Starting phenix.real_space_refine on Sun Aug 4 06:38:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g15_29662/08_2024/8g15_29662.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g15_29662/08_2024/8g15_29662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g15_29662/08_2024/8g15_29662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g15_29662/08_2024/8g15_29662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g15_29662/08_2024/8g15_29662.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g15_29662/08_2024/8g15_29662.cif" } resolution = 2.07 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= 0.001 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6352 2.51 5 N 1744 2.21 5 O 1912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 29": "OD1" <-> "OD2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B ASP 141": "OD1" <-> "OD2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D ARG 234": "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: 10056 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.55, per 1000 atoms: 0.65 Number of scatterers: 10056 At special positions: 0 Unit cell: (99.365, 102.705, 89.345, 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 48 16.00 O 1912 8.00 N 1744 7.00 C 6352 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: 3.57 Conformation dependent library (CDL) restraints added in 1.8 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 38.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.565A pdb=" N ILE A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.832A pdb=" N GLN A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.520A pdb=" N TYR A 140 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 169 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.517A pdb=" N ASN A 287 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 334 removed outlier: 3.519A pdb=" N VAL A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.566A pdb=" N ILE B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.833A pdb=" N GLN B 113 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.520A pdb=" N TYR B 140 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 169 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.517A pdb=" N ASN B 287 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 334 removed outlier: 3.518A pdb=" N VAL B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 26 Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.564A pdb=" N ILE C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.831A pdb=" N GLN C 113 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.520A pdb=" N TYR C 140 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 169 Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.516A pdb=" N ASN C 287 " --> pdb=" O SER C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 334 removed outlier: 3.516A pdb=" N VAL C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 26 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.565A pdb=" N ILE D 85 " --> pdb=" O PRO D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 110 through 115 removed outlier: 3.900A pdb=" N GLN D 113 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.521A pdb=" N TYR D 140 " --> pdb=" O HIS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 169 Proline residue: D 159 - end of helix Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.518A pdb=" N ASN D 287 " --> pdb=" O SER D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 334 removed outlier: 3.518A pdb=" N VAL D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 5.941A pdb=" N VAL A 31 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL A 8 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A 33 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 95 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.571A pdb=" N THR A 229 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 172 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 12.260A pdb=" N PHE A 307 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N GLY A 300 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N LYS A 309 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N GLY A 298 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE A 311 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 5.938A pdb=" N VAL B 31 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL B 6 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 32 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL B 95 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.531A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 172 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 12.258A pdb=" N PHE B 307 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N GLY B 300 " --> pdb=" O PHE B 307 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N LYS B 309 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLY B 298 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE B 311 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 63 removed outlier: 5.939A pdb=" N VAL C 31 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 6 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 32 