Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 12:03:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/04_2023/6pc6_20297_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/04_2023/6pc6_20297.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/04_2023/6pc6_20297_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/04_2023/6pc6_20297_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/04_2023/6pc6_20297_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/04_2023/6pc6_20297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/04_2023/6pc6_20297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/04_2023/6pc6_20297_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc6_20297/04_2023/6pc6_20297_neut_updated.pdb" } resolution = 2.5 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= -0.021 sd= 0.839 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3015 5.49 5 S 22 5.16 5 C 33503 2.51 5 N 13318 2.21 5 O 22268 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 35": "OE1" <-> "OE2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K ARG 189": "NH1" <-> "NH2" Residue "K ARG 203": "NH1" <-> "NH2" Residue "K ARG 212": "NH1" <-> "NH2" Residue "K ARG 221": "NH1" <-> "NH2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ASP 168": "OD1" <-> "OD2" Residue "M ARG 170": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 131": "OD1" <-> "OD2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "O ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 72127 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 62206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62206 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 152, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1060} Link IDs: {'rna2p': 438, 'rna3p': 2458} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2076 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1542 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Chain: "O" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'O7S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.13, per 1000 atoms: 0.39 Number of scatterers: 72127 At special positions: 0 Unit cell: (227.947, 222.145, 190.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 3015 15.00 F 1 9.00 O 22268 8.00 N 13318 7.00 C 33503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 33.93 Conformation dependent library (CDL) restraints added in 2.4 seconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 13 sheets defined 18.2% alpha, 13.8% beta 926 base pairs and 1642 stacking pairs defined. Time for finding SS restraints: 36.24 Creating SS restraints... Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'K' and resid 208 through 213 Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 79 through 85 removed outlier: 4.503A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 95 No H-bonds generated for 'chain 'L' and resid 92 through 95' Processing helix chain 'L' and resid 129 through 137 Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 38 Processing helix chain 'M' and resid 98 through 114 Processing helix chain 'M' and resid 131 through 140 Processing helix chain 'M' and resid 155 through 160 removed outlier: 3.501A pdb=" N LEU M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 Processing helix chain 'N' and resid 62 through 71 removed outlier: 3.789A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 121 through 124 No H-bonds generated for 'chain 'N' and resid 121 through 124' Processing helix chain 'O' and resid 25 through 37 removed outlier: 4.209A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 66 through 71 removed outlier: 4.541A pdb=" N ARG O 69 " --> pdb=" O GLY O 66 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP O 71 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 108 Proline residue: O 97 - end of helix removed outlier: 4.318A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY O 107 " --> pdb=" O ILE O 103 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 121 removed outlier: 4.350A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 135 No H-bonds generated for 'chain 'O' and resid 133 through 135' Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'K' and resid 101 through 105 removed outlier: 3.675A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 129 through 131 Processing sheet with id= E, first strand: chain 'K' and resid 181 through 185 removed outlier: 6.796A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.526A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.687A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'M' and resid 2 through 4 Processing sheet with id= I, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.307A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 169 through 172 removed outlier: 4.728A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP N 181 " --> pdb=" O LEU N 186 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LYS N 190 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL N 177 " --> pdb=" O LYS N 190 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 80 through 83 removed outlier: 6.387A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.483A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE O 55 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'O' and resid 73 through 76 139 hydrogen bonds defined for protein. 384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2336 hydrogen bonds 3782 hydrogen bond angles 0 basepair planarities 926 basepair parallelities 1642 stacking parallelities Total time for adding SS restraints: 143.29 Time building geometry restraints manager: 36.