Starting phenix.real_space_refine on Sun Feb 18 07:38:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/02_2024/6pcq_20304_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/02_2024/6pcq_20304.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/02_2024/6pcq_20304_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/02_2024/6pcq_20304_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/02_2024/6pcq_20304_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/02_2024/6pcq_20304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/02_2024/6pcq_20304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/02_2024/6pcq_20304_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/02_2024/6pcq_20304_neut_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.018 sd= 1.268 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 33501 2.51 5 N 13318 2.21 5 O 22269 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 TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K ARG 189": "NH1" <-> "NH2" Residue "K ARG 203": "NH1" <-> "NH2" Residue "K ARG 212": "NH1" <-> "NH2" Residue "K ARG 221": "NH1" <-> "NH2" Residue "K PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ARG 170": "NH1" <-> "NH2" Residue "M ASP 171": "OD1" <-> "OD2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N GLU 17": "OE1" <-> "OE2" 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 PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 168": "OE1" <-> "OE2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "N ASP 200": "OD1" <-> "OD2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 120": "NH1" <-> "NH2" Residue "O TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 72125 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 62206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62206 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 437, 'rna3p': 2459} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2076 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1542 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Chain: "O" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'O8J': 1} Classifications: {'undetermined': 1} Time building chain proxies: 29.41, per 1000 atoms: 0.41 Number of scatterers: 72125 At special positions: 0 Unit cell: (229.439, 221.984, 190.509, 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 22269 8.00 N 13318 7.00 C 33501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 35.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 12 sheets defined 18.7% alpha, 13.9% beta 886 base pairs and 1620 stacking pairs defined. Time for finding SS restraints: 40.82 Creating SS restraints... Processing helix chain 'K' and resid 198 through 202 removed outlier: 3.674A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 213 Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 79 through 84 removed outlier: 4.438A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 4.081A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 92 through 98' Processing helix chain 'L' and resid 129 through 138 removed outlier: 3.915A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 39 Processing helix chain 'M' and resid 98 through 114 removed outlier: 3.657A pdb=" N VAL M 113 " --> pdb=" O LEU M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 141 Processing helix chain 'M' and resid 155 through 160 removed outlier: 3.770A pdb=" N LEU M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 removed outlier: 3.550A pdb=" N GLU M 197 " --> pdb=" O VAL M 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 62 through 69 Processing helix chain 'N' and resid 98 through 101 Processing helix chain 'N' and resid 121 through 124 No H-bonds generated for 'chain 'N' and resid 121 through 124' Processing helix chain 'O' and resid 25 through 37 removed outlier: 4.382A 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: 4.534A pdb=" N ARG O 69 " --> pdb=" O GLY O 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP O 71 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 107 Proline residue: O 97 - end of helix removed outlier: 4.371A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 removed outlier: 3.847A pdb=" N PHE O 119 " --> pdb=" O GLY O 115 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 135 No H-bonds generated for 'chain 'O' and resid 133 through 135' Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'K' and resid 101 through 105 removed outlier: 6.489A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 129 through 131 Processing sheet with id= E, first strand: chain 'K' and resid 181 through 185 removed outlier: 6.438A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.318A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.826A 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 118 through 121 removed outlier: 6.003A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'N' and resid 169 through 172 removed outlier: 4.754A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL N 189 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP N 181 " --> pdb=" O LEU N 186 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LYS N 190 