Starting phenix.real_space_refine on Sun Mar 17 17:13:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/03_2024/7afa_11758_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/03_2024/7afa_11758.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/03_2024/7afa_11758_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/03_2024/7afa_11758_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/03_2024/7afa_11758_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/03_2024/7afa_11758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/03_2024/7afa_11758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/03_2024/7afa_11758_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/03_2024/7afa_11758_neut_updated.pdb" } resolution = 2.95 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= -0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 25 5.21 5 S 28 5.16 5 C 9812 2.51 5 N 3440 2.21 5 O 4720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18482 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 34, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 171} Link IDs: {'rna2p': 70, 'rna3p': 385} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "1" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Unusual residues: {' MG': 25} Classifications: {'undetermined': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.03, per 1000 atoms: 0.54 Number of scatterers: 18482 At special positions: 0 Unit cell: (136.71, 113.925, 155.155, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 456 15.00 Mg 25 11.99 O 4720 8.00 N 3440 7.00 C 9812 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: 10.35 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 9 sheets defined 43.2% alpha, 13.2% beta 139 base pairs and 235 stacking pairs defined. Time for finding SS restraints: 9.70 Creating SS restraints... Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 43 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.646A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 123 removed outlier: 3.616A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'C' and resid 7 through 10 No H-bonds generated for 'chain 'C' and resid 7 through 10' Processing helix chain 'C' and resid 29 through 46 Processing helix chain 'C' and resid 73 through 76 No H-bonds generated for 'chain 'C' and resid 73 through 76' Processing helix chain 'C' and resid 82 through 95 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 144 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 54 Processing helix chain 'G' and resid 58 through 69 removed outlier: 3.689A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 111 removed outlier: 3.566A pdb=" N ALA G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 47 Processing helix chain 'I' and resid 50 through 54 Processing helix chain 'I' and resid 72 through 90 Processing helix chain 'I' and resid 95 through 100 Processing helix chain 'J' and resid 15 through 32 Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'M' and resid 15 through 21 removed outlier: 3.836A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 62 removed outlier: 4.162A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 Processing helix chain 'M' and resid 86 through 93 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 32 removed outlier: 3.957A pdb=" N LYS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA N 22 " --> pdb=" O ASP N 18 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS N 23 " --> pdb=" O LYS N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 50 removed outlier: 4.022A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 83 through 89 Processing helix chain 'S' and resid 13 through 25 Processing helix chain 'S' and resid 42 through 44 No H-bonds generated for 'chain 'S' and resid 42 through 44' Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 71 through 74 Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.696A pdb=" N ALA B 160 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL B 187 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.929A pdb=" N ILE B 40 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 98 through 101 removed outlier: 3.678A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 164 through 171 Processing sheet with id= E, first strand: chain 'G' and resid 73 through 78 Processing sheet with id= F, first strand: chain 'I' and resid 6 through 12 Processing sheet with id= G, first strand: chain 'J' and resid 97 through 101 removed outlier: 4.543A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= I, first strand: chain 'S' and resid 31 through 33 381 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 346 hydrogen bonds 538 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 235 stacking parallelities Total time for adding SS restraints: 8.73 Time building geometry restraints manager: 10.