Starting phenix.real_space_refine on Tue Aug 6 03:48:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0p_8949/08_2024/6e0p_8949.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0p_8949/08_2024/6e0p_8949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0p_8949/08_2024/6e0p_8949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0p_8949/08_2024/6e0p_8949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0p_8949/08_2024/6e0p_8949.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0p_8949/08_2024/6e0p_8949.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 26 5.16 5 C 8921 2.51 5 N 2815 2.21 5 O 3515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "M ARG 219": "NH1" <-> "NH2" Residue "N ARG 176": "NH1" <-> "NH2" Residue "N ARG 219": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15567 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "M" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1789 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "N" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1787 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Time building chain proxies: 8.43, per 1000 atoms: 0.54 Number of scatterers: 15567 At special positions: 0 Unit cell: (132.66, 127.635, 116.58, 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 290 15.00 O 3515 8.00 N 2815 7.00 C 8921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.02 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 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: 6.91 Conformation dependent library (CDL) restraints added in 1.7 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2254 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 24 sheets defined 46.1% alpha, 20.3% beta 137 base pairs and 268 stacking pairs defined. Time for finding SS restraints: 6.98 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.723A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.598A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.646A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.806A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.276A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.566A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.702A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.724A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.599A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.647A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.807A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.308A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.535A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.526A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.735A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 84 through 87 removed outlier: 3.825A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.660A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.668A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.521A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.179A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.719A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.905A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 25 through 28 removed outlier: 3.708A pdb=" N VAL M 101 " --> pdb=" O CYS M 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 6.606A pdb=" N ILE M 56 " --> pdb=" O TYR M 72 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR M 72 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP M 58 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.725A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N SER M 122 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU M 129 " --> pdb=" O SER M 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 163 through 164 removed outlier: 4.158A pdb=" N PHE M 229 " --> pdb=" O CYS M 181 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 168 through 171 removed outlier: 3.944A pdb=" N GLU M 263 " --> pdb=" O MET M 169 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA M 171 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 168 through 171 removed outlier: 3.944A pdb=" N GLU M 263 " --> pdb=" O MET M 169 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA M 171 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR M 255 " --> pdb=" O GLN M 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 28 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.447A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE N 56 " --> pdb=" O TYR N 72 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR N 72 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP N 58 " --> pdb=" O ILE N 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.447A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 39 through 40 removed outlier: 3.553A pdb=" N VAL N 40 " --> pdb=" O LEU N 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 162 through 163 Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 Processing sheet with id=AC5, first strand: chain 'N' and resid 177 through 180 removed outlier: 3.611A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 211 through 212 removed outlier: 6.543A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR N 255 " --> pdb=" O GLN N 248 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 328 hydrogen bonds 656 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 268 stacking parallelities Total time for adding SS restraints: 6.00 Time building geometry restraints manager: 7.