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL N 177 " --> pdb=" O LYS N 190 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 80 through 83 removed outlier: 6.277A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 115 through 119 removed outlier: 5.610A pdb=" N MET N 165 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE N 118 " --> pdb=" O GLY N 163 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY N 163 " --> pdb=" O PHE N 118 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.736A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE O 55 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 73 through 76 138 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2200 hydrogen bonds 3592 hydrogen bond angles 0 basepair planarities 886 basepair parallelities 1620 stacking parallelities Total time for adding SS restraints: 136.45 Time building geometry restraints manager: 37.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.55: 73899 1.55 - 1.88: 6096 1.88 - 2.21: 0 2.21 - 2.55: 0 2.55 - 2.88: 1 Bond restraints: 79996 Sorted by residual: bond pdb=" C ASN K 226 " pdb=" N VAL K 228 " ideal model delta sigma weight residual 1.332 2.878 -1.546 1.36e-02 5.41e+03 1.29e+04 bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.410 0.392 2.00e-02 2.50e+03 3.85e+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 1.81e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.367 0.268 2.00e-02 2.50e+03 1.79e+02 ... (remaining 79991 not shown) Histogram of bond angle deviations from ideal: 52.46 - 72.58: 1 72.58 - 92.70: 0 92.70 - 112.81: 62561 112.81 - 132.93: 60582 132.93 - 153.05: 20 Bond angle restraints: 123164 Sorted by residual: angle pdb=" O ASN K 226 " pdb=" C ASN K 226 " pdb=" N VAL K 228 " ideal model delta sigma weight residual 122.59 52.46 70.13 1.33e+00 5.65e-01 2.78e+03 angle pdb=" CA ASN K 226 " pdb=" C ASN K 226 " pdb=" N VAL K 228 " ideal model delta sigma weight residual 116.84 153.05 -36.21 1.71e+00 3.42e-01 4.48e+02 angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C8 6MZ I1618 " ideal model delta sigma weight residual 91.39 126.72 -35.33 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C4 6MZ I1618 " ideal model delta sigma weight residual 154.15 125.88 28.27 3.00e+00 1.11e-01 8.88e+01 angle pdb=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C8 1MG I 745 " ideal model delta sigma weight residual 100.16 126.11 -25.95 3.00e+00 1.11e-01 7.48e+01 ... (remaining 123159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 44160 35.81 - 71.63: 6599 71.63 - 107.44: 791 107.44 - 143.26: 8 143.26 - 179.07: 6 Dihedral angle restraints: 51564 sinusoidal: 48887 harmonic: 2677 Sorted by residual: dihedral pdb=" CA ASN K 226 " pdb=" C ASN K 226 " pdb=" N VAL K 228 " pdb=" CA VAL K 228 " ideal model delta harmonic sigma weight residual 180.00 64.29 115.71 0 5.00e+00 4.00e-02 5.36e+02 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 52.93 179.07 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual 232.00 60.36 171.64 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 51561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 12418 0.030 - 0.061: 3470 0.061 - 0.091: 149 0.091 - 0.121: 81 0.121 - 0.152: 9 Chirality restraints: 16127 Sorted by residual: chirality pdb=" C30 O8J I3001 " pdb=" C29 O8J I3001 " pdb=" C31 O8J I3001 " pdb=" N34 O8J I3001 " both_signs ideal model delta sigma weight residual False -2.66 -2.51 -0.15 2.00e-01 2.50e+01 5.75e-01 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 5.67e-01 chirality pdb=" CA ILE K 135 " pdb=" N ILE K 135 " pdb=" C ILE K 135 " pdb=" CB ILE K 135 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 16124 not shown) Planarity restraints: 4341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.029 2.00e-02 2.50e+03 6.03e-01 8.19e+03 pdb=" C4' 2MG I2445 " -0.466 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.783 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.572 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.237 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.879 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.191 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.953 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " -0.045 2.00e-02 2.50e+03 6.02e-01 8.16e+03 pdb=" C4' 1MG I 745 " -0.451 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.714 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.604 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.207 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.929 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.207 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.938 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 6MZ I1618 " -0.840 2.00e-02 2.50e+03 5.76e-01 7.46e+03 pdb=" C4' 6MZ I1618 " 0.230 2.00e-02 2.50e+03 pdb=" O4' 6MZ I1618 " 0.625 2.00e-02 2.50e+03 pdb=" C3' 6MZ I1618 " -0.197 2.00e-02 2.50e+03 pdb=" O3' 6MZ I1618 " 0.929 2.00e-02 2.50e+03 pdb=" C2' 6MZ I1618 " -0.617 2.00e-02 2.50e+03 pdb=" O2' 6MZ I1618 " -0.601 2.00e-02 2.50e+03 pdb=" C1' 6MZ I1618 " 0.433 2.00e-02 2.50e+03 pdb=" N9 6MZ I1618 " 0.038 2.00e-02 2.50e+03 ... (remaining 4338 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 559 2.56 - 3.15: 53330 3.15 - 3.73: 146379 3.73 - 4.32: 206568 4.32 - 4.90: 267183 Nonbonded interactions: 674019 Sorted by model distance: nonbonded pdb=" O2' A I2799 " pdb=" OP2 G I2801 " model vdw 1.976 2.440 nonbonded pdb=" O2* PSU I1911 " pdb=" OP1 A I1912 " model vdw 1.981 3.040 nonbonded pdb=" O2' G I1715 " pdb=" O6 G I1743 " model vdw 1.986 2.440 nonbonded pdb=" O2' G I1826 " pdb=" OP2 U I1971 " model vdw 1.996 2.440 nonbonded pdb=" O2' U I1061 " pdb=" OP2 G I1063 " model vdw 2.007 2.440 ... (remaining 674014 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: 16.