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL C 95 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.585A pdb=" N THR C 229 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU C 172 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 12.256A pdb=" N PHE C 307 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 11.113A pdb=" N GLY C 300 " --> pdb=" O PHE C 307 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N LYS C 309 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N GLY C 298 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE C 311 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 63 removed outlier: 5.941A pdb=" N VAL D 31 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL D 8 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE D 33 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL D 95 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.586A pdb=" N THR D 229 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU D 172 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 12.257A pdb=" N PHE D 307 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N GLY D 300 " --> pdb=" O PHE D 307 " (cutoff:3.500A) removed outlier: 10.831A pdb=" N LYS D 309 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N GLY D 298 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE D 311 " --> pdb=" O ASP D 296 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1260 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: 2.87 Time building geometry restraints manager: 3.97 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: 3109 1.34 - 1.45: 1446 1.45 - 1.57: 5617 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 10256 Sorted by residual: bond pdb=" C SER D 312 " pdb=" N TRP D 313 " ideal model delta sigma weight residual 1.329 1.482 -0.152 1.38e-02 5.25e+03 1.22e+02 bond pdb=" C SER B 312 " pdb=" N TRP B 313 " ideal model delta sigma weight residual 1.329 1.477 -0.148 1.38e-02 5.25e+03 1.15e+02 bond pdb=" C SER C 312 " pdb=" N TRP C 313 " ideal model delta sigma weight residual 1.329 1.475 -0.146 1.38e-02 5.25e+03 1.12e+02 bond pdb=" N PRO D 208 " pdb=" CD PRO D 208 " ideal model delta sigma weight residual 1.473 1.542 -0.069 1.40e-02 5.10e+03 2.42e+01 bond pdb=" N VAL D 188 " pdb=" CA VAL D 188 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.60e+00 ... (remaining 10251 not shown) Histogram of bond angle deviations from ideal: 94.94 - 102.92: 72 102.92 - 110.91: 3656 110.91 - 118.90: 4721 118.90 - 126.89: 5331 126.89 - 134.88: 116 Bond angle restraints: 13896 Sorted by residual: angle pdb=" O SER B 312 " pdb=" C SER B 312 " pdb=" N TRP B 313 " ideal model delta sigma weight residual 123.24 94.94 28.30 1.23e+00 6.61e-01 5.30e+02 angle pdb=" O SER D 312 " pdb=" C SER D 312 " pdb=" N TRP D 313 " ideal model delta sigma weight residual 123.24 94.94 28.30 1.23e+00 6.61e-01 5.29e+02 angle pdb=" O SER C 312 " pdb=" C SER C 312 " pdb=" N TRP C 313 " ideal model delta sigma weight residual 123.24 95.09 28.15 1.23e+00 6.61e-01 5.24e+02 angle pdb=" CA SER D 312 " pdb=" C SER D 312 " pdb=" N TRP D 313 " ideal model delta sigma weight residual 115.58 134.88 -19.30 1.48e+00 4.57e-01 1.70e+02 angle pdb=" CA SER B 312 " pdb=" C SER B 312 " pdb=" N TRP B 313 " ideal model delta sigma weight residual 115.58 134.81 -19.23 1.48e+00 4.57e-01 1.69e+02 ... (remaining 13891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 5348 17.21 - 34.42: 514 34.42 - 51.63: 147 51.63 - 68.84: 53 68.84 - 86.05: 13 Dihedral angle restraints: 6075 sinusoidal: 2299 harmonic: 3776 Sorted by residual: dihedral pdb=" CA ASN B 239 " pdb=" C ASN B 239 " pdb=" N VAL B 240 " pdb=" CA VAL B 240 " ideal model delta harmonic sigma weight residual -180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN D 239 " pdb=" C ASN D 239 " pdb=" N VAL D 240 " pdb=" CA VAL D 240 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN C 239 " pdb=" C ASN C 239 " pdb=" N VAL C 240 " pdb=" CA VAL C 240 " ideal model delta harmonic sigma weight residual -180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 6072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 968 0.040 - 0.080: 381 0.080 - 0.120: 172 0.120 - 0.160: 46 0.160 - 0.200: 9 Chirality restraints: 1576 Sorted by residual: chirality pdb=" CA ILE C 207 " pdb=" N ILE C 207 " pdb=" C ILE C 207 " pdb=" CB ILE C 207 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE D 207 " pdb=" N ILE D 207 " pdb=" C ILE D 207 " pdb=" CB ILE D 207 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE A 207 " pdb=" N ILE A 207 " pdb=" C ILE A 207 " pdb=" CB ILE A 207 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 9.97e-01 ... (remaining 1573 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 312 " -0.069 2.00e-02 2.50e+03 1.08e-01 1.16e+02 pdb=" C SER C 312 " 0.187 2.00e-02 2.50e+03 pdb=" O SER C 312 " -0.058 2.00e-02 2.50e+03 pdb=" N TRP C 313 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 312 " 0.068 2.00e-02 2.50e+03 1.06e-01 1.12e+02 pdb=" C SER B 312 " -0.183 2.00e-02 2.50e+03 pdb=" O SER B 312 " 0.057 2.00e-02 2.50e+03 pdb=" N TRP B 313 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 312 " -0.068 2.00e-02 2.50e+03 1.06e-01 1.11e+02 