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3196 1.33 - 1.45: 7085 1.45 - 1.57: 8503 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19748 Sorted by residual: bond pdb=" N3 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.496 1.344 0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N3 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.496 1.345 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C2 5MC 1 967 " pdb=" N3 5MC 1 967 " ideal model delta sigma weight residual 1.493 1.350 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C2 2MG 1 966 " pdb=" N2 2MG 1 966 " ideal model delta sigma weight residual 1.475 1.342 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C2 2MG 11207 " pdb=" N2 2MG 11207 " ideal model delta sigma weight residual 1.475 1.342 0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 19743 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.39: 2734 106.39 - 113.94: 12323 113.94 - 121.50: 9295 121.50 - 129.05: 4064 129.05 - 136.60: 462 Bond angle restraints: 28878 Sorted by residual: angle pdb=" N VAL J 57 " pdb=" CA VAL J 57 " pdb=" C VAL J 57 " ideal model delta sigma weight residual 109.34 122.90 -13.56 2.08e+00 2.31e-01 4.25e+01 angle pdb=" N LYS G 114 " pdb=" CA LYS G 114 " pdb=" C LYS G 114 " ideal model delta sigma weight residual 113.51 123.15 -9.64 1.52e+00 4.33e-01 4.02e+01 angle pdb=" C1' 2MG 11207 " pdb=" N9 2MG 11207 " pdb=" C8 2MG 11207 " ideal model delta sigma weight residual 110.07 126.94 -16.87 3.00e+00 1.11e-01 3.16e+01 angle pdb=" C1' 2MG 1 966 " pdb=" N9 2MG 1 966 " pdb=" C8 2MG 1 966 " ideal model delta sigma weight residual 110.07 126.87 -16.80 3.00e+00 1.11e-01 3.14e+01 angle pdb=" N SER G 57 " pdb=" CA SER G 57 " pdb=" C SER G 57 " ideal model delta sigma weight residual 111.28 118.14 -6.86 1.35e+00 5.49e-01 2.58e+01 ... (remaining 28873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 11315 35.30 - 70.60: 1113 70.60 - 105.90: 136 105.90 - 141.20: 1 141.20 - 176.50: 3 Dihedral angle restraints: 12568 sinusoidal: 9419 harmonic: 3149 Sorted by residual: dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual 200.00 23.50 176.50 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 200.00 72.86 127.14 1 1.50e+01 4.44e-03 6.84e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual 232.00 59.36 172.64 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 12565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3383 0.107 - 0.214: 183 0.214 - 0.321: 20 0.321 - 0.428: 2 0.428 - 0.535: 2 Chirality restraints: 3590 Sorted by residual: chirality pdb=" CA VAL J 57 " pdb=" N VAL J 57 " pdb=" C VAL J 57 " pdb=" CB VAL J 57 " both_signs ideal model delta sigma weight residual False 2.44 1.91 0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CA LYS G 114 " pdb=" N LYS G 114 " pdb=" C LYS G 114 " pdb=" CB LYS G 114 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" CA ASN G 130 " pdb=" N ASN G 130 " pdb=" C ASN G 130 " pdb=" CB ASN G 130 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 ... (remaining 3587 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 1 966 " 0.032 2.00e-02 2.50e+03 5.55e-01 6.94e+03 pdb=" C4' 2MG 1 966 " 0.433 2.00e-02 2.50e+03 pdb=" O4' 2MG 1 966 " 0.574 2.00e-02 2.50e+03 pdb=" C3' 2MG 1 966 " -0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG 1 966 " -0.553 2.00e-02 2.50e+03 pdb=" C2' 2MG 1 966 " -0.212 2.00e-02 2.50e+03 pdb=" O2' 2MG 1 966 " 0.902 2.00e-02 2.50e+03 pdb=" C1' 2MG 1 966 " 0.239 2.00e-02 2.50e+03 pdb=" N9 2MG 1 966 " -0.831 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 11207 " -0.042 2.00e-02 2.50e+03 