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 44.200 Check model and map are aligned: 0.820 Set scattering table: 0.530 Process input model: 285.760 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 360.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.546 79996 Z= 0.428 Angle : 0.463 70.132 123164 Z= 0.259 Chirality : 0.024 0.152 16127 Planarity : 0.031 0.603 4341 Dihedral : 23.658 179.074 49860 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.84 % Allowed : 11.97 % Favored : 86.18 % 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: -4.00 (0.22), residues: 949 helix: -3.79 (0.21), residues: 167 sheet: -2.17 (0.40), residues: 152 loop : -2.60 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 78 HIS 0.003 0.001 HIS K 200 PHE 0.005 0.001 PHE L 50 TYR 0.007 0.001 TYR L 58 ARG 0.003 0.000 ARG O 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 218 time to evaluate : 2.120 Fit side-chains revert: symmetry clash REVERT: K 14 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7482 (ttm-80) REVERT: K 66 ASP cc_start: 0.7340 (t70) cc_final: 0.7084 (t70) REVERT: M 116 ASP cc_start: 0.8050 (t0) cc_final: 0.7624 (t0) REVERT: M 185 LYS cc_start: 0.7233 (mmtp) cc_final: 0.7020 (mptp) REVERT: M 194 LYS cc_start: 0.8243 (mptp) cc_final: 0.8017 (mmmt) REVERT: N 189 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8764 (p) outliers start: 14 outliers final: 6 residues processed: 225 average time/residue: 1.5431 time to fit residues: 458.2574 Evaluate side-chains 158 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 358 optimal weight: 2.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 134 ASN K 153 GLN M 115 GLN N 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.108 79996 Z= 0.509 Angle : 0.859 17.357 123164 Z= 0.446 Chirality : 0.045 0.353 16127 Planarity : 0.009 0.136 4341 Dihedral : 23.784 179.736 48075 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.15 % Favored : 92.53 % Rotamer: Outliers : 6.84 % Allowed : 17.24 % Favored : 75.92 % 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: -2.69 (0.24), residues: 951 helix: -2.08 (0.32), residues: 179 sheet: -1.35 (0.41), residues: 150 loop : -1.88 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 78 HIS 0.007 0.002 HIS O 76 PHE 0.017 0.003 PHE M 23 TYR 0.014 0.002 TYR L 58 ARG 0.007 0.001 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 171 time to evaluate : 2.561 Fit side-chains REVERT: K 66 ASP cc_start: 0.7709 (t70) cc_final: 0.7490 (t0) REVERT: K 153 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8503 (mt0) REVERT: K 189 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6257 (mtt-85) REVERT: K 270 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6654 (tpt-90) REVERT: M 65 THR cc_start: 0.8214 (m) cc_final: 0.7945 (p) REVERT: M 122 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6917 (mm-30) REVERT: N 105 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.8020 (mtmm) REVERT: N 159 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.6795 (tptp) REVERT: O 11 VAL cc_start: 0.9177 (p) cc_final: 0.8973 (t) outliers start: 52 outliers final: 19 residues processed: 204 average time/residue: 1.5908 time to fit residues: 428.8308 Evaluate side-chains 167 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 2.119 ------------------------------------------------------------------------------- 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 16 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 270 ARG Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 122 GLU Chi-restraints excluded: chain M residue 127 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 359 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 320 optimal weight: 0.9990 chunk 356 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 153 GLN K 239 ASN M 41 GLN M 115 GLN M 156 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 79996 Z= 0.260 Angle : 0.661 18.327 123164 Z= 0.361 Chirality : 0.034 0.327 16127 Planarity : 0.008 0.131 4341 Dihedral : 23.693 179.986 48071 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.52 % Favored : 93.27 % Rotamer: Outliers : 4.87 % Allowed : 22.37 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.26), residues: 951 helix: -0.85 (0.37), residues: 177 sheet: -1.22 (0.38), residues: 171 loop : -1.46 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 78 HIS 0.005 0.001 HIS O 76 PHE 0.014 0.002 PHE L 64 TYR 0.011 0.002 TYR K 62 ARG 0.006 0.001 ARG K 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 