Starting phenix.real_space_refine (version: dev) on Sat Feb 18 17:47:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eja_31157/02_2023/7eja_31157_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eja_31157/02_2023/7eja_31157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eja_31157/02_2023/7eja_31157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eja_31157/02_2023/7eja_31157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eja_31157/02_2023/7eja_31157_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eja_31157/02_2023/7eja_31157_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.007 sd= 0.192 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 Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "R ARG 202": "NH1" <-> "NH2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R ARG 240": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R ARG 383": "NH1" <-> "NH2" Residue "R ARG 450": "NH1" <-> "NH2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "H GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8584 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1632 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 7, 'PTRANS': 4, 'TRANS': 198} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2541 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2193 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1785 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CZX': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 5.54, per 1000 atoms: 0.65 Number of scatterers: 8584 At special positions: 0 Unit cell: (88.4, 120.7, 124.95, 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 58 16.00 O 1581 8.00 N 1458 7.00 C 5487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.4 seconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 13 sheets defined 32.1% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.912A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 209 through 217 removed outlier: 4.272A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N CYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE A 216 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLU A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.566A pdb=" N ASP A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 330 through 349 Processing helix chain 'B' and resid 8 through 24 removed outlier: 3.591A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 removed outlier: 3.802A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 46 removed outlier: 4.601A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 73 Processing helix chain 'R' and resid 82 through 107 removed outlier: 3.571A pdb=" N PHE R 86 " --> pdb=" O GLN R 83 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL R 97 " --> pdb=" O ASP R 94 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL R 101 " --> pdb=" O ALA R 98 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE R 102 " --> pdb=" O THR R 99 " (cutoff:3.500A) Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 121 through 150 Processing helix chain 'R' and resid 153 through 159 removed outlier: 4.988A pdb=" N LEU R 158 " --> pdb=" O ILE R 154 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS R 159 " --> pdb=" O GLU R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 181 Processing helix chain 'R' and resid 209 through 241 removed outlier: 3.683A pdb=" N ILE R 213 " --> pdb=" O LYS R 209 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER R 214 " --> pdb=" O TRP R 210 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ALA R 222 " --> pdb=" O GLY R 218 " (cutoff:3.500A) Proline residue: R 223 - end of helix Processing helix chain 'R' and resid 377 through 410 removed outlier: 3.698A pdb=" N ASN R 382 " --> pdb=" O ARG R 378 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE R 398 " --> pdb=" O VAL R 394 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL R 399 " --> pdb=" O ILE R 395 " (cutoff:3.500A) Proline residue: R 404 - end of helix Processing helix chain 'R' and resid 421 through 442 removed outlier: 3.950A pdb=" N ASN R 437 " --> pdb=" O SER R 434 " (cutoff:3.500A) Proline residue: R 438 - end of helix Processing helix chain 'R' and resid 446 through 456 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 264 through 269 removed outlier: 4.030A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 34 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 201 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.931A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.513A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.956A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 201 removed outlier: 3.661A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 250 through 253 Processing sheet with id= G, first strand: chain 'B' and resid 296 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.590A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.804A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 92 through 99 removed outlier: 6.315A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 134 through 136 removed outlier: 6.949A pdb=" N LYS H 232 " --> pdb=" O VAL H 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'H' and resid 143 through 148 removed outlier: 3.952A pdb=" N PHE H 200 " --> pdb=" O CYS H 147 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 214 through 219 345 hydrogen bonds defined for protein. 