Starting phenix.real_space_refine on Sat Mar 16 08:50:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/03_2024/6pch_20300_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/03_2024/6pch_20300.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/03_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_20300/03_2024/6pch_20300_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/03_2024/6pch_20300_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/03_2024/6pch_20300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/03_2024/6pch_20300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/03_2024/6pch_20300_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/03_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1542 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Chain: "O" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "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: 28.78, 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: 33.86 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: 38.31 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 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: 130.61 Time building geometry restraints manager: 36.35 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' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C8 2MA I2503 " ideal model delta sigma weight residual 106.32 126.50 -20.18 3.00e+00 1.11e-01 4.52e+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 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C8 OMG I2251 " ideal model delta sigma weight residual 142.82 125.69 17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O MET K 225 " pdb=" C MET K 225 " pdb=" N ASN K 226 " ideal model delta sigma weight residual 121.99 128.82 -6.83 1.24e+00 6.50e-01 3.04e+01 angle pdb=" C1' 2MG I1835 " pdb=" N9 2MG I1835 " pdb=" C8 2MG I1835 " ideal model delta sigma weight residual 110.07 126.11 -16.04 3.00e+00 1.11e-01 2.86e+01 ... (remaining 123173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 44218 35.70 - 71.41: 6542 71.41 - 107.11: 786 107.11 - 142.81: 6 142.81 - 178.52: 7 Dihedral angle restraints: 51559 sinusoidal: 48879 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 51556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 16043 0.086 - 0.171: 107 0.171 - 0.257: 0 0.257 - 0.342: 0 0.342 - 0.428: 2 Chirality restraints: 16152 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 16149 not shown) Planarity restraints: 4337 Sorted by residual: 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 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I1835 " -0.042 2.00e-02 2.50e+03 5.81e-01 7.60e+03 pdb=" C4' 2MG I1835 " -0.438 2.00e-02 2.50e+03 pdb=" O4' 2MG I1835 " -0.643 2.00e-02 2.50e+03 pdb=" C3' 2MG I1835 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 2MG I1835 " 0.587 2.00e-02 2.50e+03 pdb=" C2' 2MG I1835 " 0.202 2.00e-02 2.50e+03 pdb=" O2' 2MG I1835 " -0.924 2.00e-02 2.50e+03 pdb=" C1' 2MG I1835 " -0.224 2.00e-02 2.50e+03 pdb=" N9 2MG I1835 " 0.887 2.00e-02 2.50e+03 ... (remaining 4334 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 2.440 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: 9.710 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: 0.050 Extract box with map and model: 44.480 Check model and map are aligned: 0.800 Set scattering table: 0.560 Process input model: 275.760 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 345.070 ------------------------------------------------------------------------------- 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= 0.306 Angle : 0.369 20.179 123178 Z= 0.189 Chirality : 0.023 0.428 16152 Planarity : 0.023 0.601 4337 Dihedral : 23.627 178.519 49853 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 : 2.048 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: 1.7365 time to fit residues: 536.9658 Evaluate side-chains 165 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 2.087 ------------------------------------------------------------------------------- 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: 0.7816 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 80006 Z= 0.454 Angle : 0.846 16.384 123178 Z= 0.427 Chirality : 0.043 0.272 16152 Planarity : 0.008 0.139 4337 Dihedral : 23.730 175.860 48068 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.61 % Favored : 91.28 % Rotamer: Outliers : 7.62 % Allowed : 21.02 % Favored : 71.35 % 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: -3.10 (0.24), residues: 952 helix: -2.88 (0.31), residues: 175 sheet: -1.70 (0.41), residues: 146 loop : -1.98 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP K 248 HIS 0.007 0.002 HIS K 230 PHE 0.014 0.002 PHE L 66 TYR 0.011 0.002 TYR L 58 ARG 0.014 0.001 ARG O 34 *********************** 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 245 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 187 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 145 