2.703 Fit side-chains REVERT: K 66 ASP cc_start: 0.7694 (t70) cc_final: 0.7459 (t0) REVERT: K 153 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8272 (mt0) REVERT: K 189 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6021 (mtt-85) REVERT: M 65 THR cc_start: 0.8142 (m) cc_final: 0.7909 (p) REVERT: N 13 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6421 (ptm160) REVERT: N 159 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.6771 (tptp) outliers start: 37 outliers final: 17 residues processed: 184 average time/residue: 1.5494 time to fit residues: 379.3384 Evaluate side-chains 173 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 127 GLU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 128 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: 0.9990 chunk 270 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 chunk 360 optimal weight: 6.9990 chunk 381 optimal weight: 0.1980 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 239 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 79996 Z= 0.303 Angle : 0.698 18.458 123164 Z= 0.379 Chirality : 0.036 0.287 16127 Planarity : 0.008 0.132 4341 Dihedral : 23.758 179.615 48068 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.05 % Favored : 92.74 % Rotamer: Outliers : 6.05 % Allowed : 22.24 % Favored : 71.71 % 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: -1.64 (0.26), residues: 951 helix: -0.55 (0.38), residues: 179 sheet: -0.96 (0.40), residues: 159 loop : -1.32 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 78 HIS 0.004 0.001 HIS O 76 PHE 0.010 0.002 PHE N 15 TYR 0.011 0.002 TYR L 58 ARG 0.006 0.001 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 174 time to evaluate : 2.176 Fit side-chains REVERT: K 36 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8380 (ttmm) REVERT: K 66 ASP cc_start: 0.7722 (t70) cc_final: 0.7489 (t0) REVERT: K 189 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6033 (mtt-85) REVERT: M 65 THR cc_start: 0.8225 (m) cc_final: 0.7956 (p) REVERT: N 13 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6466 (ptp-170) REVERT: N 159 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.6542 (tptp) outliers start: 46 outliers final: 25 residues processed: 201 average time/residue: 1.5718 time to fit residues: 420.8426 Evaluate side-chains 184 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 36 LYS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 127 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 2.9990 chunk 216 optimal weight: 30.0000 chunk 5 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 342 optimal weight: 0.0670 chunk 96 optimal weight: 8.9990 overall best weight: 6.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN K 243 HIS M 115 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 79996 Z= 0.435 Angle : 0.796 19.965 123164 Z= 0.419 Chirality : 0.042 0.322 16127 Planarity : 0.009 0.136 4341 Dihedral : 23.927 178.834 48068 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.26 % Favored : 92.53 % Rotamer: Outliers : 6.84 % Allowed : 23.29 % Favored : 69.87 % 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: -1.78 (0.25), residues: 951 helix: -0.74 (0.37), residues: 181 sheet: -1.06 (0.40), residues: 149 loop : -1.39 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 78 HIS 0.005 0.001 HIS O 76 PHE 0.011 0.002 PHE O 119 TYR 0.011 0.002 TYR K 62 ARG 0.010 0.001 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 161 time to evaluate : 2.415 Fit side-chains REVERT: K 36 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8386 (ttmm) REVERT: K 66 ASP cc_start: 0.7738 (t70) cc_final: 0.7497 (t0) REVERT: K 175 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6559 (ttp80) REVERT: K 180 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.6851 (tm-30) REVERT: K 189 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6196 (mtt-85) REVERT: N 13 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6457 (ptm160) REVERT: N 159 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.6845 (tptp) REVERT: O 69 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.6995 (ttm110) REVERT: O 85 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8185 (mmmt) REVERT: O 91 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7771 (mt-10) outliers start: 52 outliers final: 27 residues processed: 193 average time/residue: 1.4948 time to fit residues: 386.2721 Evaluate side-chains 182 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 36 LYS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 127 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 69 ARG Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 7.9990 chunk 343 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 382 optimal weight: 5.9990 chunk 317 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN M 115 GLN M 156 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 185 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 79996 Z= 0.355 Angle : 0.730 19.182 123164 Z= 0.392 Chirality : 0.038 0.296 16127 Planarity : 0.008 0.133 4341 Dihedral : 23.862 179.176 48068 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.26 % Favored : 