5.51e-01 6.82e+03 pdb=" C4' 2MG 11207 " -0.423 2.00e-02 2.50e+03 pdb=" O4' 2MG 11207 " -0.536 2.00e-02 2.50e+03 pdb=" C3' 2MG 11207 " 0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG 11207 " 0.558 2.00e-02 2.50e+03 pdb=" C2' 2MG 11207 " 0.201 2.00e-02 2.50e+03 pdb=" O2' 2MG 11207 " -0.916 2.00e-02 2.50e+03 pdb=" C1' 2MG 11207 " -0.245 2.00e-02 2.50e+03 pdb=" N9 2MG 11207 " 0.816 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 1 967 " -0.222 2.00e-02 2.50e+03 4.35e-01 4.25e+03 pdb=" C4' 5MC 1 967 " 0.414 2.00e-02 2.50e+03 pdb=" O4' 5MC 1 967 " 0.597 2.00e-02 2.50e+03 pdb=" C3' 5MC 1 967 " -0.493 2.00e-02 2.50e+03 pdb=" O3' 5MC 1 967 " -0.159 2.00e-02 2.50e+03 pdb=" C2' 5MC 1 967 " -0.336 2.00e-02 2.50e+03 pdb=" O2' 5MC 1 967 " 0.508 2.00e-02 2.50e+03 pdb=" C1' 5MC 1 967 " 0.312 2.00e-02 2.50e+03 pdb=" N1 5MC 1 967 " -0.622 2.00e-02 2.50e+03 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.14: 26 2.14 - 2.83: 5737 2.83 - 3.52: 28503 3.52 - 4.21: 57823 4.21 - 4.90: 79844 Nonbonded interactions: 171933 Sorted by model distance: nonbonded pdb=" OP1 G 11094 " pdb="MG MG 11607 " model vdw 1.456 2.170 nonbonded pdb=" OP1 G 11068 " pdb="MG MG 11607 " model vdw 1.822 2.170 nonbonded pdb=" OP2 C 11054 " pdb="MG MG 11617 " model vdw 1.898 2.170 nonbonded pdb=" OP1 C 11303 " pdb="MG MG 11620 " model vdw 1.907 2.170 nonbonded pdb=" OP1 U 11224 " pdb="MG MG 11611 " model vdw 1.930 2.170 ... (remaining 171928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.220 Check model and map are aligned: 0.270 Set scattering table: 0.230 Process input model: 64.140 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 0.152 19748 Z= 0.516 Angle : 0.804 16.874 28878 Z= 0.527 Chirality : 0.053 0.535 3590 Planarity : 0.021 0.555 1988 Dihedral : 21.603 176.502 10530 Min Nonbonded Distance : 1.456 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1085 helix: -0.23 (0.22), residues: 492 sheet: -0.52 (0.37), residues: 183 loop : -1.27 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 42 HIS 0.005 0.001 HIS S 14 PHE 0.028 0.002 PHE B 90 TYR 0.009 0.001 TYR I 64 ARG 0.003 0.001 ARG G 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 LEU cc_start: 0.8698 (mt) cc_final: 0.8279 (mp) REVERT: C 112 ASP cc_start: 0.8233 (m-30) cc_final: 0.7910 (m-30) REVERT: C 123 GLN cc_start: 0.9196 (mt0) cc_final: 0.8994 (mt0) REVERT: C 168 TYR cc_start: 0.8444 (t80) cc_final: 0.8209 (t80) REVERT: G 17 LYS cc_start: 0.9374 (tttt) cc_final: 0.9120 (tttt) REVERT: I 60 LYS cc_start: 0.8918 (mppt) cc_final: 0.8622 (mmtm) REVERT: J 20 GLN cc_start: 0.8429 (tp-100) cc_final: 0.7725 (tm-30) REVERT: J 24 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8175 (mm-30) REVERT: J 46 LYS cc_start: 0.9266 (mttm) cc_final: 0.8955 (mtpp) REVERT: J 71 LEU cc_start: 0.9382 (tp) cc_final: 0.9172 (tm) REVERT: J 96 VAL cc_start: 0.9615 (t) cc_final: 0.9350 (m) REVERT: N 26 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8102 (tm-30) REVERT: N 30 ILE cc_start: 0.9432 (mm) cc_final: 0.9226 (mp) REVERT: N 82 ILE cc_start: 0.9713 (mm) cc_final: 0.9446 (mp) REVERT: S 17 LYS cc_start: 0.9384 (mttm) cc_final: 0.9108 (mmmm) REVERT: S 21 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8661 (mmtm) REVERT: S 65 GLU cc_start: 0.8658 (tp30) cc_final: 0.8036 (tp30) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 1.3735 time to fit residues: 472.2067 Evaluate side-chains 184 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 170 HIS B 227 GLN C 102 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN J 64 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS N 60 GLN S 56 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19748 Z= 0.202 Angle : 0.689 13.310 28878 Z= 0.384 Chirality : 0.037 0.217 3590 Planarity : 0.006 0.122 1988 Dihedral : 22.531 176.056 8316 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.16 % Allowed : 21.70 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1085 helix: 0.51 (0.22), residues: 498 sheet: -0.18 (0.38), residues: 175 loop : -0.76 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 42 HIS 0.012 0.001 HIS B 94 PHE 0.015 0.002 PHE B 32 TYR 0.028 0.002 TYR B 213 ARG 0.010 0.000 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 221 