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7085 (mt-10) REVERT: K 185 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: K 187 ASP cc_start: 0.7770 (m-30) cc_final: 0.7374 (m-30) REVERT: K 270 ARG cc_start: 0.6599 (ptm160) cc_final: 0.6039 (ttm110) REVERT: L 66 PHE cc_start: 0.8753 (p90) cc_final: 0.8509 (p90) REVERT: M 94 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8578 (mt0) REVERT: M 111 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6619 (tm-30) REVERT: M 144 GLU cc_start: 0.4255 (OUTLIER) cc_final: 0.3523 (tp30) REVERT: N 13 ARG cc_start: 0.5200 (ptp-170) cc_final: 0.4635 (pmt170) REVERT: N 40 LEU cc_start: 0.8451 (mp) cc_final: 0.7696 (tt) REVERT: N 62 LYS cc_start: 0.8462 (ptpt) cc_final: 0.8246 (ptmm) REVERT: N 105 LYS cc_start: 0.7797 (ttmm) cc_final: 0.7117 (mmmt) REVERT: N 160 LYS cc_start: 0.8972 (mtmm) cc_final: 0.8710 (mtmm) REVERT: N 190 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7813 (tmmm) REVERT: O 111 LYS cc_start: 0.7029 (mptt) cc_final: 0.6395 (mttp) outliers start: 58 outliers final: 28 residues processed: 220 average time/residue: 1.6075 time to fit residues: 465.3791 Evaluate side-chains 186 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 2.014 ------------------------------------------------------------------------------- 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 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 145 GLU 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 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: 3.9990 chunk 98 optimal weight: 7.9990 chunk 359 optimal weight: 4.9990 chunk 388 optimal weight: 4.9990 chunk 320 optimal weight: 3.9990 chunk 356 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 80006 Z= 0.319 Angle : 0.678 13.877 123178 Z= 0.351 Chirality : 0.036 0.268 16152 Planarity : 0.007 0.134 4337 Dihedral : 23.694 171.433 48063 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.46 % Favored : 92.44 % Rotamer: Outliers : 8.41 % Allowed : 24.31 % Favored : 67.28 % 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: -2.66 (0.24), residues: 952 helix: -2.51 (0.32), residues: 177 sheet: -1.46 (0.41), residues: 147 loop : -1.66 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.016 0.002 PHE M 19 TYR 0.013 0.002 TYR O 44 ARG 0.006 0.001 ARG L 126 *********************** 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 248 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 184 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 145 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: L 129 LYS cc_start: 0.7937 (mtmm) cc_final: 0.7728 (pttt) REVERT: M 94 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8652 (mt0) REVERT: M 111 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6444 (tm-30) REVERT: M 144 GLU cc_start: 0.4401 (OUTLIER) cc_final: 0.3936 (tp30) REVERT: M 157 LEU cc_start: 0.8660 (pt) cc_final: 0.8100 (tp) REVERT: N 13 ARG cc_start: 0.5207 (ptp-170) cc_final: 0.4530 (pmt170) REVERT: N 40 LEU cc_start: 0.8333 (mp) cc_final: 0.7663 (tt) REVERT: N 62 LYS cc_start: 0.8455 (ptpt) cc_final: 0.8235 (ptmm) REVERT: N 105 LYS cc_start: 0.7721 (ttmm) cc_final: 0.7254 (mmmt) REVERT: N 190 LYS cc_start: 0.8403 (ttmt) cc_final: 0.7834 (tmmm) REVERT: O 111 LYS cc_start: 0.7058 (mptt) cc_final: 0.6389 (mttp) REVERT: O 142 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.5955 (mp) outliers start: 64 outliers final: 33 residues processed: 222 average time/residue: 1.6092 time to fit residues: 471.0106 Evaluate side-chains 207 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 170 time to evaluate : 2.027 ------------------------------------------------------------------------------- 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 53 HIS Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain K residue 125 LYS 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 14 LYS Chi-restraints excluded: chain L residue 61 LEU 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 58 LYS Chi-restraints excluded: chain M residue 77 ILE 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 116 ASP 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 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 170 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 0.9980 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: 3.9990 chunk 381 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- 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** K 53 HIS N 49 GLN O 80 HIS O 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3445 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= 0.371 Angle : 0.748 13.986 123178 Z= 0.386 Chirality : 0.039 0.264 16152 Planarity : 0.008 0.133 4337 Dihedral : 23.878 172.924 48062 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.93 % Favored : 90.97 % Rotamer: Outliers : 8.54 % Allowed : 26.81 % Favored : 64.65 % 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: -2.45 (0.24), residues: 