Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 16 18:11:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wub_21909/10_2023/6wub_21909.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wub_21909/10_2023/6wub_21909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wub_21909/10_2023/6wub_21909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wub_21909/10_2023/6wub_21909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wub_21909/10_2023/6wub_21909.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wub_21909/10_2023/6wub_21909.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.005 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 1121 5.49 5 S 26 5.16 5 C 16918 2.51 5 N 6288 2.21 5 O 9596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d GLU 25": "OE1" <-> "OE2" Residue "d ASP 169": "OD1" <-> "OD2" Residue "d GLU 182": "OE1" <-> "OE2" Residue "f GLU 8": "OE1" <-> "OE2" Residue "h GLU 23": "OE1" <-> "OE2" Residue "k GLU 94": "OE1" <-> "OE2" Residue "l ASP 122": "OD1" <-> "OD2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 53": "OE1" <-> "OE2" Residue "q GLU 4": "OE1" <-> "OE2" Residue "q GLU 66": "OE1" <-> "OE2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 33949 Number of models: 1 Model: "" Number of chains: 12 Chain: "a" Number of atoms: 24077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 24077 Classifications: {'RNA': 1121} Modifications used: {'rna2p_pur': 85, 'rna2p_pyr': 50, 'rna3p_pur': 562, 'rna3p_pyr': 424} Link IDs: {'rna2p': 135, 'rna3p': 985} Chain breaks: 3 Chain: "d" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1620 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain: "e" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1204 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "f" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "h" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 125} Chain: "k" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 863 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "l" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1065 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 127} Chain: "o" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 741 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 708 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "q" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 681 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "r" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 537 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "t" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 617 Classifications: {'peptide': 82} Link IDs: {'TRANS': 81} Time building chain proxies: 17.19, per 1000 atoms: 0.51 Number of scatterers: 33949 At special positions: 0 Unit cell: (161.259, 189.781, 173.326, 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 26 16.00 P 1121 15.00 O 9596 8.00 N 6288 7.00 C 16918 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=0, symmetry=0 Time building additional restraints: 19.03 Conformation dependent library (CDL) restraints added in 1.6 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 12 sheets defined 36.5% alpha, 21.3% beta 375 base pairs and 632 stacking pairs defined. Time for finding SS restraints: 18.74 Creating SS restraints... Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 45 through 61 removed outlier: 3.510A pdb=" N MET d 49 " --> pdb=" O SER d 45 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN d 50 " --> pdb=" O GLU d 46 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 76 Processing helix chain 'd' and resid 83 through 91 removed outlier: 3.589A pdb=" N PHE d 87 " --> pdb=" O HIS d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 103 Processing helix chain 'd' and resid 107 through 117 removed outlier: 3.806A pdb=" N ALA d 111 " --> pdb=" O THR d 107 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 158 removed outlier: 3.586A pdb=" N GLU d 157 " --> pdb=" O LYS d 153 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA d 158 " --> pdb=" O GLU d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 186 Processing helix chain 'd' and resid 193 through 199 removed outlier: 3.540A pdb=" N TYR d 199 " --> pdb=" O VAL d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 69 removed outlier: 3.838A pdb=" N LYS e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 117 removed outlier: 3.643A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL e 114 " --> pdb=" O PRO e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 145 Processing helix chain 'e' and resid 149 through 157 removed outlier: 3.666A pdb=" N VAL e 153 " --> pdb=" O ARG e 149 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA e 154 " --> pdb=" O ALA e 150 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 35 Processing helix chain 'f' and