pdb=" C SER D 312 " 0.183 2.00e-02 2.50e+03 pdb=" O SER D 312 " -0.056 2.00e-02 2.50e+03 pdb=" N TRP D 313 " -0.058 2.00e-02 2.50e+03 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1932 2.77 - 3.31: 8802 3.31 - 3.84: 16550 3.84 - 4.37: 20098 4.37 - 4.90: 35079 Nonbonded interactions: 82461 Sorted by model distance: nonbonded pdb=" O ASN B 239 " pdb=" OD1 ASN B 316 " model vdw 2.243 3.040 nonbonded pdb=" O ASN D 239 " pdb=" OD1 ASN D 316 " model vdw 2.243 3.040 nonbonded pdb=" O ASN C 239 " pdb=" OD1 ASN C 316 " model vdw 2.251 3.040 nonbonded pdb=" O ASN A 239 " pdb=" OD1 ASN A 316 " model vdw 2.255 3.040 nonbonded pdb=" NH2 ARG C 118 " pdb=" OD1 ASN C 142 " model vdw 2.257 3.120 ... (remaining 82456 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 'B' selection = chain 'C' 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 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 30.020 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 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 : 0.005 0.152 10256 Z= 0.364 Angle : 0.963 28.304 13896 Z= 0.638 Chirality : 0.054 0.200 1576 Planarity : 0.009 0.120 1804 Dihedral : 16.072 86.054 3667 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.59 % Allowed : 16.21 % Favored : 82.19 % 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: -1.62 (0.22), residues: 1328 helix: -2.29 (0.18), residues: 388 sheet: 0.29 (0.40), residues: 220 loop : -0.71 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 87 HIS 0.003 0.001 HIS B 53 PHE 0.009 0.001 PHE B 233 TYR 0.010 0.002 TYR D 42 ARG 0.021 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.163 Fit side-chains outliers start: 17 outliers final: 15 residues processed: 104 average time/residue: 1.4241 time to fit residues: 157.8388 Evaluate side-chains 97 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN B 149 ASN C 149 ASN D 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10256 Z= 0.264 Angle : 0.589 6.925 13896 Z= 0.326 Chirality : 0.048 0.155 1576 Planarity : 0.006 0.054 1804 Dihedral : 6.106 46.822 1431 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.00 % Allowed : 14.71 % Favored : 82.29 % 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: -0.43 (0.23), residues: 1328 helix: -0.06 (0.24), residues: 392 sheet: 0.49 (0.40), residues: 212 loop : -0.59 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 87 HIS 0.002 0.001 HIS B 53 PHE 0.010 0.001 PHE A 286 TYR 0.014 0.001 TYR C 314 ARG 0.008 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 78 time to evaluate : 1.395 Fit side-chains outliers start: 32 outliers final: 23 residues processed: 101 average time/residue: 1.4266 time to fit residues: 153.8671 Evaluate side-chains 94 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 10256 Z= 0.438 Angle : 0.675 9.640 13896 Z= 0.372 Chirality : 0.053 0.152 1576 Planarity : 0.006 0.055 1804 Dihedral : 6.816 56.845 1423 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.00 % Allowed : 15.46 % Favored : 81.54 % 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: -0.13 (0.24), residues: 1328 helix: 0.62 (0.25), residues: 372 sheet: 0.46 (0.39), residues: 204 loop : -0.57 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 87 HIS 0.003 0.001 HIS D 53 PHE 0.015 0.002 PHE D 318 TYR 0.015 0.002 TYR D 314 ARG 0.006 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 1.114 Fit side-chains outliers start: 32 outliers final: 23 residues processed: 97 average time/residue: 1.6912 time to fit residues: 173.9041 Evaluate side-chains 95 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 72 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10256 Z= 0.193 Angle : 0.541 7.725 13896 Z= 0.296 Chirality : 0.047 0.140 1576 Planarity : 0.005 0.053 1804 Dihedral : 6.484 59.624 1423 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.19 % Allowed : 15.93 % Favored : 80.88 % 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: 0.11 (0.24), residues: 1328 helix: 0.99 (0.26), residues: 380 sheet: 0.31 (0.37), residues: 228 loop : -0.45 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 313 HIS 0.002 0.001 HIS A 179 PHE 0.007 0.001 PHE B 318 TYR 0.010 0.001 TYR D 314 ARG 0.009 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 78 time to evaluate : 1.182 Fit side-chains outliers start: 34 outliers final: 23 residues processed: 106 average time/residue: 1.3450 time to fit residues: 152.9255 Evaluate side-chains 94 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10256 Z= 0.355 Angle : 0.630 9.182 13896 Z= 0.346 Chirality : 0.051 0.147 1576 Planarity : 0.006 0.064 1804 Dihedral : 6.205 50.726 1423 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.81 % Allowed : 15.56 % Favored : 81.63 % 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: 0.02 (0.24), residues: 1328 helix: 0.94 (0.26), residues: 376 sheet: 0.41 (0.38), residues: 204 loop : -0.56 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 87 HIS 0.003 0.001 HIS C 53 PHE 0.010 0.002 PHE C 286 TYR 0.014 0.002 TYR C 314 ARG 0.009 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 72 time to evaluate : 1.225 Fit side-chains outliers start: 30 outliers final: 24 residues processed: 98 average