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.55: 73903 1.55 - 1.88: 6094 1.88 - 2.21: 0 2.21 - 2.55: 0 2.55 - 2.88: 1 Bond restraints: 79998 Sorted by residual: bond pdb=" C ASN K 226 " pdb=" N VAL K 228 " ideal model delta sigma weight residual 1.332 2.883 -1.551 1.36e-02 5.41e+03 1.30e+04 bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.409 0.393 2.00e-02 2.50e+03 3.86e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.410 0.392 2.00e-02 2.50e+03 3.85e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.364 0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.367 0.268 2.00e-02 2.50e+03 1.79e+02 ... (remaining 79993 not shown) Histogram of bond angle deviations from ideal: 51.92 - 72.30: 1 72.30 - 92.68: 0 92.68 - 113.07: 63518 113.07 - 133.45: 59628 133.45 - 153.83: 19 Bond angle restraints: 123166 Sorted by residual: angle pdb=" O ASN K 226 " pdb=" C ASN K 226 " pdb=" N VAL K 228 " ideal model delta sigma weight residual 122.59 51.92 70.67 1.33e+00 5.65e-01 2.82e+03 angle pdb=" CA ASN K 226 " pdb=" C ASN K 226 " pdb=" N VAL K 228 " ideal model delta sigma weight residual 116.84 153.83 -36.99 1.71e+00 3.42e-01 4.68e+02 angle pdb=" C06 O7S I3001 " pdb=" C07 O7S I3001 " pdb=" C08 O7S I3001 " ideal model delta sigma weight residual 68.57 120.15 -51.58 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C07 O7S I3001 " pdb=" C09 O7S I3001 " pdb=" C10 O7S I3001 " ideal model delta sigma weight residual 85.73 128.50 -42.77 3.00e+00 1.11e-01 2.03e+02 angle pdb=" C04 O7S I3001 " pdb=" C05 O7S I3001 " pdb=" C06 O7S I3001 " ideal model delta sigma weight residual 85.76 124.50 -38.74 3.00e+00 1.11e-01 1.67e+02 ... (remaining 123161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 39489 35.67 - 71.34: 1121 71.34 - 107.01: 123 107.01 - 142.68: 13 142.68 - 178.35: 11 Dihedral angle restraints: 40757 sinusoidal: 38080 harmonic: 2677 Sorted by residual: dihedral pdb=" CA ASN K 226 " pdb=" C ASN K 226 " pdb=" N VAL K 228 " pdb=" CA VAL K 228 " ideal model delta harmonic sigma weight residual 180.00 62.45 117.55 0 5.00e+00 4.00e-02 5.53e+02 dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual 232.00 53.65 178.35 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 42.89 -170.89 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 40754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 12081 0.030 - 0.059: 3783 0.059 - 0.089: 163 0.089 - 0.119: 89 0.119 - 0.148: 7 Chirality restraints: 16123 Sorted by residual: chirality pdb=" C3' G I 271 " pdb=" C4' G I 271 " pdb=" O3' G I 271 " pdb=" C2' G I 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" C1' A I1395 " pdb=" O4' A I1395 " pdb=" C2' A I1395 " pdb=" N9 A I1395 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE K 135 " pdb=" N ILE K 135 " pdb=" C ILE K 135 " pdb=" CB ILE K 135 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 16120 not shown) Planarity restraints: 4340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " -0.040 2.00e-02 2.50e+03 5.94e-01 7.94e+03 pdb=" C4' 1MG I 745 " -0.447 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.692 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.595 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.206 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.924 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.213 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.921 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.033 2.00e-02 2.50e+03 5.91e-01 7.86e+03 pdb=" C4' OMG I2251 " 0.446 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.706 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.594 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.579 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.216 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.908 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.212 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.916 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.020 2.00e-02 2.50e+03 5.87e-01 7.75e+03 pdb=" C4' 2MG I2445 " -0.454 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.731 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.560 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.231 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.878 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.207 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.914 2.00e-02 2.50e+03 ... (remaining 4337 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 436 2.52 - 3.12: 49800 3.12 - 3.71: 145264 3.71 - 4.31: 210862 4.31 - 4.90: 270771 Nonbonded interactions: 677133 Sorted by model distance: nonbonded pdb=" O2' G I1475 " pdb=" O6 G I1514 " model vdw 1.930 2.440 nonbonded pdb=" O2' A I1084 " pdb=" O2' U I1105 " model vdw 1.943 2.440 nonbonded pdb=" O2* PSU I1911 " pdb=" OP1 A I1912 " model vdw 1.951 3.040 nonbonded pdb=" O2' G I1715 " pdb=" O6 G I1743 " model vdw 1.972 2.440 nonbonded pdb=" O2' A I1508 " pdb=" O4' A I1509 " model vdw 2.003 2.440 ... (remaining 677128 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.200 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: 0.080 Extract box with map and model: 47.260 Check model and map are aligned: 0.790 Set scattering table: 0.480 Process input model: 286.380 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:10.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 358.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.551 79998 Z= 0.495 Angle : 0.562 70.672 123166 Z= 0.281 Chirality : 0.025 0.148 16123 Planarity : 0.031 0.594 4340 Dihedral : 13.076 178.353 39053 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.22), residues: 949 helix: -2.95 (0.27), residues: 176 sheet: -1.72 (0.40), residues: 134 loop : -2.49 (0.20), residues: 639 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 2.098 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 212 average time/residue: 1.7857 time to fit residues: 488.4791 Evaluate side-chains 153 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 2.117 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.9631 ------------------------------------------------------------------------------- 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: 0.6980 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 201 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 309 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 358 optimal weight: 4.