Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:27:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agg_11779/12_2022/7agg_11779.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agg_11779/12_2022/7agg_11779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agg_11779/12_2022/7agg_11779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agg_11779/12_2022/7agg_11779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agg_11779/12_2022/7agg_11779.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agg_11779/12_2022/7agg_11779.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 196": "OE1" <-> "OE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F GLU 240": "OE1" <-> "OE2" Residue "F PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 268": "OE1" <-> "OE2" Residue "F TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 300": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8252 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "D" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1819 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1819 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Time building chain proxies: 4.93, per 1000 atoms: 0.60 Number of scatterers: 8252 At special positions: 0 Unit cell: (113.75, 110.5, 101.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1669 8.00 N 1344 7.00 C 5206 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: 3.04 Conformation dependent library (CDL) restraints added in 1.3 seconds 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 17 sheets defined 7.5% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.558A pdb=" N GLY A 234 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 5.642A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.558A pdb=" N GLY B 234 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 5.642A pdb=" N LYS B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 252 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.557A pdb=" N GLY C 234 " --> pdb=" O ASN C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 5.642A pdb=" N LYS C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 252 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 296 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.573A pdb=" N TYR A 320 " --> pdb=" O VAL A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 199 removed outlier: 5.896A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA4, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.990A pdb=" N THR D 187 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 154 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR D 189 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 130 through 131 removed outlier: 3.579A pdb=" N MET D 130 " --> pdb=" O ILE D 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 222 through 223 Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 231 removed outlier: 6.723A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 135 removed outlier: 3.573A pdb=" N TYR B 320 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 190 through 199 removed outlier: 5.896A pdb=" N ASN B 297 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AB2, first strand: chain 'C' and resid 133 through 135 removed outlier: 3.572A pdb=" N TYR C 320 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 190 through 199 removed outlier: 5.897A pdb=" N ASN C 297 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AB5, first strand: chain 'F' and resid 114 through 120 removed outlier: 6.991A pdb=" N THR F 187 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU F 154 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR F 189 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 130 through 131 removed outlier: 3.578A pdb=" N MET F 130 " --> pdb=" O ILE F 171 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 222 through 223 Processing sheet with id=AB8, first strand: chain 'F' and resid 229 through 231 removed outlier: 6.725A pdb=" N SER F 302 " --> pdb=" O ALA F 264 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 537 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2700 1.34 - 1.46: 1662 1.46 - 1.57: 4002 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 8418 Sorted by residual: bond pdb=" CB TRP C 135 " pdb=" CG TRP C 135 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.10e+00 bond pdb=" CB TRP A 135 " pdb=" CG TRP A 135 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.06e+00 bond pdb=" CB TRP B 135 " pdb=" CG TRP B 135 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.03e+00 bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.09e+00 bond pdb=" CG1 ILE A 273 " pdb=" CD1 ILE A 273 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.08e+00 ... (remaining 8413 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.92: 169 105.92 - 112.95: 4640 112.95 - 119.97: 2729 119.97 - 127.00: 3867 127.00 - 134.02: 85 Bond angle restraints: 11490 Sorted by residual: angle pdb=" N TRP A 135 " pdb=" CA TRP A 135 " pdb=" CB TRP A 135 " ideal model delta sigma weight residual 111.56 106.66 4.90 1.52e+00 4.33e-01 1.04e+01 angle pdb=" N TRP C 135 " pdb=" CA TRP C 135 " pdb=" CB TRP C 135 " ideal model delta sigma weight residual 111.56 106.66 4.90 1.52e+00 4.33e-01 1.04e+01 angle pdb=" N TRP B 135 " pdb=" CA TRP B 135 " pdb=" CB TRP B 135 " ideal model delta sigma weight residual 111.56 106.68 4.88 1.52e+00 4.33e-01 1.03e+01 angle pdb=" C LYS D 313 " pdb=" CA LYS D 313 " pdb=" CB LYS D 313 " ideal model delta sigma weight residual 110.96 106.03 4.93 1.54e+00 4.22e-01 1.03e+01 angle pdb=" C LYS F 313 " pdb=" CA LYS F 313 " pdb=" CB LYS F 313 " ideal model delta sigma weight residual 110.96 106.03 4.93 1.54e+00 4.22e-01 1.02e+01 ... (remaining 11485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 4637 17.28 - 34.56: 311 34.56 - 51.85: 44 51.85 - 69.13: 19 69.13 - 86.41: 8 Dihedral angle restraints: 5019 sinusoidal: 1907 harmonic: 3112 Sorted by residual: dihedral pdb=" CA GLU D 240 " pdb=" C GLU D 240 " pdb=" N VAL D 241 " pdb=" CA VAL D 241 " ideal model delta harmonic sigma weight residual 180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA GLU F 240 " pdb=" C GLU F 240 " pdb=" N VAL F 