Starting phenix.real_space_refine on Fri Jan 19 01:34:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahe_11784/01_2024/7ahe_11784_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahe_11784/01_2024/7ahe_11784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahe_11784/01_2024/7ahe_11784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahe_11784/01_2024/7ahe_11784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahe_11784/01_2024/7ahe_11784_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahe_11784/01_2024/7ahe_11784_updated.pdb" } resolution = 4.1 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 2 5.49 5 S 50 5.16 5 C 6470 2.51 5 N 1676 2.21 5 O 1862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 173": "NH1" <-> "NH2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 382": "NH1" <-> "NH2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D ARG 318": "NH1" <-> "NH2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D ARG 382": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10060 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "B" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "C" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2992 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "D" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2992 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Classifications: {'RNA': 1} Time building chain proxies: 5.73, per 1000 atoms: 0.57 Number of scatterers: 10060 At special positions: 0 Unit cell: (102.212, 86.02, 122.452, 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 50 16.00 P 2 15.00 O 1862 8.00 N 1676 7.00 C 6470 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: 4.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 4 sheets defined 56.7% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 27 through 50 Processing helix chain 'A' and resid 54 through 67 Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 92 through 121 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 123 through 138 removed outlier: 3.593A pdb=" N LYS A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Proline residue: A 131 - end of helix Processing helix chain 'A' and resid 141 through 151 removed outlier: 3.795A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 197 through 203 Processing helix chain 'A' and resid 205 through 233 removed outlier: 5.810A pdb=" N GLY A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N MET A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 249 Processing helix chain 'A' and resid 252 through 276 removed outlier: 3.877A pdb=" N LYS A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 276 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 Processing helix chain 'B' and resid 27 through 50 Processing helix chain 'B' and resid 54 through 67 Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 92 through 121 Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 123 through 138 removed outlier: 3.593A pdb=" N LYS B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 141 through 151 removed outlier: 3.795A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Proline residue: B 147 - end of helix Processing helix chain 'B' and resid 156 through 180 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 184 through 192 Processing helix chain 'B' and resid 197 through 203 Processing helix chain 'B' and resid 205 through 233 removed outlier: 5.809A pdb=" N GLY B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N MET B 233 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 252 through 276 removed outlier: 3.876A pdb=" N LYS B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 276 " --> pdb=" O PHE B 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 25 Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 123 through 134 removed outlier: 4.947A pdb=" N GLY C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN C 134 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 152 Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 167 through 179 Processing helix chain 'C' and resid 191 through 194 removed outlier: 3.802A pdb=" N ALA C 194 " --> pdb=" O ALA C 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 197 through 213 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 251 through 254 No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 261 through 264 No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 357 through 360 No H-bonds generated for 'chain 'C' and resid 357 through 360' Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.131A pdb=" N GLU C 387 " --> pdb=" O GLY C 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 25 Processing helix chain 'D' and resid 31 through 38 Processing helix chain 'D' and resid 68 through 74 Processing helix chain 'D' and resid 97 through 106 Processing helix chain 'D' and resid 123 through 134 removed outlier: 4.948A pdb=" N GLY D 130 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN D 134 