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 60 GLN K 163 GLN M 30 GLN M 41 GLN M 90 GLN M 115 GLN M 195 GLN N 32 ASN N 130 GLN O 128 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 79998 Z= 0.344 Angle : 0.708 18.000 123166 Z= 0.383 Chirality : 0.036 0.288 16123 Planarity : 0.008 0.135 4340 Dihedral : 13.937 179.930 37257 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.57 % Favored : 94.11 % Rotamer Outliers : 4.08 % 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: -1.96 (0.25), residues: 951 helix: -0.83 (0.35), residues: 171 sheet: -0.90 (0.39), residues: 156 loop : -1.61 (0.23), residues: 624 *********************** 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 178 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 2.130 Fit side-chains outliers start: 31 outliers final: 18 residues processed: 168 average time/residue: 1.7322 time to fit residues: 382.2361 Evaluate side-chains 154 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 2.137 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.5953 time to fit residues: 7.3099 ------------------------------------------------------------------------------- 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: 8.9990 chunk 298 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 359 optimal weight: 0.9980 chunk 388 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 chunk 356 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 60 GLN K 163 GLN M 90 GLN M 115 GLN M 136 GLN N 130 GLN N 167 ASN O 58 ASN O 128 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 79998 Z= 0.378 Angle : 0.690 16.511 123166 Z= 0.373 Chirality : 0.037 0.282 16123 Planarity : 0.008 0.138 4340 Dihedral : 14.284 177.044 37257 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.38 % Rotamer Outliers : 5.00 % 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: -1.36 (0.26), residues: 951 helix: -0.13 (0.39), residues: 167 sheet: -0.68 (0.37), residues: 172 loop : -1.22 (0.24), residues: 612 *********************** 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 191 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 2.136 Fit side-chains outliers start: 38 outliers final: 21 residues processed: 176 average time/residue: 1.7455 time to fit residues: 400.1095 Evaluate side-chains 172 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 2.089 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 7 average time/residue: 0.7496 time to fit residues: 10.3176 ------------------------------------------------------------------------------- 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: 5.9990 chunk 270 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 360 optimal weight: 1.9990 chunk 381 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 60 GLN K 115 GLN M 90 GLN M 115 GLN N 130 GLN N 167 ASN O 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 79998 Z= 0.317 Angle : 0.671 16.306 123166 Z= 0.367 Chirality : 0.035 0.279 16123 Planarity : 0.008 0.135 4340 Dihedral : 14.288 177.504 37257 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.10 % Favored : 93.69 % Rotamer Outliers : 4.34 % 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: -1.14 (0.26), residues: 951 helix: 0.04 (0.39), residues: 168 sheet: -0.50 (0.38), residues: 172 loop : -1.08 (0.24), residues: 611 *********************** 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 186 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 2.127 Fit side-chains outliers start: 33 outliers final: 22 residues processed: 175 average time/residue: 1.7424 time to fit residues: 399.0373 Evaluate side-chains 167 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 6 average time/residue: 0.6063 time to fit residues: 8.4336 ------------------------------------------------------------------------------- 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: 40.0000 chunk 5 optimal weight: 7.9990 chunk 284 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 342 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 90 GLN M 115 GLN N 130 GLN N 149 ASN O 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 79998 Z= 0.343 Angle : 0.673 16.687 123166 Z= 0.368 Chirality : 0.036 0.282 16123 Planarity : 0.008 0.136 4340 Dihedral : 14.335 177.010 37257 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.31 % Favored : 93.48 % Rotamer Outliers : 5.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 951 helix: 0.17 (0.39), residues: 168 sheet: -0.50 (0.37), residues: 176 loop : -0.90 (0.25), residues: 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 152 time to evaluate : 2.132 Fit side-chains outliers start: 39 outliers final: 24 residues processed: 180 average time/residue: 1.7679 time to fit residues: 415.2353 Evaluate side-chains 177 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 2.158 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 6 average time/residue: 0.5785 time to fit residues: 8.1042 ------------------------------------------------------------------------------- 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: 1.9990 chunk 75 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 382 optimal weight: 5.9990 chunk 317 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 90 GLN M 115 GLN N 130 GLN N 167 ASN O 58 ASN O 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 79998 Z= 0.345 Angle : 0.673 16.674 123166 Z= 0.368 Chirality : 0.036 0.285 16123 Planarity : 0.008 0.135 4340 Dihedral : 14.384 177.390 37257 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.62 % Favored : 93.17 % Rotamer Outliers : 4.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 951 helix: 0.24 (0.39), residues: 169 sheet: -0.46 (0.37), residues: 176 loop : -0.84 (0.25), residues: 606 *********************** 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 189 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 2.163 Fit side-chains outliers start: 36 outliers final: 26 residues processed: 176 average time/residue: 1.7383 time to fit residues: 402.3558 Evaluate side-chains 175 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 2.151 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 0.6014 time to fit residues: 9.6264 ------------------------------------------------------------------------------- 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: 0.9990 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 40.0000 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 40.0000 chunk 321 optimal weight: 0.0270 chunk 213 optimal weight: 50.0000 chunk 380 optimal weight: 0.4980 chunk 238 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 overall best weight: 3.