952 helix: -2.28 (0.34), residues: 168 sheet: -1.30 (0.40), residues: 148 loop : -1.57 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 15 HIS 0.005 0.001 HIS K 230 PHE 0.016 0.002 PHE L 66 TYR 0.014 0.002 TYR O 44 ARG 0.008 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 242 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 177 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 125 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7975 (ttpt) REVERT: K 145 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: K 270 ARG cc_start: 0.6697 (ptm160) cc_final: 0.6019 (ttm110) REVERT: L 115 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: M 94 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8651 (mt0) REVERT: M 111 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6349 (tm-30) REVERT: M 123 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.5888 (ptmt) REVERT: M 157 LEU cc_start: 0.8817 (pt) cc_final: 0.8402 (tp) REVERT: M 195 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: N 13 ARG cc_start: 0.5305 (ptp-170) cc_final: 0.4964 (pmt170) REVERT: N 40 LEU cc_start: 0.8402 (mp) cc_final: 0.7763 (tt) REVERT: N 105 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7259 (mmmt) REVERT: N 190 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7881 (tmmm) REVERT: O 111 LYS cc_start: 0.7067 (mptt) cc_final: 0.6318 (mttm) REVERT: O 142 ILE cc_start: 0.6508 (OUTLIER) cc_final: 0.5986 (mp) outliers start: 65 outliers final: 36 residues processed: 212 average time/residue: 1.6049 time to fit residues: 450.0178 Evaluate side-chains 199 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 2.067 ------------------------------------------------------------------------------- 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 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 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 77 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 58 LYS 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 123 LYS Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 GLN 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 112 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 4.9990 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: 9.9990 chunk 263 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 25 HIS K 251 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN O 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 80006 Z= 0.529 Angle : 0.902 13.822 123178 Z= 0.452 Chirality : 0.047 0.329 16152 Planarity : 0.008 0.140 4337 Dihedral : 24.156 170.584 48059 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.77 % Favored : 90.13 % Rotamer: Outliers : 10.78 % Allowed : 25.62 % 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: -2.66 (0.24), residues: 952 helix: -2.38 (0.34), residues: 166 sheet: -1.16 (0.42), residues: 141 loop : -1.82 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP K 248 HIS 0.006 0.002 HIS K 230 PHE 0.013 0.002 PHE M 85 TYR 0.016 0.002 TYR O 44 ARG 0.007 0.001 ARG K 14 *********************** 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 252 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 170 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7670 (tp30) cc_final: 0.7257 (tp30) REVERT: K 125 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8072 (ttpt) REVERT: K 145 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: K 175 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6890 (ptm-80) REVERT: K 270 ARG cc_start: 0.6727 (ptm160) cc_final: 0.6034 (ttm110) REVERT: M 94 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8669 (mt0) REVERT: M 111 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6573 (tm-30) REVERT: M 123 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.5714 (ptmt) REVERT: M 157 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8522 (tp) REVERT: N 13 ARG cc_start: 0.5468 (ptp-170) cc_final: 0.5094 (pmt170) REVERT: N 40 LEU cc_start: 0.8377 (mp) cc_final: 0.7728 (tt) REVERT: N 105 LYS cc_start: 0.7712 (ttmm) cc_final: 0.7239 (mmmt) REVERT: O 7 LYS cc_start: 0.8705 (mptp) cc_final: 0.8389 (mppt) REVERT: O 111 LYS cc_start: 0.7057 (mptt) cc_final: 0.6308 (mttm) REVERT: O 142 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6471 (mp) outliers start: 82 outliers final: 42 residues processed: 219 average time/residue: 1.5706 time to fit residues: 453.2875 Evaluate side-chains 204 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 155 time to evaluate : 2.051 ------------------------------------------------------------------------------- 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 175 ARG Chi-restraints excluded: chain K residue 184 VAL 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 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 58 LYS 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 M residue 197 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 8.9990 