resid 76 through 85 removed outlier: 3.738A pdb=" N ASP f 81 " --> pdb=" O ILE f 77 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 20 Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 115 through 122 Processing helix chain 'k' and resid 48 through 51 Processing helix chain 'k' and resid 53 through 58 Processing helix chain 'k' and resid 59 through 75 removed outlier: 3.747A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL k 73 " --> pdb=" O ALA k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 102 removed outlier: 3.667A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 21 through 25 Processing helix chain 'o' and resid 4 through 13 removed outlier: 3.901A pdb=" N ASN o 9 " --> pdb=" O GLN o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.938A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.667A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 removed outlier: 3.713A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 61 removed outlier: 3.551A pdb=" N SER p 61 " --> pdb=" O LEU p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 76 Processing helix chain 'p' and resid 78 through 88 removed outlier: 3.937A pdb=" N LYS p 82 " --> pdb=" O GLY p 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 15 through 20 removed outlier: 3.722A pdb=" N ASN r 20 " --> pdb=" O TYR r 16 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 34 Processing helix chain 'r' and resid 45 through 50 removed outlier: 3.643A pdb=" N THR r 49 " --> pdb=" O PRO r 45 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 69 removed outlier: 3.565A pdb=" N ARG r 57 " --> pdb=" O ALA r 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE r 68 " --> pdb=" O LYS r 64 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 40 removed outlier: 3.524A pdb=" N ILE t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA t 38 " --> pdb=" O LYS t 34 " (cutoff:3.500A) Processing helix chain 't' and resid 46 through 63 removed outlier: 3.648A pdb=" N TYR t 50 " --> pdb=" O VAL t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 80 Processing sheet with id=AA1, first strand: chain 'd' and resid 125 through 126 Processing sheet with id=AA2, first strand: chain 'd' and resid 166 through 169 Processing sheet with id=AA3, first strand: chain 'e' and resid 14 through 24 removed outlier: 5.688A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 85 through 88 Processing sheet with id=AA5, first strand: chain 'f' and resid 39 through 50 removed outlier: 6.062A pdb=" N ASN f 67 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER f 43 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE f 65 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP f 45 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR f 63 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU f 47 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY f 61 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL f 68 " --> pdb=" O TYR f 7 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET f 10 " --> pdb=" O HIS f 93 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS f 93 " --> pdb=" O MET f 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE f 12 " --> pdb=" O ILE f 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 39 through 50 removed outlier: 6.062A pdb=" N ASN f 67 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER f 43 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE f 65 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP f 45 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR f 63 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU f 47 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY f 61 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL f 68 " --> pdb=" O TYR f 7 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS f 6 " --> pdb=" O VAL f 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'h' and resid 25 through 27 removed outlier: 3.650A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 77 through 79 removed outlier: 6.805A pdb=" N ILE h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY h 111 " --> pdb=" O THR h 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'k' and resid 41 through 46 removed outlier: 6.344A pdb=" N VAL k 82 " --> pdb=" O VAL k 107 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA k 109 " --> pdb=" O VAL k 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'l' and resid 43 through 53 removed outlier: 5.875A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG l 49 " --> pdb=" O ARG l 67 " (cutoff:3.500A) removed outlier: 13.538A pdb=" N GLU l 75 " --> pdb=" O VAL l 106 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N TYR l 108 " --> pdb=" O GLU l 75 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR l 77 " --> pdb=" O TYR l 108 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE l 110 " --> pdb=" O THR l 77 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR l 79 " --> pdb=" O ILE l 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'p' and resid 48 through 50 removed outlier: 3.595A pdb=" N GLU p 48 " --> pdb=" O ASN p 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU p 35 " --> pdb=" O VAL p 22 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE p 20 " --> pdb=" O VAL p 37 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'q' and resid 10 through 17 removed outlier: 17.366A pdb=" N VAL q 10 " --> pdb=" O LYS q 31 " (cutoff:3.500A) removed outlier: 14.270A pdb=" N LYS q 31 " --> pdb=" O VAL q 10 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLN q 12 " --> pdb=" O GLU q 29 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU q 29 " --> pdb=" O GLN q 12 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR q 25 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU q 78 " --> pdb=" O MET q 65 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET q 65 " --> pdb=" O LEU q 78 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU q 80 " --> pdb=" O LYS q 63 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE q 61 " --> pdb=" O VAL q 82 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 946 hydrogen bonds 1510 hydrogen bond angles 0 basepair planarities 375 basepair parallelities 632 stacking parallelities Total time for adding SS restraints: 33.07 Time building geometry restraints manager: 20.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3684 1.32 - 1.44: 16134 1.44 - 1.56: 14868 1.56 - 1.68: 2238 1.68 - 1.81: 50 Bond restraints: 36974 Sorted by residual: bond pdb=" C ARG q 68 " pdb=" N PRO q 69 " ideal model delta sigma weight residual 1.332 1.307 0.025 1.12e-02 7.97e+03 5.04e+00 bond pdb=" N9 G a 183 " pdb=" C4 G a 183 " ideal model delta sigma weight residual 1.375 1.333 0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" P G a 35 " pdb=" O5' G a 35 " ideal model delta sigma weight residual 1.593 1.564 0.029 1.50e-02 4.44e+03 3.73e+00 bond pdb=" CB VAL p 37 " pdb=" CG1 VAL p 37 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.27e+00 bond pdb=" C2 G a 183 " pdb=" N3 G a 183 " ideal model delta sigma weight residual 1.323 1.287 0.036 2.00e-02 2.50e+03 3.21e+00 ... (remaining 36969 not shown) Histogram of bond angle deviations from ideal: 94.45 - 102.60: 1884 102.60 - 110.74: 18982 110.74 - 118.88: 16417 118.88 - 127.02: 15436 127.02 - 135.17: 2790 Bond angle restraints: 55509 Sorted by residual: angle pdb=" O3' U a 34 " pdb=" P G a 35 " pdb=" O5' G a 35 " ideal model delta sigma weight residual 104.00 112.98 -8.98 1.50e+00 4.44e-01 3.59e+01 angle pdb=" C3' U a 34 " pdb=" O3' U a 34 " pdb=" P G a 35 " ideal model delta sigma weight residual 120.20 111.59 8.61 1.50e+00 4.44e-01 3.29e+01 angle pdb=" C2' C a 31 " pdb=" C1' C a 31 " pdb=" N1 C a 31 " ideal model delta sigma weight residual 114.00 106.92 7.08 1.50e+00 4.44e-01 2.23e+01 angle pdb=" OP1 G a 35 " pdb=" P G a 35 " pdb=" O5' G a 35 " ideal model delta sigma weight residual 108.00 94.45 13.55 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C2' C a 201 " pdb=" C1' C a 201 " pdb=" N1 C a 201 " ideal model delta sigma weight residual 112.00 118.53 -6.53 1.50e+00 4.44e-01 1.89e+01 ... (remaining 55504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 18602 34.08 - 68.15: 980 68.15 - 102.23: 72 102.23 - 136.30: 5 136.30 - 170.38: 11 Dihedral angle restraints: 19670 sinusoidal: 16069 harmonic: 3601 Sorted by residual: dihedral pdb=" O4' U a 586 " pdb=" C1' U a 586 " pdb=" N1 U a 586 " pdb=" C2 U a 586 " ideal model delta sinusoidal sigma weight residual 200.00 29.62 170.38 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U a 579 " pdb=" C1' U a 579 " pdb=" N1 U a 579 " pdb=" C2 U a 579 " ideal model delta sinusoidal sigma weight residual -160.00 9.15 -169.15 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" C4' G a1447 " pdb=" C3' G a1447 " pdb=" C2' G a1447 " pdb=" C1' G a1447 " ideal model delta sinusoidal sigma weight residual 36.00 -24.66 60.66 1 8.00e+00 1.56e-02 7.65e+01 ... (remaining 19667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 6312 0.082 - 0.165: 739 0.165 - 0.247: 63 0.247 - 0.329: 8 0.329 - 0.411: 2 Chirality restraints: 7124 Sorted by residual: chirality pdb=" C1' C a 201 " pdb=" O4' C a 201 " pdb=" C2' C a 201 " pdb=" N1 C a 201 " both_signs ideal model delta sigma weight residual False 2.47 2.05 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C3' U a 214 " pdb=" C4' U a 214 " pdb=" O3' U a 214 " pdb=" C2' U a 214 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C3' C a 37 " pdb=" C4' C a 37 " pdb=" O3' C a 37 " pdb=" C2' C a 37 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 7121 not shown) Planarity restraints: 2853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C