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.5370 (OUTLIER) cc_final: 0.4212 (ptpt) REVERT: B 120 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6222 (tm-30) REVERT: B 132 LYS cc_start: 0.9045 (tppp) cc_final: 0.8776 (tppp) REVERT: B 147 SER cc_start: 0.9054 (t) cc_final: 0.8824 (p) REVERT: B 154 MET cc_start: 0.7050 (tpt) cc_final: 0.6643 (mmm) REVERT: C 83 ASP cc_start: 0.7805 (p0) cc_final: 0.7600 (p0) REVERT: C 123 GLN cc_start: 0.9131 (mt0) cc_final: 0.8909 (mt0) REVERT: C 168 TYR cc_start: 0.8374 (t80) cc_final: 0.8158 (t80) REVERT: C 181 ASP cc_start: 0.8845 (t70) cc_final: 0.8324 (p0) REVERT: J 20 GLN cc_start: 0.8378 (tp-100) cc_final: 0.7485 (tm-30) REVERT: J 24 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8010 (mm-30) REVERT: J 46 LYS cc_start: 0.9313 (mttm) cc_final: 0.8961 (mtpp) REVERT: N 26 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7923 (tm-30) REVERT: N 30 ILE cc_start: 0.9374 (mm) cc_final: 0.9115 (mp) REVERT: N 38 ASP cc_start: 0.8733 (p0) cc_final: 0.8310 (p0) REVERT: N 82 ILE cc_start: 0.9689 (mm) cc_final: 0.9462 (mp) REVERT: S 17 LYS cc_start: 0.9299 (mttm) cc_final: 0.8726 (mtpp) REVERT: S 21 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8548 (mttt) REVERT: S 65 GLU cc_start: 0.8408 (tp30) cc_final: 0.7701 (tp30) outliers start: 29 outliers final: 7 residues processed: 235 average time/residue: 1.2435 time to fit residues: 328.9255 Evaluate side-chains 204 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 195 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain S residue 12 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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: 71.2881 > 50: distance: 11 - 15: 34.969 distance: 15 - 16: 48.170 distance: 16 - 17: 42.608 distance: 16 - 19: 46.974 distance: 17 - 18: 40.391 distance: 17 - 29: 41.120 distance: 19 - 20: 39.236 distance: 20 - 21: 40.642 distance: 22 - 24: 39.896 distance: 22 - 25: 26.488 distance: 24 - 26: 37.534 distance: 25 - 27: 39.729 distance: 26 - 28: 15.605 distance: 27 - 28: 46.303 distance: 29 - 30: 39.447 distance: 30 - 31: 57.572 distance: 30 - 33: 40.836 distance: 31 - 32: 47.743 distance: 31 - 37: 12.595 distance: 33 - 34: 40.744 distance: 34 - 36: 55.970 distance: 37 - 38: 62.784 distance: 37 - 43: 42.965 distance: 38 - 39: 51.788 distance: 38 - 41: 54.152 distance: 39 - 40: 43.243 distance: 39 - 44: 52.089 distance: 40 - 61: 66.137 distance: 41 - 42: 19.905 distance: 42 - 43: 24.124 distance: 44 - 45: 40.071 distance: 45 - 46: 40.205 distance: 45 - 48: 17.422 distance: 46 - 47: 56.557 distance: 46 - 53: 41.449 distance: 48 - 49: 35.570 distance: 49 - 50: 43.491 distance: 50 - 51: 48.734 distance: 51 - 52: 34.235 distance: 53 - 54: 35.650 distance: 54 - 55: 44.451 distance: 54 - 57: 34.445 distance: 55 - 56: 68.642 distance: 55 - 61: 57.330 distance: 57 - 58: 43.745 distance: 58 - 59: 46.326 distance: 59 - 60: 21.588 distance: 61 - 62: 40.074 distance: 62 - 63: 39.629 distance: 62 - 65: 55.427 distance: 63 - 64: 41.247 distance: 63 - 70: 56.708 distance: 65 - 66: 63.156 distance: 66 - 67: 36.386 distance: 67 - 68: 27.514 distance: 68 - 69: 47.747 distance: 70 - 71: 45.937 distance: 70 - 76: 56.422 distance: 71 - 72: 38.648 distance: 71 - 74: 28.401 distance: 72 - 73: 32.967 distance: 72 - 77: 58.975 distance: 74 - 75: 52.274 distance: 75 - 76: 55.920 distance: 77 - 78: 15.563 distance: 78 - 79: 34.881 distance: 78 - 81: 32.693 distance: 79 - 80: 48.374 distance: 79 - 88: 34.890 distance: 81 - 82: 54.437 distance: 82 - 83: 47.229 distance: 82 - 84: 39.720 distance: 83 - 85: 34.912 distance: 84 - 86: 56.945 distance: 85 - 87: 29.185 distance: 86 - 87: 36.604 distance: 88 - 89: 44.122 distance: 89 - 90: 39.036 distance: 89 - 92: 21.769 distance: 90 - 91: 55.789 distance: 90 - 96: 3.339 distance: 92 - 93: 44.269 distance: 92 - 94: 37.695 distance: 93 - 95: 40.502 distance: 96 - 97: 39.598 distance: 96 - 121: 30.279 distance: 97 - 98: 38.899 distance: 97 - 100: 39.944 distance: 98 - 99: 30.209 distance: 98 - 107: 35.554 distance: 100 - 101: 45.073 distance: 101 - 102: 38.927 distance: 101 - 103: 29.638 distance: 102 - 104: 39.065 distance: 103 - 105: 31.406 distance: 104 - 106: 29.353 distance: 105 - 106: 38.766