chunk 343 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 382 optimal weight: 7.9990 chunk 317 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 80006 Z= 0.390 Angle : 0.764 13.838 123178 Z= 0.394 Chirality : 0.041 0.288 16152 Planarity : 0.008 0.134 4337 Dihedral : 24.045 174.513 48058 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.45 % Favored : 90.44 % Rotamer: Outliers : 9.33 % Allowed : 27.99 % Favored : 62.68 % 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: -2.49 (0.25), residues: 952 helix: -2.20 (0.35), residues: 166 sheet: -1.06 (0.43), residues: 139 loop : -1.71 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP K 248 HIS 0.004 0.001 HIS K 142 PHE 0.014 0.002 PHE L 66 TYR 0.016 0.002 TYR O 44 ARG 0.007 0.001 ARG K 14 *********************** 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 234 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 163 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7672 (tp30) cc_final: 0.7213 (tp30) REVERT: K 125 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8021 (ttpt) REVERT: K 145 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: K 270 ARG cc_start: 0.6617 (ptm160) cc_final: 0.5917 (ttm110) REVERT: M 94 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8662 (mt0) REVERT: M 111 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6226 (tm-30) REVERT: M 123 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.5713 (ptmt) REVERT: M 157 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8500 (tp) REVERT: N 13 ARG cc_start: 0.5402 (ptp-170) cc_final: 0.5074 (pmt170) REVERT: N 40 LEU cc_start: 0.8390 (mp) cc_final: 0.7735 (tt) REVERT: N 105 LYS cc_start: 0.7745 (ttmm) cc_final: 0.7269 (mmmt) REVERT: N 190 LYS cc_start: 0.8423 (tttt) cc_final: 0.7925 (tmmm) REVERT: O 7 LYS cc_start: 0.8698 (mptp) cc_final: 0.8373 (mtmt) REVERT: O 142 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6434 (mp) outliers start: 71 outliers final: 49 residues processed: 210 average time/residue: 1.5396 time to fit residues: 431.1751 Evaluate side-chains 209 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 154 time to evaluate : 2.059 ------------------------------------------------------------------------------- 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 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 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 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 17 THR Chi-restraints excluded: chain M residue 58 LYS 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 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 59 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 40.0000 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: 1.9990 chunk 238 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 overall best weight: 5.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 49 GLN ** N 173 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: 0.7843 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 80006 Z= 0.350 Angle : 0.722 13.834 123178 Z= 0.374 Chirality : 0.038 0.264 16152 Planarity : 0.008 0.132 4337 Dihedral : 23.986 176.292 48058 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.82 % Favored : 91.07 % Rotamer: Outliers : 8.41 % Allowed : 30.49 % Favored : 61.10 % 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: -2.26 (0.25), residues: 952 helix: -1.84 (0.37), residues: 166 sheet: -1.01 (0.42), residues: 141 loop : -1.58 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.005 0.001 HIS K 200 PHE 0.014 0.002 PHE O 89 TYR 0.016 0.002 TYR O 44 ARG 0.009 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 230 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 166 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7675 (tp30) cc_final: 0.7250 (tp30) REVERT: K 125 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7980 (ttpt) REVERT: K 175 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.6883 (ptm-80) REVERT: K 270 ARG cc_start: 0.6612 (ptm160) cc_final: 0.5944 (ttm110) REVERT: M 94 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8664 (mt0) REVERT: M 111 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6466 (tm-30) REVERT: M 157 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8466 (tp) REVERT: N 13 ARG cc_start: 0.5392 (ptp-170) cc_final: 0.5070 (pmt170) REVERT: N 40 LEU cc_start: 0.8392 (mp) cc_final: 0.7758 (tt) REVERT: N 105 LYS cc_start: 0.7751 (ttmm) cc_final: 0.7484 (mtpp) REVERT: O 7 LYS cc_start: 0.8691 (mptp) cc_final: 0.8387 (mtmt) REVERT: O 92 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7952 (mtp) REVERT: O 111 LYS cc_start: 0.7092 (mptt) cc_final: 0.6461 (mttp) REVERT: O 142 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6399 (mp) outliers start: 64 outliers final: 44 residues processed: 209 average time/residue: 1.5666 time to fit residues: 435.2692 Evaluate side-chains 207 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 157 