840 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: 2.34 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1385 1.31 - 1.44: 2457 1.44 - 1.56: 4847 1.56 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 8768 Sorted by residual: bond pdb=" N ILE R 123 " pdb=" CA ILE R 123 " ideal model delta sigma weight residual 1.461 1.396 0.065 1.17e-02 7.31e+03 3.07e+01 bond pdb=" N ASN A 346 " pdb=" CA ASN A 346 " ideal model delta sigma weight residual 1.459 1.400 0.060 1.20e-02 6.94e+03 2.47e+01 bond pdb=" CA TYR R 156 " pdb=" C TYR R 156 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.29e-02 6.01e+03 2.45e+01 bond pdb=" CA ASN A 346 " pdb=" C ASN A 346 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.26e-02 6.30e+03 2.30e+01 bond pdb=" N PRO R 438 " pdb=" CD PRO R 438 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.22e+01 ... (remaining 8763 not shown) Histogram of bond angle deviations from ideal: 99.74 - 107.23: 241 107.23 - 114.71: 5135 114.71 - 122.19: 4958 122.19 - 129.67: 1483 129.67 - 137.16: 64 Bond angle restraints: 11881 Sorted by residual: angle pdb=" N ARG R 378 " pdb=" CA ARG R 378 " pdb=" C ARG R 378 " ideal model delta sigma weight residual 111.28 121.19 -9.91 1.09e+00 8.42e-01 8.27e+01 angle pdb=" N LYS A 211 " pdb=" CA LYS A 211 " pdb=" C LYS A 211 " ideal model delta sigma weight residual 111.14 119.75 -8.61 1.08e+00 8.57e-01 6.36e+01 angle pdb=" N HIS A 214 " pdb=" CA HIS A 214 " pdb=" C HIS A 214 " ideal model delta sigma weight residual 111.28 119.83 -8.55 1.09e+00 8.42e-01 6.16e+01 angle pdb=" N LYS R 159 " pdb=" CA LYS R 159 " pdb=" C LYS R 159 " ideal model delta sigma weight residual 113.15 122.41 -9.26 1.19e+00 7.06e-01 6.06e+01 angle pdb=" N CYS R 121 " pdb=" CA CYS R 121 " pdb=" C CYS R 121 " ideal model delta sigma weight residual 112.90 103.56 9.34 1.31e+00 5.83e-01 5.08e+01 ... (remaining 11876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4741 17.69 - 35.39: 349 35.39 - 53.08: 70 53.08 - 70.78: 7 70.78 - 88.47: 7 Dihedral angle restraints: 5174 sinusoidal: 1996 harmonic: 3178 Sorted by residual: dihedral pdb=" N ILE R 123 " pdb=" C ILE R 123 " pdb=" CA ILE R 123 " pdb=" CB ILE R 123 " ideal model delta harmonic sigma weight residual 123.40 109.48 13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" C PHE A 216 " pdb=" N PHE A 216 " pdb=" CA PHE A 216 " pdb=" CB PHE A 216 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" CA ILE G 25 " pdb=" C ILE G 25 " pdb=" N ASP G 26 " pdb=" CA ASP G 26 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 5171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1292 0.110 - 0.219: 39 0.219 - 0.329: 12 0.329 - 0.438: 4 0.438 - 0.548: 2 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA PHE A 216 " pdb=" N PHE A 216 " pdb=" C PHE A 216 " pdb=" CB PHE A 216 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" CA GLU A 217 " pdb=" N GLU A 217 " pdb=" C GLU A 217 " pdb=" CB GLU A 217 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA LYS R 159 " pdb=" N LYS R 159 " pdb=" C LYS R 159 " pdb=" CB LYS R 159 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 1346 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 161 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO R 162 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 162 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 162 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 183 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C THR A 183 " -0.034 2.00e-02 2.50e+03 pdb=" O THR A 183 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 184 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 282 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO A 283 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.026 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 4 2.21 - 2.88: 3396 2.88 - 3.55: 12495 3.55 - 4.23: 18707 4.23 - 4.90: 31496 Nonbonded interactions: 66098 Sorted by model distance: nonbonded pdb=" CE2 PHE H 32 " pdb=" NH2 ARG H 98 " model vdw 1.533 3.420 nonbonded pdb=" OE1 GLN R 83 " pdb=" NH2 ARG R 160 " model vdw 1.893 2.520 nonbonded pdb=" CZ PHE H 32 " pdb=" NH2 ARG H 98 " model vdw 2.085 3.420 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.175 2.440 nonbonded pdb=" OG SER H 192 " pdb=" OG1 THR H 203 " model vdw 2.215 2.440 ... (remaining 66093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5487 2.51 5 N 1458 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.390 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: 4.690 Check model and map are aligned: 0.130 Process input model: 26.540 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 0.066 8768 Z= 0.292 Angle : 0.845 14.408 11881 Z= 0.532 Chirality : 0.059 0.548 1349 Planarity : 0.004 0.055 1496 Dihedral : 13.050 88.469 3113 Min Nonbonded Distance : 1.533 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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 (0.26), residues: 1075 helix: 1.20 (0.28), residues: 341 sheet: -0.37 (0.33), residues: 263 loop : -1.32 (0.29), residues: 471 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.2491 time to fit residues: 75.1141 Evaluate side-chains 147 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0270 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 55 optimal weight: 0.0060 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 40.0000 overall best weight: 0.