241 " pdb=" CA VAL F 241 " ideal model delta harmonic sigma weight residual -180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ILE F 315 " pdb=" C ILE F 315 " pdb=" N ARG F 316 " pdb=" CA ARG F 316 " ideal model delta harmonic sigma weight residual 180.00 155.57 24.43 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1024 0.057 - 0.115: 292 0.115 - 0.172: 39 0.172 - 0.230: 0 0.230 - 0.287: 2 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CB VAL D 204 " pdb=" CA VAL D 204 " pdb=" CG1 VAL D 204 " pdb=" CG2 VAL D 204 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB VAL F 204 " pdb=" CA VAL F 204 " pdb=" CG1 VAL F 204 " pdb=" CG2 VAL F 204 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA TYR F 158 " pdb=" N TYR F 158 " pdb=" C TYR F 158 " pdb=" CB TYR F 158 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 1354 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 135 " -0.040 2.00e-02 2.50e+03 4.40e-02 4.83e+01 pdb=" CG TRP A 135 " 0.113 2.00e-02 2.50e+03 pdb=" CD1 TRP A 135 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP A 135 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 135 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 135 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 135 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 135 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 135 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 135 " -0.040 2.00e-02 2.50e+03 4.39e-02 4.82e+01 pdb=" CG TRP C 135 " 0.113 2.00e-02 2.50e+03 pdb=" CD1 TRP C 135 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP C 135 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 135 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 135 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 135 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 135 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP C 135 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 135 " 0.040 2.00e-02 2.50e+03 4.39e-02 4.81e+01 pdb=" CG TRP B 135 " -0.113 2.00e-02 2.50e+03 pdb=" CD1 TRP B 135 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP B 135 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 135 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 135 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 135 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 135 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 135 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 135 " 0.002 2.00e-02 2.50e+03 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 74 2.56 - 3.15: 6661 3.15 - 3.73: 12795 3.73 - 4.32: 18999 4.32 - 4.90: 30816 Nonbonded interactions: 69345 Sorted by model distance: nonbonded pdb=" OH TYR A 319 " pdb=" OH TYR B 319 " model vdw 1.980 2.440 nonbonded pdb=" O HIS F 273 " pdb=" OG1 THR F 286 " model vdw 2.236 2.440 nonbonded pdb=" O HIS D 273 " pdb=" OG1 THR D 286 " model vdw 2.237 2.440 nonbonded pdb=" OG SER A 238 " pdb=" OE1 GLN B 222 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR B 165 " pdb=" OG1 THR B 170 " model vdw 2.292 2.440 ... (remaining 69340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 5206 2.51 5 N 1344 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.880 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: 0.010 Extract box with map and model: 7.210 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 26.790 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.056 8418 Z= 0.463 Angle : 0.785 6.289 11490 Z= 0.455 Chirality : 0.052 0.287 1357 Planarity : 0.005 0.050 1484 Dihedral : 13.158 86.411 3001 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.00 % 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: -1.18 (0.26), residues: 1046 helix: -2.40 (0.61), residues: 54 sheet: -0.53 (0.26), residues: 370 loop : -0.73 (0.25), residues: 622 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2228 time to fit residues: 66.6108 Evaluate side-chains 145 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 66.8732 > 50: distance: 60 - 153: 14.823 distance: 105 - 164: 17.858 distance: 108 - 161: 20.271 distance: 135 - 140: 24.837 distance: 140 - 141: 15.250 distance: 141 - 142: 19.081 distance: 142 - 143: 18.545 distance: 142 - 144: 26.761 distance: 144 - 145: 7.250 distance: 145 - 146: 27.419 distance: 145 - 148: 14.814 distance: 146 - 147: 22.310 distance: 146 - 153: 24.682 distance: 148 - 149: 19.470 distance: 149 - 150: 24.192 distance: 150 - 151: 18.067 distance: 150 - 152: 15.213 distance: 153 - 154: 15.756 distance: 154 - 155: 7.273 distance: 154 - 157: 23.801 distance: 155 - 156: 10.781 distance: 155 - 161: 12.988 distance: 157 - 158: 33.653 distance: 157 - 159: 15.193 distance: 158 - 160: 15.264 distance: 161 - 162: 21.263 distance: 162 - 163: 22.439 distance: 162 - 165: 9.059 distance: 163 - 164: 29.548 distance: 163 - 173: 30.602 distance: 165 - 166: 6.794 distance: 166 - 167: 7.135 distance: 166 - 168: 14.998 distance: 167 - 169: 7.346 distance: 168 - 170: 17.594 distance: 169 - 171: 15.316 distance: 170 - 171: 7.169 distance: 171 - 172: 19.655 distance: 173 - 174: 14.824 distance: 174 - 175: 20.913 distance: 174 - 177: 21.342 distance: 175 - 176: 4.379 distance: 175 - 180: 14.451 distance: 177 - 178: 48.660 distance: 177 - 179: 35.888 distance: 180 - 181: 16.953 distance: 181 - 182: 11.794 distance: 181 - 184: 27.889 distance: 182 - 183: 14.008 distance: 182 - 187: 18.501 distance: 184 - 185: 42.448 distance: 184 - 186: 10.392 distance: 187 - 188: 13.898 distance: 188 - 189: 23.511 distance: 188 - 191: 24.610 distance: 189 - 190: 28.238 distance: 189 - 193: 27.585 distance: 191 - 192: 19.806 distance: 193 - 194: 17.512 distance: 194 - 195: 11.421 distance: 194 - 197: 22.654 distance: 195 - 196: 28.496 distance: 195 - 200: 33.990 distance: 197 - 198: 12.083 distance: 197 - 199: 25.722 distance: 200 - 201: 23.190 distance: 201 - 202: 38.778 distance: 201 - 204: 16.647 distance: 202 - 203: 23.859 distance: 202 - 207: 43.201 distance: 204 - 205: 36.494 distance: 204 - 206: 4.248 distance: 207 - 208: 18.679 distance: 208 - 209: 19.475 distance: 208 - 211: 21.993 distance: 209 - 210: 26.577 distance: 211 - 212: 20.195 distance: 212 - 213: 15.616 distance: 212 - 214: 3.753