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3679 1.34 - 1.46: 5588 1.46 - 1.58: 6571 1.58 - 1.71: 578 1.71 - 1.83: 42 Bond restraints: 16458 Sorted by residual: bond pdb=" CG1 ILE A 132 " pdb=" CD1 ILE A 132 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.76e+00 bond pdb=" CG1 ILE E 132 " pdb=" CD1 ILE E 132 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.76e+00 bond pdb=" CB THR H 96 " pdb=" CG2 THR H 96 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.32e+00 bond pdb=" C3' DG J 93 " pdb=" O3' DG J 93 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.19e+00 bond pdb=" CG LEU A 112 " pdb=" CD2 LEU A 112 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.05e+00 ... (remaining 16453 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.29: 1378 105.29 - 112.47: 8875 112.47 - 119.65: 5450 119.65 - 126.83: 6868 126.83 - 134.01: 909 Bond angle restraints: 23480 Sorted by residual: angle pdb=" C TYR M 208 " pdb=" N ALA M 209 " pdb=" CA ALA M 209 " ideal model delta sigma weight residual 121.54 129.66 -8.12 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C TYR N 208 " pdb=" N ALA N 209 " pdb=" CA ALA N 209 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C GLU N 251 " pdb=" N SER N 252 " pdb=" CA SER N 252 " ideal model delta sigma weight residual 120.06 124.78 -4.72 1.19e+00 7.06e-01 1.57e+01 angle pdb=" C3' DG J 93 " pdb=" O3' DG J 93 " pdb=" P DA J 94 " ideal model delta sigma weight residual 120.20 125.29 -5.09 1.50e+00 4.44e-01 1.15e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 110.86 116.55 -5.69 1.84e+00 2.95e-01 9.56e+00 ... (remaining 23475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 7721 35.86 - 71.72: 1463 71.72 - 107.57: 15 107.57 - 143.43: 1 143.43 - 179.29: 1 Dihedral angle restraints: 9201 sinusoidal: 5679 harmonic: 3522 Sorted by residual: dihedral pdb=" CA ASP N 186 " pdb=" C ASP N 186 " pdb=" N ILE N 187 " pdb=" CA ILE N 187 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LYS H 46 " pdb=" C LYS H 46 " pdb=" N GLN H 47 " pdb=" CA GLN H 47 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA GLU M 251 " pdb=" C GLU M 251 " pdb=" N SER M 252 " pdb=" CA SER M 252 " ideal model delta harmonic sigma weight residual 180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 9198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1662 0.040 - 0.079: 692 0.079 - 0.119: 213 0.119 - 0.159: 58 0.159 - 0.198: 16 Chirality restraints: 2641 Sorted by residual: chirality pdb=" CB THR G 101 " pdb=" CA THR G 101 " pdb=" OG1 THR G 101 " pdb=" CG2 THR G 101 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CG LEU A 94 " pdb=" CB LEU A 94 " pdb=" CD1 LEU A 94 " pdb=" CD2 LEU A 94 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA LYS H 46 " pdb=" N LYS H 46 " pdb=" C LYS H 46 " pdb=" CB LYS H 46 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 2638 not shown) Planarity restraints: 1956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 74 " -0.024 2.00e-02 2.50e+03 1.85e-02 6.82e+00 pdb=" CG TYR M 74 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR M 74 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR M 74 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR M 74 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR M 74 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR M 74 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR M 74 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 74 " 0.024 2.00e-02 2.50e+03 1.83e-02 6.73e+00 pdb=" CG TYR N 74 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR N 74 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR N 74 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR N 74 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR N 74 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR N 74 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 74 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.019 2.00e-02 2.50e+03 1.95e-02 6.65e+00 pdb=" CG PHE G 25 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.003 2.00e-02 2.50e+03 ... (remaining 1953 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2999 2.78 - 3.31: 12515 3.31 - 3.84: 30175 3.84 - 4.37: 36172 4.37 - 4.90: 52624 Nonbonded interactions: 134485 Sorted by model distance: nonbonded pdb=" OG SER M 165 " pdb=" OG1 THR M 180 " model vdw 2.253 3.040 nonbonded pdb=" OG SER D 32 " pdb=" OP1 DT J 103 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR E 79 " pdb=" O VAL E 82 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR A 79 " pdb=" O