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS R 138 HIS R 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8768 Z= 0.165 Angle : 0.722 14.487 11881 Z= 0.355 Chirality : 0.044 0.157 1349 Planarity : 0.005 0.056 1496 Dihedral : 4.340 21.298 1185 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.46 (0.26), residues: 1075 helix: 0.91 (0.27), residues: 346 sheet: -0.06 (0.34), residues: 255 loop : -1.34 (0.28), residues: 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 190 average time/residue: 0.2312 time to fit residues: 59.1774 Evaluate side-chains 155 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1251 time to fit residues: 3.7378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.0040 chunk 30 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 333 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 8768 Z= 0.282 Angle : 0.729 13.292 11881 Z= 0.367 Chirality : 0.043 0.144 1349 Planarity : 0.005 0.054 1496 Dihedral : 4.500 19.944 1185 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.54 (0.26), residues: 1075 helix: 0.86 (0.28), residues: 340 sheet: -0.19 (0.34), residues: 263 loop : -1.33 (0.29), residues: 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 164 average time/residue: 0.2321 time to fit residues: 52.0374 Evaluate side-chains 146 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0795 time to fit residues: 3.1539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 104 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN G 18 GLN G 24 ASN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 8768 Z= 0.365 Angle : 0.766 13.963 11881 Z= 0.389 Chirality : 0.044 0.163 1349 Planarity : 0.005 0.047 1496 Dihedral : 4.807 20.299 1185 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.86 (0.26), residues: 1075 helix: 0.63 (0.28), residues: 338 sheet: -0.40 (0.33), residues: 274 loop : -1.54 (0.28), residues: 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 157 average time/residue: 0.2100 time to fit residues: 45.8357 Evaluate side-chains 150 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0836 time to fit residues: 3.6860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8768 Z= 0.210 Angle : 0.742 17.122 11881 Z= 0.358 Chirality : 0.044 0.179 1349 Planarity : 0.004 0.049 1496 Dihedral : 4.575 21.286 1185 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.73 (0.26), residues: 1075 helix: 0.75 (0.29), residues: 334 sheet: -0.28 (0.33), residues: 265 loop : -1.48 (0.28), residues: 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 165 average time/residue: 0.2174 time to fit residues: 49.2837 Evaluate side-chains 146 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1170 time to fit residues: 3.0963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.0170 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8768 Z= 0.173 Angle : 0.747 14.431 11881 Z= 0.352 Chirality : 0.043 0.169 1349 Planarity : 0.004 0.049 1496 Dihedral : 4.394 21.126 1185 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.74 (0.26), residues: 1075 helix: 0.66 (0.29), residues: 335 sheet: -0.24 (0.34), residues: 250 loop : -1.44 (0.28), residues: 490 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 1.094 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 outliers start: 9 outliers final: 3 residues processed: 166 average time/residue: 0.2187 time to fit residues: 49.4888 Evaluate side-chains 142 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0801 time to fit residues: 1.8927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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-4877/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-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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: 64.9018 > 50: distance: 0 - 1: 38.672 distance: 1 - 2: 20.641 distance: 1 - 4: 19.234 distance: 2 - 3: 23.457 distance: 4 - 5: 16.174 distance: 5 - 6: 17.111 distance: 5 - 7: 22.447 distance: 6 - 8: 16.196 distance: 7 - 9: 4.567 distance: 8 - 10: 9.122 distance: 9 - 10: 9.065 distance: 10 - 11: 8.384 distance: 12 - 13: 38.498 distance: 13 - 14: 18.688 distance: 13 - 16: 27.954 distance: 14 - 15: 11.181 distance: 14 - 18: 19.828 distance: 16 - 17: 44.409 distance: 18 - 19: 19.223 distance: 19 - 20: 34.019 distance: 19 - 22: 56.974 distance: 20 - 21: 7.440 distance: 20 - 26: 9.792 distance: 23 - 25: 15.577 distance: 26 - 27: 19.495 distance: 27 - 28: 38.311 distance: 27 - 30: 16.082 distance: 28 - 29: 39.817 distance: 28 - 35: 30.438 distance: 30 - 31: 24.416 distance: 31 - 32: 28.499 distance: 32 - 33: 20.071 distance: 32 - 34: 20.598 distance: 35 - 36: 7.244 distance: 36 - 37: 7.706 distance: 37 - 38: 20.845 distance: 37 - 42: 10.964 distance: 38 - 57: 47.259 distance: 39 - 40: 9.412 distance: 42 - 43: 16.139 distance: 43 - 44: 29.611 distance: 43 - 46: 20.729 distance: 44 - 45: 10.228 distance: 44 - 49: 44.446 distance: 45 - 64: 28.049 distance: 46 - 47: 4.004 distance: 46 - 48: 7.149 distance: 49 - 50: 39.050 distance: 50 - 51: 41.710 distance: 50 - 53: 38.808 distance: 51 - 52: 32.571 distance: 51 - 57: 15.450 distance: 52 - 72: 30.668 distance: 53 - 54: 8.478 distance: 54 - 55: 6.119 distance: 54 - 56: 52.335 distance: 57 - 58: 14.478 distance: 58 - 59: 29.183 distance: 58 - 61: 18.246 distance: 59 - 60: 17.817 distance: 59 - 64: 10.447 distance: 60 - 79: 33.622 distance: 61 - 62: 5.306 distance: 61 - 63: 30.427 distance: 64 - 65: 28.856 distance: 65 - 66: 5.877 distance: 65 - 68: 42.153 distance: 66 - 67: 14.583 distance: 66 - 72: 32.493 distance: 67 - 85: 28.472 distance: 68 - 69: 11.731 distance: 69 - 70: 17.648 distance: 69 - 71: 10.974 distance: 75 - 93: 3.001