a 31 " -0.068 2.00e-02 2.50e+03 3.64e-02 2.99e+01 pdb=" N1 C a 31 " 0.081 2.00e-02 2.50e+03 pdb=" C2 C a 31 " 0.005 2.00e-02 2.50e+03 pdb=" O2 C a 31 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C a 31 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C a 31 " -0.016 2.00e-02 2.50e+03 pdb=" N4 C a 31 " -0.013 2.00e-02 2.50e+03 pdb=" C5 C a 31 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C a 31 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U a 255 " 0.064 2.00e-02 2.50e+03 3.51e-02 2.77e+01 pdb=" N1 U a 255 " -0.080 2.00e-02 2.50e+03 pdb=" C2 U a 255 " -0.005 2.00e-02 2.50e+03 pdb=" O2 U a 255 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U a 255 " 0.008 2.00e-02 2.50e+03 pdb=" C4 U a 255 " 0.017 2.00e-02 2.50e+03 pdb=" O4 U a 255 " 0.011 2.00e-02 2.50e+03 pdb=" C5 U a 255 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U a 255 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G a1447 " 0.061 2.00e-02 2.50e+03 2.77e-02 2.30e+01 pdb=" N9 G a1447 " -0.070 2.00e-02 2.50e+03 pdb=" C8 G a1447 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G a1447 " 0.008 2.00e-02 2.50e+03 pdb=" C5 G a1447 " 0.011 2.00e-02 2.50e+03 pdb=" C6 G a1447 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G a1447 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G a1447 " 0.011 2.00e-02 2.50e+03 pdb=" C2 G a1447 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G a1447 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G a1447 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G a1447 " -0.013 2.00e-02 2.50e+03 ... (remaining 2850 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 631 2.60 - 3.18: 24582 3.18 - 3.75: 61162 3.75 - 4.33: 89739 4.33 - 4.90: 118572 Nonbonded interactions: 294686 Sorted by model distance: nonbonded pdb=" O2 U a 858 " pdb=" N4 C a 860 " model vdw 2.029 2.520 nonbonded pdb=" O2' A a 26 " pdb=" O2 C a 27 " model vdw 2.108 2.440 nonbonded pdb=" NH1 ARG e 61 " pdb=" OE2 GLU e 65 " model vdw 2.125 2.520 nonbonded pdb=" O2' C a 483 " pdb=" O4' U a 484 " model vdw 2.137 2.440 nonbonded pdb=" O2' A a1508 " pdb=" O5' A a1509 " model vdw 2.142 2.440 ... (remaining 294681 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: 4.140 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: 0.020 Extract box with map and model: 21.740 Check model and map are aligned: 0.480 Set scattering table: 0.310 Process input model: 123.280 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.009 0.072 36974 Z= 0.546 Angle : 0.966 13.545 55509 Z= 0.486 Chirality : 0.054 0.411 7124 Planarity : 0.007 0.060 2853 Dihedral : 16.483 170.377 17348 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.41 % Allowed : 13.40 % Favored : 86.19 % Rotamer: Outliers : 18.19 % Allowed : 15.65 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -4.06 (0.20), residues: 1231 helix: -2.07 (0.21), residues: 419 sheet: -1.85 (0.29), residues: 250 loop : -3.62 (0.22), residues: 562 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 268 time to evaluate : 1.851 Fit side-chains revert: symmetry clash outliers start: 193 outliers final: 108 residues processed: 401 average time/residue: 0.5215 time to fit residues: 324.6987 Evaluate side-chains 310 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 202 time to evaluate : 2.023 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 0 residues processed: 108 average time/residue: 0.3692 time to fit residues: 73.5228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 181 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 55 GLN d 59 HIS d 113 GLN d 147 GLN e 8 HIS e 43 ASN l 5 ASN l 109 HIS l 125 GLN o 38 GLN o 42 HIS o 46 HIS p 65 GLN t 45 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36974 Z= 0.210 Angle : 0.621 8.993 55509 Z= 0.327 Chirality : 0.038 0.263 7124 Planarity : 0.005 0.061 2853 Dihedral : 14.187 168.973 14828 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.77 % Favored : 91.06 % Rotamer: Outliers : 4.62 % Allowed : 23.47 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % 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: -2.70 (0.22), residues: 1231 helix: -0.50 (0.24), residues: 428 sheet: -1.18 (0.32), residues: 232 loop : -3.16 (0.22), residues: 571 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 210 time to evaluate : 1.934 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 26 residues processed: 242 average time/residue: 0.5052 time to fit residues: 190.8825 Evaluate side-chains 214 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3319 time to fit residues: 17.8075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 228 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 169 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 65 GLN p 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 36974 Z= 0.284 Angle : 0.690 9.584 