Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 12:08:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2023/6pcq_20304_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2023/6pcq_20304.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2023/6pcq_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_20304/04_2023/6pcq_20304_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2023/6pcq_20304_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2023/6pcq_20304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2023/6pcq_20304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2023/6pcq_20304_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2023/6pcq_20304_neut_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 29.82, 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: 33.60 Conformation dependent library (CDL) restraints added in 1.3 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: 33.53 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: 134.65 Time building geometry restraints manager: 35.93 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: 39496 35.81 - 71.63: 1111 71.63 - 107.44: 109 107.44 - 143.26: 7 143.26 - 179.07: 5 Dihedral angle restraints: 40728 sinusoidal: 38051 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 40725 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: 9.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 46.580 Check model and map are aligned: 0.790 Set scattering table: 0.480 Process input model: 272.240 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.170 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 344.190 ------------------------------------------------------------------------------- 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 : 12.764 179.074 39024 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 % 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 *********************** 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 : 2.102 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 225 average time/residue: 1.6663 time to fit residues: 496.2644 Evaluate side-chains 149 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 2.098 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 4 average time/residue: 0.5937 time to fit residues: 6.1000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.109 79996 Z= 0.503 Angle : 0.860 17.601 123164 Z= 0.447 Chirality : 0.045 0.342 16127 Planarity : 0.009 0.138 4341 Dihedral : 14.267 179.772 37228 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.94 % Favored : 92.74 % Rotamer Outliers : 6.71 % 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: -2.68 (0.24), residues: 951 helix: -2.06 (0.32), residues: 179 sheet: -1.32 (0.41), residues: 145 loop : -1.89 (0.22), residues: 627 *********************** 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 217 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 166 time to evaluate : 2.177 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 18 residues processed: 199 average time/residue: 1.6595 time to fit residues: 437.4568 Evaluate side-chains 158 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 2.056 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.5792 time to fit residues: 8.0148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 388 optimal weight: 2.9990 chunk 320 optimal weight: 0.9990 chunk 356 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8191 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 79996 Z= 0.206 Angle : 0.625 18.171 123164 Z= 0.346 Chirality : 0.031 0.298 16127 Planarity : 0.008 0.129 4341 Dihedral : 13.895 178.886 37228 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.31 % Favored : 93.59 % Rotamer Outliers : 4.61 % 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: -1.75 (0.26), residues: 951 helix: -0.73 (0.38), residues: 177 sheet: -0.98 (0.40), residues: 154 loop : -1.39 (0.24), residues: 620 *********************** 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 198 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 2.076 Fit side-chains outliers start: 35 outliers final: 17 residues processed: 184 average time/residue: 1.6074 time to fit residues: 392.0237 Evaluate side-chains 169 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 2.102 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 6 average time/residue: 0.7846 time to fit residues: 9.2922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 0.3980 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: 10.0000 chunk 360 optimal weight: 0.9990 chunk 381 optimal weight: 0.0980 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 0.0570 chunk 102 optimal weight: 10.0000 overall best weight: 2.3104 ------------------------------------------------------------------------------- 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** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 79996 Z= 0.187 Angle : 0.617 17.785 123164 Z= 0.344 Chirality : 0.031 0.271 16127 Planarity : 0.008 0.127 4341 Dihedral : 13.893 178.751 37228 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.73 % Favored : 93.17 % Rotamer Outliers : 5.13 % 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: -1.27 (0.26), residues: 951 helix: -0.14 (0.40), residues: 171 sheet: -0.66 (0.41), residues: 154 loop : -1.12 (0.24), residues: 626 *********************** 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 199 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 160 time to evaluate : 2.109 Fit side-chains outliers start: 39 outliers final: 22 residues processed: 186 average time/residue: 1.5667 time to fit residues: 388.7953 Evaluate side-chains 178 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 2.071 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 6 average time/residue: 0.9347 time to fit residues: 10.3176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 0.9990 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: 0.5980 chunk 263 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 342 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 ASN O 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3098 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= 0.426 Angle : 0.779 19.162 123164 Z= 0.413 Chirality : 0.042 0.316 16127 Planarity : 0.009 0.135 4341 Dihedral : 14.398 179.627 37228 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.05 % Favored : 92.74 % Rotamer Outliers : 5.13 % 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: -1.55 (0.26), residues: 951 helix: -0.67 (0.37), residues: 182 sheet: -0.67 (0.42), residues: 140 loop : -1.27 (0.24), residues: 629 *********************** 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 204 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 2.129 Fit side-chains outliers start: 39 outliers final: 24 residues processed: 189 average time/residue: 1.5634 time to fit residues: 394.9228 Evaluate side-chains 171 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 2.041 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 6 average time/residue: 0.7135 time to fit residues: 8.8370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 75 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 382 optimal weight: 