VAL A 82 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.292 3.040 ... (remaining 134480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 116) } ncs_group { reference = (chain 'D' and resid 31 through 124) selection = chain 'H' } ncs_group { reference = (chain 'M' and (resid 23 through 141 or resid 157 through 265)) selection = (chain 'N' and (resid 23 through 141 or resid 157 through 265)) } 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: 0.970 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: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 47.430 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 0.007 0.085 16458 Z= 0.409 Angle : 0.852 12.286 23480 Z= 0.489 Chirality : 0.049 0.198 2641 Planarity : 0.007 0.057 1956 Dihedral : 25.474 179.291 6935 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: -2.18 (0.20), residues: 1196 helix: -1.22 (0.17), residues: 514 sheet: -0.66 (0.35), residues: 237 loop : -1.99 (0.24), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP M 132 HIS 0.016 0.003 HIS B 75 PHE 0.045 0.004 PHE G 25 TYR 0.045 0.003 TYR M 74 ARG 0.020 0.002 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: G 91 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7109 (tm-30) REVERT: N 112 ASP cc_start: 0.7859 (m-30) cc_final: 0.7571 (m-30) REVERT: N 185 GLN cc_start: 0.8598 (mt0) cc_final: 0.8340 (mt0) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 1.8272 time to fit residues: 528.6966 Evaluate side-chains 191 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN D 63 ASN D 84 ASN D 95 GLN E 127 GLN H 84 ASN N 134 GLN N 164 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16458 Z= 0.203 Angle : 0.614 9.447 23480 Z= 0.357 Chirality : 0.036 0.161 2641 Planarity : 0.005 0.047 1956 Dihedral : 29.458 174.473 4618 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.43 % Allowed : 11.68 % Favored : 85.88 % 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: -0.32 (0.23), residues: 1196 helix: 0.87 (0.21), residues: 520 sheet: -0.13 (0.37), residues: 216 loop : -1.48 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 132 HIS 0.003 0.001 HIS B 75 PHE 0.012 0.002 PHE C 25 TYR 0.017 0.001 TYR N 74 ARG 0.005 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8209 (ttpt) REVERT: C 91 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: M 219 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7688 (ptm160) REVERT: N 173 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8178 (tt) outliers start: 25 outliers final: 6 residues processed: 226 average time/residue: 1.8724 time to fit residues: 452.2279 Evaluate side-chains 207 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 60.7504 > 50: distance: 41 - 139: 33.408 distance: 53 - 126: 13.268 distance: 55 - 62: 15.955 distance: 56 - 123: 33.852 distance: 62 - 63: 5.714 distance: 62 - 201: 18.769 distance: 63 - 64: 10.442 distance: 63 - 66: 10.129 distance: 64 - 65: 14.337 distance: 64 - 71: 17.135 distance: 65 - 198: 28.875 distance: 66 - 67: 19.830 distance: 67 - 68: 15.583 distance: 68 - 69: 36.767 distance: 68 - 70: 15.294 distance: 71 - 72: 13.539 distance: 72 - 73: 16.761 distance: 72 - 75: 15.786 distance: 73 - 74: 19.903 distance: 73 - 80: 17.440 distance: 75 - 76: 40.227 distance: 76 - 77: 54.856 distance: 77 - 78: 16.111 distance: 78 - 79: 15.492 distance: 80 - 81: 15.930 distance: 80 - 86: 40.326 distance: 81 - 82: 20.628 distance: 81 - 84: 26.012 distance: 82 - 83: 23.279 distance: 82 - 87: 10.022 distance: 84 - 85: 27.871 distance: 87 - 88: 32.036 distance: 89 - 90: 6.174 distance: 89 - 101: 28.716 distance: 91 - 92: 38.583 distance: 92 - 94: 11.633 distance: 94 - 96: 11.675 distance: 94 - 97: 37.617 distance: 96 - 98: 4.262 distance: 97 - 99: 15.047 distance: 98 - 100: 32.154 distance: 99 - 100: 25.131 distance: 101 - 102: 9.547 distance: 102 - 103: 16.137 distance: 102 - 105: 9.475 distance: 103 - 110: 13.604 distance: 105 - 106: 9.780 distance: 106 - 107: 20.058 distance: 107 - 108: 17.651 distance: 108 - 109: 13.531 distance: 110 - 111: 36.056 distance: 111 - 112: 19.220 distance: 111 - 114: 5.234 distance: 112 - 113: 23.698 distance: 112 - 116: 10.131 distance: 114 - 115: 23.868 distance: 116 - 117: 13.224 distance: 116 - 122: 10.086 distance: 117 - 118: 24.751 distance: 117 - 120: 7.029 distance: 118 - 119: 10.047 distance: 120 - 121: 16.509 distance: 121 - 122: 26.575 distance: 123 - 124: 31.465 distance: 124 - 125: 7.326 distance: 125 - 126: 23.492 distance: 127 - 128: 34.644 distance: 128 - 129: 28.686 distance: 129 - 130: 33.536 distance: 130 - 131: 44.115 distance: 132 - 133: 16.914 distance: 133 - 134: 33.180 distance: 133 - 136: 36.303 distance: 134 - 135: 16.595 distance: 134 - 139: 10.238 distance: 136 - 137: 13.739 distance: 136 - 138: 27.588 distance: 139 - 140: 15.919 distance: 140 - 141: 27.749 distance: 140 - 143: 27.788 distance: 141 - 142: 7.629 distance: 141 - 147: 18.606 distance: 143 - 144: 30.248 distance: 144 - 145: 39.533 distance: 144 - 146: 15.225