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 191 through 194 removed outlier: 3.802A pdb=" N ALA D 194 " --> pdb=" O ALA D 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 191 through 194' Processing helix chain 'D' and resid 197 through 213 Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 251 through 254 No H-bonds generated for 'chain 'D' and resid 251 through 254' Processing helix chain 'D' and resid 261 through 264 No H-bonds generated for 'chain 'D' and resid 261 through 264' Processing helix chain 'D' and resid 293 through 303 Processing helix chain 'D' and resid 323 through 331 Processing helix chain 'D' and resid 359 through 362 No H-bonds generated for 'chain 'D' and resid 359 through 362' Processing helix chain 'D' and resid 383 through 389 removed outlier: 4.131A pdb=" N GLU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= B, first strand: chain 'C' and resid 307 through 311 Processing sheet with id= C, first strand: chain 'D' and resid 57 through 59 Processing sheet with id= D, first strand: chain 'D' and resid 307 through 311 474 hydrogen bonds defined for protein. 1416 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: 2.68 Time building geometry restraints manager: 4.61 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: 3207 1.34 - 1.45: 1180 1.45 - 1.57: 5721 1.57 - 1.69: 4 1.69 - 1.81: 100 Bond restraints: 10212 Sorted by residual: bond pdb=" C5' 2BA C 501 " pdb=" O5' 2BA C 501 " ideal model delta sigma weight residual 1.433 1.357 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb="C3'1 2BA C 501 " pdb="O3'1 2BA C 501 " ideal model delta sigma weight residual 1.418 1.350 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb="C5'1 2BA C 501 " pdb="O5'1 2BA C 501 " ideal model delta sigma weight residual 1.427 1.363 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" N VAL D 353 " pdb=" CA VAL D 353 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.14e-02 7.69e+03 9.17e+00 bond pdb=" N LEU C 352 " pdb=" CA LEU C 352 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.22e-02 6.72e+03 9.11e+00 ... (remaining 10207 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.14: 214 105.14 - 112.36: 5424 112.36 - 119.58: 3280 119.58 - 126.80: 4766 126.80 - 134.02: 144 Bond angle restraints: 13828 Sorted by residual: angle pdb=" C SER A 16 " pdb=" N SER A 17 " pdb=" CA SER A 17 " ideal model delta sigma weight residual 120.54 132.77 -12.23 1.35e+00 5.49e-01 8.21e+01 angle pdb=" C SER B 16 " pdb=" N SER B 17 " pdb=" CA SER B 17 " ideal model delta sigma weight residual 120.54 132.76 -12.22 1.35e+00 5.49e-01 8.19e+01 angle pdb=" C LEU B 40 " pdb=" N MET B 41 " pdb=" CA MET B 41 " ideal model delta sigma weight residual 120.44 131.09 -10.65 1.30e+00 5.92e-01 6.71e+01 angle pdb=" C GLY A 43 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta sigma weight residual 120.60 131.11 -10.51 1.29e+00 6.01e-01 6.64e+01 angle pdb=" C LEU A 40 " pdb=" N MET A 41 " pdb=" CA MET A 41 " ideal model delta sigma weight residual 120.44 131.03 -10.59 1.30e+00 5.92e-01 6.64e+01 ... (remaining 13823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.05: 5988 23.05 - 46.10: 223 46.10 - 69.16: 47 69.16 - 92.21: 6 92.21 - 115.26: 6 Dihedral angle restraints: 6270 sinusoidal: 2536 harmonic: 3734 Sorted by residual: dihedral pdb=" CA ILE D 218 " pdb=" C ILE D 218 " pdb=" N ILE D 219 " pdb=" CA ILE D 219 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ILE C 218 " pdb=" C ILE C 218 " pdb=" N ILE C 219 " pdb=" CA ILE C 219 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C5' 2BA C 501 " pdb=" O5' 2BA C 501 " pdb=" P 2BA C 501 " pdb=" O2P 2BA C 501 " ideal model delta sinusoidal sigma weight residual -34.39 80.87 -115.26 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 6267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 1647 0.172 - 0.345: 22 0.345 - 0.517: 11 0.517 - 0.690: 2 0.690 - 0.862: 6 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CG LEU A 66 " pdb=" CB LEU A 66 " pdb=" CD1 LEU A 66 " pdb=" CD2 LEU A 66 " both_signs ideal model delta sigma weight residual False -2.59 -1.73 -0.86 2.00e-01 2.50e+01 1.86e+01 chirality pdb=" CG LEU B 66 " pdb=" CB LEU B 66 " pdb=" CD1 LEU B 66 " pdb=" CD2 LEU B 66 " both_signs ideal model delta sigma weight residual False -2.59 -1.73 -0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" CG LEU B 208 " pdb=" CB LEU B 208 " pdb=" CD1 LEU B 208 " pdb=" CD2 LEU B 208 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.35e+01 ... (remaining 1685 not shown) Planarity restraints: 1732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 34 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C GLN A 34 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN A 34 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS A 35 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 34 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C GLN B 34 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN B 34 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS B 35 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 61 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C THR A 61 " 0.032 2.00e-02 2.50e+03 pdb=" O THR A 61 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE A 62 " -0.011 2.00e-02 2.50e+03 ... (remaining 1729 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1330 2.74 - 3.28: 11559 3.28 - 3.82: 16411 3.82 - 4.36: 20037 4.36 - 4.90: 33918 Nonbonded interactions: 83255 Sorted by model distance: nonbonded pdb=" O ASP B 20 " pdb=" OG SER B 24 " model vdw 2.205 2.440 nonbonded pdb=" O ASP A 20 " pdb=" OG SER A 24 " model vdw 2.205 2.440 nonbonded pdb=" O LYS D 158 " pdb=" OD1 ASP D 159 " model vdw 2.219 3.040 nonbonded pdb=" O LYS C 158 " pdb=" OD1 ASP C 159 " model vdw 2.220 3.040 nonbonded pdb=" N ASP C 371 " pdb=" O PHE C 375 " model vdw 2.228 2.520 ... (remaining 83250 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' } ncs_group { reference = (chain 'C' and resid 3 through 391) selection = chain 'D' } 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 group one per residue 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: 0.830 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: 4.240 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.940 Find NCS groups from input model: 0.580 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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 0.076 10212 Z= 0.427 Angle : 1.010 12.232 13828 Z= 0.616 Chirality : 0.085 0.862 1688 Planarity : 0.004 0.034 1732 Dihedral : 13.736 115.258 3850 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 0.45 % Allowed : 1.18 % Favored : 98.37 % 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: -5.40 (0.17), residues: 1296 helix: -2.87 (0.14), residues: 764 sheet: -5.40 (0.25), residues: 98 loop : -4.16 (0.23), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 21 HIS 0.004 0.002 HIS C 223 PHE 0.012 0.001 PHE D 115 TYR 0.005 0.001 TYR B 144 ARG 0.004 0.000 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 348 time to evaluate : 1.239 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 93 ASP cc_start: 0.7838 (m-30) cc_final: 0.7175 (m-30) REVERT: C 284 LEU cc_start: 0.8771 (mt) cc_final: 0.8321 (mm) REVERT: C 353 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7192 (m) REVERT: D 24 MET cc_start: 0.8969 (mtt) cc_final: 0.8225 (mmm) REVERT: D 129 TYR cc_start: 0.8633 (t80) cc_final: 0.8377 (t80) REVERT: D 160 GLN cc_start: 0.7918 (mt0) cc_final: 0.7653 (mt0) REVERT: D 313 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8388 (tptt) outliers start: 5 outliers final: 0 residues processed: 352 average time/residue: 0.2505 time to fit residues: 117.9749 Evaluate side-chains 193 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 56.8751 > 50: distance: 84 - 103: 6.530 distance: 88 - 114: 22.768 distance: 94 - 121: 28.844 distance: 97 - 103: 6.621 distance: 98 - 125: 24.015 distance: 103 - 104: 5.285 distance: 104 - 105: 19.056 distance: 104 - 107: 22.622 distance: 105 - 106: 14.628 distance: 105 - 114: 5.629 distance: 106 - 133: 5.698 distance: 107 - 108: 34.166 distance: 108 - 109: 22.915 distance: 109 - 110: 25.676 distance: 110 - 111: 19.906 distance: 111 - 112: 18.573 distance: 111 - 113: 14.212 distance: 114 - 115: 17.669 distance: 115 - 116: 18.326 distance: 115 - 118: 30.778 distance: 116 - 117: 20.349 distance: 116 - 121: 31.063 distance: 117 - 138: 46.780 distance: 118 - 119: 21.471 distance: 118 - 120: 19.725 distance: 121 - 122: 32.838 distance: 122 - 123: 14.782 distance: 123 - 124: 10.070 distance: 123 - 125: 12.199 distance: 124 - 149: 23.022 distance: 125 - 126: 10.015 distance: 126 - 127: 6.575 distance: 126 - 129: 12.615 distance: 127 - 128: 6.262 distance: 127 - 133: 27.369 distance: 128 - 154: 25.191 distance: 129 - 130: 7.593 distance: 130 - 131: 10.435 distance: 130 - 132: 5.212 distance: 133 - 134: 15.693 distance: 134 - 135: 19.373 distance: 134 - 137: 24.543 distance: 135 - 136: 18.794 distance: 135 - 138: 19.736 distance: 138 - 139: 13.054 distance: 139 - 140: 25.133 distance: 139 - 142: 23.478 distance: 140 - 141: 15.708 distance: 140 - 149: 9.137 distance: 142 - 143: 20.829 distance: 143 - 144: 25.957 distance: 144 - 145: 14.562 distance: 145 - 146: 3.929 distance: 146 - 147: 16.285 distance: 146 - 148: 16.514 distance: 149 - 150: 13.783 distance: 150 - 151: 11.213 distance: 150 - 153: 8.484 distance: 151 - 152: 4.505 distance: 151 - 154: 4.984 distance: 154 - 155: 14.512 distance: 155 - 156: 18.472 distance: 155 - 158: 22.785 distance: 156 - 157: 15.799 distance: 156 - 162: 23.507 distance: 158 - 159: 13.651 distance: 159 - 160: 32.331 distance: 159 - 161: 16.998 distance: 162 - 163: 7.153 distance: 163 - 164: 17.142 distance: 163 - 166: 11.482 distance: 164 - 165: 10.939 distance: 164 - 167: 20.041 distance: 167 - 168: 6.688 distance: 168 - 169: 8.933 distance: 168 - 171: 36.967 distance: 169 - 170: 27.330 distance: 171 - 172: 36.210 distance: 172 - 173: 44.319 distance: 172 - 174: 15.038