time to evaluate : 2.067 ------------------------------------------------------------------------------- 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 184 VAL 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 77 ILE Chi-restraints excluded: chain L residue 80 SER 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 17 THR Chi-restraints excluded: chain M residue 58 LYS 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 113 VAL Chi-restraints excluded: chain M residue 121 VAL 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 91 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 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 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: ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.112 80006 Z= 0.578 Angle : 0.941 13.819 123178 Z= 0.467 Chirality : 0.049 0.336 16152 Planarity : 0.009 0.141 4337 Dihedral : 24.202 171.182 48058 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.50 % Favored : 89.39 % Rotamer: Outliers : 9.07 % Allowed : 30.22 % 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: -2.52 (0.25), residues: 952 helix: -1.99 (0.37), residues: 163 sheet: -1.38 (0.41), residues: 140 loop : -1.73 (0.23), residues: 649 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 0.020 0.003 PHE L 66 TYR 0.019 0.003 TYR O 44 ARG 0.006 0.001 ARG N 128 *********************** 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 227 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 158 time to evaluate : 2.050 Fit side-chains revert: symmetry clash REVERT: K 100 GLU cc_start: 0.7740 (tp30) cc_final: 0.7359 (tp30) REVERT: K 125 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8068 (ttpt) REVERT: K 135 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7968 (tp) REVERT: K 145 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: K 175 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6750 (ptm-80) REVERT: K 187 ASP cc_start: 0.8016 (m-30) cc_final: 0.7790 (m-30) REVERT: K 270 ARG cc_start: 0.6631 (ptm160) cc_final: 0.5975 (ttm110) REVERT: M 94 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8636 (mt0) REVERT: M 111 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: M 157 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8562 (tp) REVERT: N 13 ARG cc_start: 0.5456 (ptp-170) cc_final: 0.5077 (pmt170) REVERT: N 40 LEU cc_start: 0.8375 (mp) cc_final: 0.7751 (tt) REVERT: N 105 LYS cc_start: 0.7734 (ttmm) cc_final: 0.7427 (mtpp) REVERT: N 164 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: O 7 LYS cc_start: 0.8670 (mptp) cc_final: 0.8396 (mtmt) REVERT: O 111 LYS cc_start: 0.7087 (mptt) cc_final: 0.6399 (mttp) REVERT: O 142 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6567 (mp) outliers start: 69 outliers final: 48 residues processed: 206 average time/residue: 1.5478 time to fit residues: 422.5945 Evaluate side-chains 210 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 153 time to evaluate : 2.058 ------------------------------------------------------------------------------- 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 135 ILE 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 184 VAL 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 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 17 THR Chi-restraints excluded: chain M residue 58 LYS 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 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 109 VAL 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 164 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.9980 chunk 364 optimal weight: 9.9990 chunk 332 optimal weight: 7.9990 chunk 354 optimal weight: 7.9990 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: 0.0870 overall best weight: 2.1962 ------------------------------------------------------------------------------- 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: 0.7750 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 80006 Z= 0.166 Angle : 0.607 13.681 123178 Z= 0.326 Chirality : 0.031 0.245 16152 Planarity : 0.007 0.126 4337 Dihedral : 23.929 178.882 48058 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.30 % Favored : 91.60 % Rotamer: Outliers : 5.39 % Allowed : 34.03 % Favored : 60.58 % 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: -2.12 (0.26), residues: 952 helix: -1.40 (0.38), residues: 175 sheet: -1.12 (0.42), residues: 148 loop : -1.53 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 78 HIS 0.006 0.001 HIS K 142 PHE 0.014 0.001 PHE L 66 TYR 0.014 0.001 TYR O 44 ARG 0.005 0.001 ARG O 13 *********************** 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 218 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 177 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LYS cc_start: 0.6191 (OUTLIER) cc_final: 0.5932 (mttm) REVERT: K 153 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: K 264 ASP cc_start: 0.5125 (OUTLIER) cc_final: 0.4853 (m-30) REVERT: K 270 