to fit residues: 438.6958 Evaluate side-chains 213 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 161 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 53 HIS Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 123 LYS Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 30 THR 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 131 ASN 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: 10.0000 chunk 152 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 overall best weight: 9.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 53 HIS ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.110 80006 Z= 0.582 Angle : 0.967 17.854 123178 Z= 0.489 Chirality : 0.048 0.330 16128 Planarity : 0.010 0.142 4343 Dihedral : 24.252 171.059 48072 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.82 % Favored : 88.97 % Rotamer: Outliers : 9.20 % Allowed : 29.43 % Favored : 61.37 % 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: -2.48 (0.25), residues: 952 helix: -1.97 (0.37), residues: 167 sheet: -1.18 (0.41), residues: 146 loop : -1.74 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP K 248 HIS 0.007 0.002 HIS K 200 PHE 0.019 0.002 PHE O 89 TYR 0.018 0.002 TYR O 44 ARG 0.006 0.001 ARG K 189 *********************** 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 238 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 168 time to evaluate : 2.159 Fit side-chains revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7716 (tp30) cc_final: 0.7332 (tp30) REVERT: K 125 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8079 (ttpt) REVERT: K 145 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6966 (mp0) REVERT: K 175 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6878 (ptm-80) REVERT: K 270 ARG cc_start: 0.6636 (ptm160) cc_final: 0.6020 (ttm110) REVERT: M 94 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8634 (mt0) REVERT: M 111 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6583 (tm-30) REVERT: M 123 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.5734 (ptmt) REVERT: M 157 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8492 (tp) REVERT: N 13 ARG cc_start: 0.5453 (ptp-170) cc_final: 0.5065 (pmt170) REVERT: N 40 LEU cc_start: 0.8380 (mp) cc_final: 0.7754 (tt) REVERT: N 62 LYS cc_start: 0.8481 (ptpt) cc_final: 0.8210 (ptmm) REVERT: N 105 LYS cc_start: 0.7730 (ttmm) cc_final: 0.7450 (mtpp) REVERT: O 7 LYS cc_start: 0.8649 (mptp) cc_final: 0.8354 (mtmt) REVERT: O 111 LYS cc_start: 0.7074 (mptt) cc_final: 0.6396 (mttp) REVERT: O 142 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6482 (mp) outliers start: 70 outliers final: 51 residues processed: 213 average time/residue: 1.5731 time to fit residues: 445.6472 Evaluate side-chains 213 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 155 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 123 LYS Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 30 THR 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 131 ASN Chi-restraints excluded: chain O residue 141 ASP 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: 1.9990 chunk 364 optimal weight: 6.9990 chunk 332 optimal weight: 0.0570 chunk 354 optimal weight: 0.9990 chunk 213 optimal weight: 30.0000 chunk 154 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 0.9990 chunk 335 optimal weight: 0.8980 chunk 353 optimal weight: 2.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 153 GLN N 49 GLN ** N 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.111 80006 Z= 0.127 Angle : 0.629 16.605 123178 Z= 0.350 Chirality : 0.029 0.259 16128 Planarity : 0.008 0.124 4343 Dihedral : 23.966 177.140 48072 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.77 % Favored : 92.12 % Rotamer: Outliers : 4.47 % Allowed : 34.17 % Favored : 61.37 % 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: -1.97 (0.26), residues: 952 helix: -1.39 (0.38), residues: 176 sheet: -0.82 (0.44), residues: 144 loop : -1.45 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 78 HIS 0.004 0.001 HIS K 142 PHE 0.013 0.001 PHE L 66 TYR 0.013 0.001 TYR O 44 ARG 0.010 0.001 ARG O 95 *********************** 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 216 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 182 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 5 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.4754 (ttpt) REVERT: K 100 GLU cc_start: 0.7506 (tp30) cc_final: 0.7113 (tp30) REVERT: K 264 ASP cc_start: 0.5025 (OUTLIER) cc_final: 0.4798 (m-30) REVERT: K 270 ARG cc_start: 0.6488 (ptm160) cc_final: 0.5819 (ttm110) REVERT: M 111 GLU cc_start: 0.6585 (mm-30) cc_final: 0.6255 (tm-30) REVERT: M 157 LEU cc_start: 0.8699 (pt) cc_final: 0.8212 (tp) REVERT: N 13 ARG cc_start: 0.5140 (ptp-170) cc_final: 0.4707 (pmt170) REVERT: N 40 LEU cc_start: 0.8306 (mp) cc_final: 0.7757 (tt) REVERT: N 62 LYS cc_start: 0.8497 (ptpt) cc_final: 0.8204 (ptmm) REVERT: N 105 LYS cc_start: 0.7742 (ttmm) cc_final: 0.7477 (mtpp) REVERT: N 160 LYS cc_start: 0.9085 (mtpp) cc_final: 0.8742 (mtpp) REVERT: N 190 LYS cc_start: 0.8449 (tttt) cc_final: 0.7813 (tmmm) REVERT: O 7 LYS cc_start: 0.8556 (mptp) cc_final: 0.8197 (mtmt) REVERT: O 118 MET cc_start: 0.7730 (mmm) cc_final: 0.7448 (mpm) outliers start: 34 outliers final: 20 residues processed: 199 average time/residue: 1.5840 time to fit residues: 416.5494 Evaluate side-chains 191 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 169 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain O residue 5 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 10.0000 chunk 375 optimal weight: 0.4980 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 393 optimal weight: 5.9990 chunk 362 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 7.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 153 GLN N 49 GLN N 173 GLN O 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 80006 Z= 0.442 Angle : 0.815 17.455 123178 Z= 0.424 Chirality : 0.041 0.274 16128 Planarity : 0.009 0.136 4343 Dihedral : 24.029 175.281 48072 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.03 % Favored : 90.86 % Rotamer: Outliers : 3.94 % Allowed : 35.35 % Favored : 60.71 % 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: -2.14 (0.25), residues: 952 helix: -1.49 (0.38), residues: 167 sheet: -0.83 (0.43), residues: 134 loop : -1.60 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP M 78 HIS 0.005 0.001 HIS K 142 PHE 0.013 0.002 PHE O 119 TYR 0.017 0.002 TYR O 44 ARG 0.005 0.001 ARG N 46 ********************** 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 192 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 2.194 Fit side-chains revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7681 (tp30) cc_final: 0.7255 (tp30) REVERT: K 181 MET cc_start: 0.7575 (mmm) cc_final: 0.7286 (mmt) REVERT: K 270 ARG cc_start: 0.6563 (ptm160) cc_final: 0.5937 (ttm110) REVERT: M 111 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6398 (tm-30) REVERT: M 157 LEU cc_start: 0.8915 (pt) cc_final: 0.8438 (tp) REVERT: N 13 ARG cc_start: 0.5413 (ptp-170) cc_final: 0.5095 (pmt170) REVERT: N 40 LEU cc_start: 0.8306 (mp) cc_final: 0.7720 (tt) REVERT: N 62 LYS cc_start: 0.8502 (ptpt) cc_final: 0.8217 (ptmm) REVERT: N 105 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7455 (mtpp) REVERT: O 111 LYS cc_start: 0.7104 (mptt) cc_final: 0.6364 (mttm) REVERT: O 142 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.6326 (mp) outliers start: 30 outliers final: 22 residues processed: 182 average time/residue: 1.6302 time to fit residues: 389.8246 Evaluate side-chains 179 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain O residue 5 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 10.0000 chunk 333 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 57 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: K 153 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.148643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.126597 restraints weight = 143039.138| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 0.67 r_work: 0.3672 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 80006 Z= 0.261 Angle : 0.702 17.192 123178 Z= 0.380 Chirality : 0.035 0.251 16128 Planarity : 0.008 0.130 4343 Dihedral : 24.042 176.889 48072 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.61 % Favored : 91.28 % Rotamer: Outliers : 4.34 % Allowed : 34.82 % Favored : 60.84 % 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: -2.05 (0.26), residues: 952 helix: -1.39 (0.39), residues: 167 sheet: -0.81 (0.43), residues: 136 loop : -1.55 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 78 HIS 0.004 0.001 HIS K 142 PHE 0.022 0.002 PHE L 66 TYR 0.015 0.002 TYR O 44 ARG 0.008 0.001 ARG N 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11554.19 seconds wall clock time: 208 minutes 9.44 seconds (12489.44 seconds total)