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 90 GLN M 115 GLN N 130 GLN N 167 ASN O 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 79998 Z= 0.294 Angle : 0.660 16.626 123166 Z= 0.363 Chirality : 0.034 0.278 16123 Planarity : 0.008 0.134 4340 Dihedral : 14.385 177.328 37257 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.38 % Rotamer Outliers : 4.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.27), residues: 951 helix: 0.30 (0.40), residues: 169 sheet: -0.44 (0.37), residues: 176 loop : -0.80 (0.25), residues: 606 *********************** 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 183 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 2.186 Fit side-chains outliers start: 36 outliers final: 27 residues processed: 172 average time/residue: 1.6569 time to fit residues: 377.0689 Evaluate side-chains 175 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 7 average time/residue: 0.8258 time to fit residues: 11.0698 ------------------------------------------------------------------------------- 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: 6.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 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: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 90 GLN M 115 GLN N 130 GLN O 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.091 79998 Z= 0.580 Angle : 0.810 17.055 123166 Z= 0.426 Chirality : 0.045 0.337 16123 Planarity : 0.009 0.146 4340 Dihedral : 14.680 176.561 37257 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.05 % Favored : 92.74 % Rotamer Outliers : 4.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.26), residues: 951 helix: 0.11 (0.40), residues: 166 sheet: -0.55 (0.37), residues: 170 loop : -0.83 (0.25), residues: 615 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 2.170 Fit side-chains outliers start: 36 outliers final: 26 residues processed: 176 average time/residue: 1.7539 time to fit residues: 406.0735 Evaluate side-chains 172 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 2.105 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 23 residues processed: 3 average time/residue: 0.6406 time to fit residues: 5.1684 ------------------------------------------------------------------------------- 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: 1.9990 chunk 364 optimal weight: 0.9990 chunk 332 optimal weight: 0.9990 chunk 354 optimal weight: 4.9990 chunk 213 optimal weight: 40.0000 chunk 154 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 6.9990 chunk 335 optimal weight: 0.9990 chunk 353 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 90 GLN M 115 GLN N 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 79998 Z= 0.208 Angle : 0.668 16.649 123166 Z= 0.368 Chirality : 0.034 0.271 16123 Planarity : 0.008 0.129 4340 Dihedral : 14.586 178.114 37257 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.20 % Favored : 93.59 % Rotamer Outliers : 3.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.27), residues: 951 helix: 0.09 (0.40), residues: 174 sheet: -0.43 (0.38), residues: 165 loop : -0.71 (0.25), residues: 612 *********************** 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 176 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 2.166 Fit side-chains outliers start: 27 outliers final: 23 residues processed: 171 average time/residue: 1.7246 time to fit residues: 387.7419 Evaluate side-chains 173 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 2.079 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.5489 time to fit residues: 4.8038 ------------------------------------------------------------------------------- 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: 7.9990 chunk 375 optimal weight: 0.7980 chunk 228 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 393 optimal weight: 8.9990 chunk 362 optimal weight: 0.0170 chunk 313 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 242 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 overall best weight: 3.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 90 GLN M 115 GLN N 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 79998 Z= 0.310 Angle : 0.668 16.465 123166 Z= 0.368 Chirality : 0.036 0.278 16123 Planarity : 0.008 0.134 4340 Dihedral : 14.505 177.658 37257 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.52 % Favored : 93.27 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.27), residues: 951 helix: 0.28 (0.39), residues: 169 sheet: -0.47 (0.37), residues: 176 loop : -0.72 (0.26), residues: 606 ********************** 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 169 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 2.115 Fit side-chains outliers start: 23 outliers final: 22 residues processed: 169 average time/residue: 1.6662 time to fit residues: 371.1052 Evaluate side-chains 168 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 2.131 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 1.6272 ------------------------------------------------------------------------------- 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: 7.9990 chunk 333 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 322 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 90 GLN M 115 GLN N 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.104002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079295 restraints weight = 143547.737| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 0.53 r_work: 0.2965 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 79998 Z= 0.298 Angle : 0.667 16.460 123166 Z= 0.366 Chirality : 0.035 0.276 16123 Planarity : 0.008 0.134 4340 Dihedral : 14.501 177.563 37257 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.62 % Favored : 93.17 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.27), residues: 951 helix: 0.09 (0.39), residues: 176 sheet: -0.43 (0.37), residues: 171 loop : -0.74 (0.25), residues: 604 =============================================================================== Job complete usr+sys time: 11033.30 seconds wall clock time: 198 minutes 43.47 seconds (11923.47 seconds total)