4.9990 chunk 317 optimal weight: 0.9980 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: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 239 ASN M 115 GLN M 156 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 185 ASN O 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 79996 Z= 0.369 Angle : 0.728 19.496 123164 Z= 0.391 Chirality : 0.039 0.292 16127 Planarity : 0.009 0.133 4341 Dihedral : 14.398 179.927 37228 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.15 % Favored : 92.64 % Rotamer Outliers : 5.39 % 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: -1.53 (0.26), residues: 951 helix: -0.55 (0.37), residues: 179 sheet: -0.77 (0.40), residues: 156 loop : -1.25 (0.24), residues: 616 *********************** 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 197 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 2.184 Fit side-chains outliers start: 41 outliers final: 25 residues processed: 187 average time/residue: 1.4872 time to fit residues: 376.7224 Evaluate side-chains 161 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 2.074 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 5 average time/residue: 0.5740 time to fit residues: 7.0095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 213 optimal weight: 40.0000 chunk 380 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- 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 K 243 HIS M 156 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 126 ASN N 185 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.086 79996 Z= 0.403 Angle : 0.773 19.269 123164 Z= 0.411 Chirality : 0.041 0.310 16127 Planarity : 0.009 0.135 4341 Dihedral : 14.684 179.181 37228 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.68 % Favored : 92.11 % Rotamer Outliers : 5.53 % 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: -1.56 (0.26), residues: 951 helix: -0.70 (0.37), residues: 182 sheet: -0.67 (0.41), residues: 146 loop : -1.27 (0.24), residues: 623 *********************** 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 192 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 2.128 Fit side-chains outliers start: 42 outliers final: 29 residues processed: 180 average time/residue: 1.4432 time to fit residues: 355.2029 Evaluate side-chains 169 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 2.069 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 6 average time/residue: 0.6467 time to fit residues: 9.1028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 239 ASN M 115 GLN M 156 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 185 ASN O 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.117 79996 Z= 0.554 Angle : 0.894 19.466 123164 Z= 0.459 Chirality : 0.048 0.352 16127 Planarity : 0.009 0.139 4341 Dihedral : 15.076 179.193 37228 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.52 % Favored : 91.27 % Rotamer Outliers : 5.79 % 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: -1.92 (0.25), residues: 951 helix: -1.12 (0.36), residues: 189 sheet: -0.67 (0.42), residues: 141 loop : -1.52 (0.23), residues: 621 *********************** 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 187 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 143 time to evaluate : 2.079 Fit side-chains outliers start: 44 outliers final: 28 residues processed: 179 average time/residue: 1.4518 time to fit residues: 354.9514 Evaluate side-chains 164 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 2.119 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 5 average time/residue: 0.8269 time to fit residues: 8.6271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.0470 chunk 364 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 213 optimal weight: 40.0000 chunk 154 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 0.2980 chunk 335 optimal weight: 0.9990 chunk 353 optimal weight: 3.9990 overall best weight: 1.4684 ------------------------------------------------------------------------------- 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 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: 0.8173 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 79996 Z= 0.150 Angle : 0.615 18.121 123164 Z= 0.343 Chirality : 0.030 0.262 16127 Planarity : 0.008 0.126 4341 Dihedral : 14.397 179.971 37228 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.31 % Favored : 93.48 % Rotamer Outliers : 3.82 % 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: -1.35 (0.26), residues: 951 helix: -0.20 (0.39), residues: 179 sheet: -0.87 (0.40), residues: 151 loop : -1.13 (0.25), residues: 621 *********************** 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: 29 poor density : 157 time to evaluate : 2.091 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 184 average time/residue: 1.4265 time to fit residues: 360.1513 Evaluate side-chains 163 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 1.6307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 10.0000 chunk 375 optimal weight: 0.9980 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 chunk 393 optimal weight: 8.9990 chunk 362 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 overall best weight: 5.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN O 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.096 79996 Z= 0.431 Angle : 0.781 18.174 123164 Z= 0.413 Chirality : 0.041 0.316 16127 Planarity : 0.009 0.135 4341 Dihedral : 14.700 179.818 37228 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.20 % Favored : 91.59 % Rotamer Outliers : 3.42 % 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: -0.76 (0.37), residues: 188 sheet: -0.67 (0.41), residues: 143 loop : -1.31 (0.24), residues: 620 ********************** 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 171 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 2.104 Fit side-chains outliers start: 26 outliers final: 25 residues processed: 168 average time/residue: 1.4894 time to fit residues: 342.7260 Evaluate side-chains 168 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 2.134 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 3 average time/residue: 0.5991 time to fit residues: 5.2397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0270 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: 8.9990 chunk 131 optimal weight: 7.9990 chunk 322 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.125173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099487 restraints weight = 132053.752| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 0.62 r_work: 0.3239 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 79996 Z= 0.327 Angle : 0.727 18.141 123164 Z= 0.393 Chirality : 0.037 0.293 16127 Planarity : 0.008 0.134 4341 Dihedral : 14.691 179.562 37228 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.78 % Favored : 92.01 % Rotamer Outliers : 3.82 % 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: -1.58 (0.26), residues: 951 helix: -0.72 (0.37), residues: 187 sheet: -0.59 (0.41), residues: 141 loop : -1.30 (0.24), residues: 623 =============================================================================== Job complete usr+sys time: 11453.78 seconds wall clock time: 205 minutes 57.93 seconds (12357.93 seconds total)