55509 Z= 0.357 Chirality : 0.041 0.276 7124 Planarity : 0.005 0.056 2853 Dihedral : 14.284 171.376 14828 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.91 % Favored : 89.93 % Rotamer: Outliers : 5.75 % Allowed : 24.03 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % 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: -2.19 (0.23), residues: 1231 helix: -0.06 (0.24), residues: 435 sheet: -0.74 (0.31), residues: 242 loop : -3.03 (0.23), residues: 554 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 182 time to evaluate : 1.715 Fit side-chains outliers start: 61 outliers final: 44 residues processed: 223 average time/residue: 0.5005 time to fit residues: 176.3261 Evaluate side-chains 220 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 176 time to evaluate : 2.063 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2963 time to fit residues: 27.1581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 224 optimal weight: 0.0670 chunk 110 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 87 ASN o 38 GLN p 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 36974 Z= 0.296 Angle : 0.694 9.445 55509 Z= 0.358 Chirality : 0.041 0.275 7124 Planarity : 0.005 0.055 2853 Dihedral : 14.274 171.865 14828 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.02 % Favored : 90.82 % Rotamer: Outliers : 4.43 % Allowed : 24.22 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.90 (0.23), residues: 1231 helix: 0.20 (0.25), residues: 435 sheet: -0.68 (0.32), residues: 239 loop : -2.81 (0.24), residues: 557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 172 time to evaluate : 1.993 Fit side-chains outliers start: 47 outliers final: 23 residues processed: 207 average time/residue: 0.5147 time to fit residues: 167.6176 Evaluate side-chains 193 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 1.903 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3051 time to fit residues: 15.2944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 166 optimal weight: 0.5980 chunk 92 optimal weight: 20.0000 chunk 191 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 18 ASN p 65 GLN q 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 36974 Z= 0.278 Angle : 0.672 9.411 55509 Z= 0.349 Chirality : 0.040 0.258 7124 Planarity : 0.005 0.064 2853 Dihedral : 14.205 171.346 14828 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.42 % Favored : 90.41 % Rotamer: Outliers : 4.24 % Allowed : 25.16 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.67 (0.23), residues: 1231 helix: 0.41 (0.25), residues: 430 sheet: -0.42 (0.33), residues: 233 loop : -2.71 (0.24), residues: 568 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 179 time to evaluate : 1.937 Fit side-chains outliers start: 45 outliers final: 23 residues processed: 205 average time/residue: 0.5223 time to fit residues: 167.5881 Evaluate side-chains 200 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 2.090 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3383 time to fit residues: 16.3256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1482 > 50: distance: 13 - 16: 3.031 distance: 44 - 49: 35.633 distance: 49 - 50: 39.012 distance: 49 - 154: 35.255 distance: 50 - 51: 23.565 distance: 51 - 52: 43.157 distance: 51 - 53: 14.633 distance: 52 - 151: 29.564 distance: 53 - 54: 40.048 distance: 54 - 55: 55.860 distance: 54 - 57: 56.606 distance: 55 - 56: 41.224 distance: 55 - 60: 39.363 distance: 57 - 59: 39.674 distance: 60 - 61: 39.751 distance: 60 - 137: 35.637 distance: 61 - 62: 70.070 distance: 61 - 64: 39.067 distance: 62 - 63: 55.608 distance: 62 - 68: 10.528 distance: 63 - 134: 36.425 distance: 64 - 65: 36.914 distance: 65 - 66: 36.134 distance: 68 - 69: 31.970 distance: 69 - 70: 50.611 distance: 69 - 72: 40.205 distance: 70 - 71: 39.865 distance: 70 - 75: 51.765 distance: 72 - 73: 39.022 distance: 72 - 74: 41.039 distance: 75 - 76: 49.525 distance: 76 - 77: 42.065 distance: 76 - 79: 41.373 distance: 77 - 82: 39.910 distance: 80 - 81: 39.830 distance: 83 - 84: 39.953 distance: 83 - 86: 40.554 distance: 84 - 91: 55.528 distance: 86 - 87: 56.810 distance: 88 - 89: 40.078 distance: 89 - 90: 39.384 distance: 91 - 92: 39.343 distance: 92 - 93: 38.866 distance: 92 - 95: 57.764 distance: 93 - 94: 57.325 distance: 93 - 100: 40.523 distance: 95 - 96: 39.227 distance: 98 - 99: 69.547 distance: 101 - 102: 39.755 distance: 101 - 104: 40.200 distance: 102 - 103: 39.682 distance: 102 - 107: 41.782 distance: 104 - 105: 41.507 distance: 107 - 108: 15.401 distance: 108 - 109: 38.668 distance: 109 - 110: 41.057 distance: 109 - 115: 68.926 distance: 111 - 112: 48.731 distance: 112 - 113: 12.699 distance: 112 - 114: 41.735 distance: 115 - 116: 41.030 distance: 116 - 117: 38.651 distance: 116 - 119: 40.345 distance: 117 - 118: 41.148 distance: 117 - 121: 34.607 distance: 119 - 120: 40.339