time/residue: 1.4151 time to fit residues: 147.9645 Evaluate side-chains 96 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN C 149 ASN D 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10256 Z= 0.188 Angle : 0.544 7.745 13896 Z= 0.296 Chirality : 0.047 0.139 1576 Planarity : 0.005 0.056 1804 Dihedral : 5.754 48.597 1420 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.72 % Allowed : 15.18 % Favored : 82.10 % 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: 0.27 (0.25), residues: 1328 helix: 1.25 (0.27), residues: 376 sheet: 0.28 (0.36), residues: 236 loop : -0.39 (0.26), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 313 HIS 0.002 0.001 HIS D 179 PHE 0.007 0.001 PHE D 286 TYR 0.010 0.001 TYR B 314 ARG 0.010 0.001 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 76 time to evaluate : 1.061 Fit side-chains outliers start: 29 outliers final: 24 residues processed: 100 average time/residue: 1.3616 time to fit residues: 145.7311 Evaluate side-chains 99 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 79 optimal weight: 0.2980 chunk 77 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10256 Z= 0.293 Angle : 0.602 8.849 13896 Z= 0.329 Chirality : 0.050 0.145 1576 Planarity : 0.006 0.065 1804 Dihedral : 5.971 48.423 1420 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.09 % Allowed : 14.81 % Favored : 82.10 % 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: 0.11 (0.24), residues: 1328 helix: 1.14 (0.27), residues: 376 sheet: 0.43 (0.38), residues: 204 loop : -0.56 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 87 HIS 0.002 0.001 HIS C 53 PHE 0.009 0.001 PHE B 286 TYR 0.012 0.001 TYR D 314 ARG 0.011 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 72 time to evaluate : 1.175 Fit side-chains outliers start: 33 outliers final: 28 residues processed: 97 average time/residue: 1.4505 time to fit residues: 150.0953 Evaluate side-chains 100 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10256 Z= 0.171 Angle : 0.537 7.245 13896 Z= 0.292 Chirality : 0.046 0.137 1576 Planarity : 0.005 0.059 1804 Dihedral : 5.525 45.166 1420 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.06 % Allowed : 16.12 % Favored : 81.82 % 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: 0.22 (0.25), residues: 1328 helix: 1.09 (0.27), residues: 396 sheet: 0.43 (0.39), residues: 212 loop : -0.44 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.002 0.000 HIS D 179 PHE 0.006 0.001 PHE C 286 TYR 0.009 0.001 TYR C 314 ARG 0.012 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 74 time to evaluate : 1.172 Fit side-chains outliers start: 22 outliers final: 20 residues processed: 91 average time/residue: 1.4360 time to fit residues: 139.4877 Evaluate side-chains 93 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10256 Z= 0.168 Angle : 0.524 6.800 13896 Z= 0.285 Chirality : 0.046 0.137 1576 Planarity : 0.006 0.077 1804 Dihedral : 5.277 43.312 1416 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.62 % Allowed : 16.68 % Favored : 80.69 % 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: 0.21 (0.25), residues: 1328 helix: 1.13 (0.27), residues: 396 sheet: 0.45 (0.39), residues: 212 loop : -0.49 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 313 HIS 0.001 0.000 HIS C 53 PHE 0.006 0.001 PHE A 286 TYR 0.008 0.001 TYR D 314 ARG 0.019 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 71 time to evaluate : 1.138 Fit side-chains REVERT: A 335 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6176 (mp0) REVERT: D 335 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6190 (mp0) outliers start: 28 outliers final: 20 residues processed: 93 average time/residue: 1.4041 time to fit residues: 139.7920 Evaluate side-chains 93 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 335 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 70.9682 > 50: distance: 41 - 46: 28.476 distance: 46 - 47: 30.687 distance: 46 - 135: 30.884 distance: 47 - 48: 41.787 distance: 47 - 50: 27.896 distance: 48 - 49: 56.456 distance: 48 - 54: 8.139 distance: 50 - 51: 25.878 distance: 50 - 52: 27.346 distance: 51 - 53: 31.185 distance: 55 - 56: 7.782 distance: 55 - 58: 7.984 distance: 56 - 57: 59.208 distance: 56 - 60: 56.017 distance: 58 - 59: 50.709 distance: 60 - 61: 40.798 distance: 61 - 64: 27.748 distance: 65 - 66: 56.893 distance: 65 - 71: 56.164 distance: 66 - 69: 40.984 distance: 69 - 70: 40.520 distance: 73 - 74: 39.872 distance: 73 - 76: 38.970 distance: 74 - 75: 39.288 distance: 74 - 78: 40.902 distance: 78 - 79: 40.691 distance: 80 - 81: 39.654 distance: 83 - 84: 37.638 distance: 84 - 85: 40.153 distance: 85 - 86: 40.851 distance: 85 - 91: 55.785 distance: 87 - 88: 38.590 distance: 88 - 89: 40.750 distance: 88 - 90: 39.822 distance: 93 - 94: 56.137 distance: 93 - 96: 39.396 distance: 96 - 97: 31.067 distance: 97 - 98: 40.642 distance: 97 - 100: 64.971 distance: 98 - 99: 23.883 distance: 98 - 103: 3.614 distance: 100 - 101: 40.336 distance: 101 - 102: 39.931 distance: 103 - 104: 5.654 distance: 104 - 105: 25.280 distance: 104 - 107: 46.531 distance: 105 - 106: 28.213 distance: 105 - 111: 24.892 distance: 107 - 108: 29.609 distance: 109 - 110: 6.170