ARG cc_start: 0.6551 (ptm160) cc_final: 0.5862 (ttm110) REVERT: M 157 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8362 (tp) REVERT: M 183 PHE cc_start: 0.8292 (m-10) cc_final: 0.8087 (m-10) REVERT: N 13 ARG cc_start: 0.5298 (ptp-170) cc_final: 0.4807 (pmt170) REVERT: N 40 LEU cc_start: 0.8297 (mp) cc_final: 0.7731 (tt) REVERT: N 105 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7488 (mtpp) REVERT: O 142 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6217 (mp) outliers start: 41 outliers final: 24 residues processed: 198 average time/residue: 1.5752 time to fit residues: 413.8375 Evaluate side-chains 197 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 2.058 ------------------------------------------------------------------------------- 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 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 216 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 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 157 LEU 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 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 141 ASP 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: 9.9990 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 260 optimal weight: 9.9990 chunk 393 optimal weight: 10.0000 chunk 362 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.107 80006 Z= 0.567 Angle : 0.914 13.865 123178 Z= 0.454 Chirality : 0.048 0.316 16152 Planarity : 0.008 0.141 4337 Dihedral : 24.101 172.645 48058 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.71 % Favored : 89.18 % Rotamer: Outliers : 5.26 % Allowed : 34.30 % Favored : 60.45 % 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: -2.43 (0.25), residues: 952 helix: -1.87 (0.36), residues: 164 sheet: -1.18 (0.41), residues: 146 loop : -1.72 (0.23), residues: 642 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 0.012 0.002 PHE L 50 TYR 0.019 0.003 TYR O 44 ARG 0.006 0.001 ARG N 128 ********************** 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 193 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 2.118 Fit side-chains revert: symmetry clash REVERT: K 5 LYS cc_start: 0.6082 (OUTLIER) cc_final: 0.5869 (mttm) REVERT: K 100 GLU cc_start: 0.7779 (tp30) cc_final: 0.7397 (tp30) REVERT: K 145 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6990 (mp0) REVERT: K 181 MET cc_start: 0.7704 (mmm) cc_final: 0.7392 (mmt) REVERT: K 270 ARG cc_start: 0.6682 (ptm160) cc_final: 0.6011 (ttm110) REVERT: M 157 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8527 (tp) REVERT: M 195 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: N 13 ARG cc_start: 0.5490 (ptp-170) cc_final: 0.5099 (pmt170) REVERT: N 40 LEU cc_start: 0.8379 (mp) cc_final: 0.7767 (tt) REVERT: N 105 LYS cc_start: 0.7727 (ttmm) cc_final: 0.7429 (mtpp) REVERT: O 111 LYS cc_start: 0.7073 (mptt) cc_final: 0.6388 (mttp) outliers start: 40 outliers final: 31 residues processed: 183 average time/residue: 1.5775 time to fit residues: 383.8334 Evaluate side-chains 186 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 2.229 ------------------------------------------------------------------------------- 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 88 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 184 VAL 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 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 17 THR Chi-restraints excluded: chain M residue 107 SER 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 M residue 195 GLN Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 109 VAL 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 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 141 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 5.9990 chunk 333 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 322 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 49 GLN ** N 173 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 = 0.4087 r_free = 0.4087 target = 0.149672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.127597 restraints weight = 143783.488| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 0.65 r_work: 0.3689 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 80006 Z= 0.236 Angle : 0.641 13.838 123178 Z= 0.341 Chirality : 0.034 0.309 16152 Planarity : 0.007 0.127 4337 Dihedral : 23.981 178.873 48058 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.82 % Favored : 91.07 % Rotamer: Outliers : 4.07 % Allowed : 35.61 % Favored : 60.32 % 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: -2.16 (0.26), residues: 952 helix: -1.45 (0.38), residues: 170 sheet: -1.19 (0.40), residues: 158 loop : -1.55 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.005 0.001 HIS K 142 PHE 0.011 0.001 PHE O 119 TYR 0.016 0.002 TYR O 44 ARG 0.005 0.001 ARG O 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11109.78 seconds wall clock time: 199 minutes 46.75 seconds (11986.75 seconds total)