92.53 % Rotamer: Outliers : 6.05 % Allowed : 24.61 % Favored : 69.34 % 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: -1.60 (0.26), residues: 951 helix: -0.49 (0.38), residues: 179 sheet: -0.92 (0.39), residues: 159 loop : -1.30 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 78 HIS 0.005 0.001 HIS O 76 PHE 0.011 0.002 PHE O 119 TYR 0.011 0.002 TYR K 62 ARG 0.009 0.001 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 150 time to evaluate : 2.187 Fit side-chains REVERT: K 36 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8383 (ttmm) REVERT: K 66 ASP cc_start: 0.7725 (t70) cc_final: 0.7489 (t0) REVERT: K 175 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6599 (ttp80) REVERT: K 189 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6064 (mtt-85) REVERT: M 65 THR cc_start: 0.8177 (m) cc_final: 0.7963 (p) REVERT: N 13 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6436 (ptm160) REVERT: N 89 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6789 (mt-10) REVERT: N 159 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.6748 (tptp) REVERT: O 69 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7012 (ttm110) REVERT: O 85 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8157 (mmmt) outliers start: 46 outliers final: 25 residues processed: 183 average time/residue: 1.5174 time to fit residues: 372.0201 Evaluate side-chains 176 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 36 LYS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 127 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 69 ARG Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 40.0000 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 30.0000 chunk 321 optimal weight: 4.9990 chunk 213 optimal weight: 40.0000 chunk 380 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 chunk 232 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 21 ASN K 239 ASN M 115 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 79996 Z= 0.458 Angle : 0.819 19.261 123164 Z= 0.429 Chirality : 0.043 0.332 16127 Planarity : 0.009 0.136 4341 Dihedral : 24.000 178.566 48068 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.20 % Favored : 91.59 % Rotamer: Outliers : 6.97 % Allowed : 23.68 % Favored : 69.34 % 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: -1.71 (0.26), residues: 951 helix: -0.68 (0.38), residues: 181 sheet: -0.89 (0.40), residues: 156 loop : -1.38 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 78 HIS 0.006 0.001 HIS O 76 PHE 0.015 0.002 PHE K 240 TYR 0.013 0.002 TYR K 62 ARG 0.009 0.001 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 151 time to evaluate : 2.168 Fit side-chains REVERT: K 36 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8399 (ttmm) REVERT: K 66 ASP cc_start: 0.7780 (t70) cc_final: 0.7527 (t0) REVERT: K 175 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6636 (ttp80) REVERT: K 189 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6169 (mtt-85) REVERT: K 201 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7899 (OUTLIER) REVERT: N 13 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6471 (ptm160) REVERT: N 159 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.6834 (tptp) REVERT: O 69 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6998 (ttm110) REVERT: O 85 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8216 (mmmt) REVERT: O 91 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7763 (mt-10) outliers start: 53 outliers final: 35 residues processed: 187 average time/residue: 1.5411 time to fit residues: 386.2756 Evaluate side-chains 186 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 36 LYS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 201 MET Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 127 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 69 ARG Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 239 ASN K 260 ASN M 115 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 79996 Z= 0.485 Angle : 0.830 18.484 123164 Z= 0.433 Chirality : 0.044 0.335 16127 Planarity : 0.009 0.137 4341 Dihedral : 24.014 179.037 48068 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.89 % Favored : 91.90 % Rotamer: Outliers : 6.84 % Allowed : 24.61 % Favored : 68.55 % 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: -1.88 (0.25), residues: 951 helix: -0.86 (0.37), residues: 187 sheet: -0.88 (0.40), residues: 154 loop : -1.53 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 78 HIS 0.006 0.001 HIS O 76 PHE 0.013 0.003 PHE O 119 TYR 0.012 0.002 TYR O 16 ARG 0.013 0.001 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 147 time to evaluate : 2.179 Fit side-chains REVERT: K 36 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8400 (ttmm) REVERT: K 66 ASP cc_start: 0.7835 (t70) cc_final: 0.7584 (t0) REVERT: K 175 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6631 (ttp80) REVERT: K 189 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6158 (mtt-85) REVERT: N 13 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6316 (ptp-170) REVERT: N 88 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: N 89 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6778 (mt-10) REVERT: N 159 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.6887 (tptp) REVERT: N 185 ASN cc_start: 0.8256 (m-40) cc_final: 0.8016 (m110) REVERT: O 69 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7002 (ttm110) REVERT: O 85 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8171 (mmmt) REVERT: O 91 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7778 (mt-10) outliers start: 52 outliers final: 32 residues processed: 181 average time/residue: 1.5440 time to fit residues: 371.9729 Evaluate side-chains 187 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 145 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 36 LYS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 225 MET Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 127 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 69 ARG Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.0770 chunk 364 optimal weight: 2.9990 chunk 332 optimal weight: 2.9990 chunk 354 optimal weight: 1.9990 chunk 213 optimal weight: 40.0000 chunk 154 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 0.6980 chunk 335 optimal weight: 3.9990 chunk 353 optimal weight: 6.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 239 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 79996 Z= 0.160 Angle : 0.616 17.653 123164 Z= 0.344 Chirality : 0.030 0.259 16127 Planarity : 0.008 0.126 4341 Dihedral : 23.813 179.706 48068 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.73 % Favored : 93.06 % Rotamer: Outliers : 4.08 % Allowed : 28.03 % Favored : 67.89 % 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: -1.23 (0.27), residues: 951 helix: 0.07 (0.40), residues: 178 sheet: -0.77 (0.39), residues: 166 loop : -1.12 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 78 HIS 0.004 0.001 HIS O 47 PHE 0.030 0.002 PHE K 240 TYR 0.014 0.001 TYR K 62 ARG 0.015 0.001 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 2.142 Fit side-chains REVERT: K 66 ASP cc_start: 0.7742 (t70) cc_final: 0.7475 (t0) REVERT: N 13 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6439 (ptm160) REVERT: N 159 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.6549 (tptp) REVERT: O 69 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6989 (ttm110) outliers start: 31 outliers final: 18 residues processed: 175 average time/residue: 1.5137 time to fit residues: 353.5300 Evaluate side-chains 172 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 127 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 69 ARG Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 10.0000 chunk 375 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 chunk 393 optimal weight: 6.9990 chunk 362 optimal weight: 5.9990 chunk 313 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 126 ASN N 185 ASN O 128 ASN O 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 79996 Z= 0.444 Angle : 0.795 17.773 123164 Z= 0.418 Chirality : 0.042 0.325 16127 Planarity : 0.009 0.136 4341 Dihedral : 23.946 179.235 48068 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.31 % Favored : 91.48 % Rotamer: Outliers : 4.47 % Allowed : 28.03 % Favored : 67.50 % 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: -1.62 (0.26), residues: 951 helix: -0.64 (0.37), residues: 189 sheet: -0.83 (0.40), residues: 154 loop : -1.32 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.005 0.002 HIS O 76 PHE 0.013 0.002 PHE N 90 TYR 0.015 0.002 TYR O 16 ARG 0.009 0.001 ARG M 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 153 time to evaluate : 2.315 Fit side-chains REVERT: K 66 ASP cc_start: 0.7745 (t70) cc_final: 0.7514 (t0) REVERT: N 13 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6513 (ptm160) REVERT: N 159 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.6735 (tptp) REVERT: O 69 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.6997 (ttm110) outliers start: 34 outliers final: 20 residues processed: 173 average time/residue: 1.5100 time to fit residues: 351.7043 Evaluate side-chains 173 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 127 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 69 ARG Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 8.9990 chunk 333 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099542 restraints weight = 131997.452| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 0.65 r_work: 0.3229 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 79996 Z= 0.341 Angle : 0.738 17.741 123164 Z= 0.397 Chirality : 0.038 0.302 16127 Planarity : 0.009 0.134 4341 Dihedral : 23.968 178.980 48068 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.99 % Favored : 91.80 % Rotamer: Outliers : 4.34 % Allowed : 28.68 % Favored : 66.97 % 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: -1.59 (0.26), residues: 951 helix: -0.62 (0.38), residues: 187 sheet: -0.82 (0.40), residues: 154 loop : -1.28 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 78 HIS 0.005 0.001 HIS O 76 PHE 0.040 0.003 PHE K 240 TYR 0.013 0.002 TYR O 16 ARG 0.014 0.001 ARG M 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11634.36 seconds wall clock time: 209 minutes 52.18 seconds (12592.18 seconds total)