Starting phenix.real_space_refine on Thu Mar 14 22:01:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfc_33785/03_2024/7yfc_33785_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfc_33785/03_2024/7yfc_33785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfc_33785/03_2024/7yfc_33785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfc_33785/03_2024/7yfc_33785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfc_33785/03_2024/7yfc_33785_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfc_33785/03_2024/7yfc_33785_updated.pdb" } resolution = 3.0 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= 1.000 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 59 5.16 5 C 6294 2.51 5 N 1686 2.21 5 O 1843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 182": "OE1" <-> "OE2" Residue "R TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9882 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1912 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1799 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2096 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 252} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'CLR': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.50, per 1000 atoms: 0.56 Number of scatterers: 9882 At special positions: 0 Unit cell: (88.88, 126.72, 127.6, 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 59 16.00 O 1843 8.00 N 1686 7.00 C 6294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " 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: 3.58 Conformation dependent library (CDL) restraints added in 1.8 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 14 sheets defined 30.7% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.004A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 275 through 278 No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 299 through 318 removed outlier: 3.522A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.816A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 49 through 75 removed outlier: 4.471A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 84 through 117 Processing helix chain 'R' and resid 119 through 123 Processing helix chain 'R' and resid 132 through 154 removed outlier: 3.570A pdb=" N TRP R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 184 through 203 Processing helix chain 'R' and resid 301 through 328 removed outlier: 4.010A pdb=" N LEU R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 4.073A pdb=" N ILE R 324 " --> pdb=" O SER R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 357 removed outlier: 3.796A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 359 through 361 No H-bonds generated for 'chain 'R' and resid 359 through 361' Processing helix chain 'R' and resid 365 through 372 Processing sheet with id= A, first strand: chain 'A' and resid 326 through 330 removed outlier: 7.226A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.823A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.829A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.087A 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: 6.862A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.905A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.784A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.687A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.812A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'C' and resid 115 through 117 removed outlier: 3.610A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU C 45 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.964A pdb=" N LYS C 244 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 189 " --> pdb=" O TRP C 176 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C 178 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU C 187 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= N, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.122A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1227 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: 2.53 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1590 1.27 - 1.40: 2602 1.40 - 1.54: 5747 1.54 - 1.68: 73 1.68 - 1.81: 85 Bond restraints: 10097 Sorted by residual: bond pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 1.503 1.132 0.371 3.40e-02 8.65e+02 1.19e+02 bond pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " ideal model delta sigma weight residual 1.492 1.218 0.274 5.00e-02 4.00e+02 2.99e+01 bond pdb=" N PRO R 355 " pdb=" CA PRO R 355 " ideal model delta sigma weight residual 1.471 1.521 -0.050 1.32e-02 5.74e+03 1.43e+01 bond pdb=" N PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.51e+00 bond pdb=" C3 CLR R 602 " pdb=" O1 CLR R 602 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.09e+00 ... (remaining 10092 not shown) Histogram of bond angle deviations from ideal: 71.73 - 84.43: 2 84.43 - 97.12: 0 97.12 - 109.81: 1188 109.81 - 122.50: 11112 122.50 - 135.19: 1391 Bond angle restraints: 13693 Sorted by residual: angle pdb=" N PRO R 355 " pdb=" CD PRO R 355 " pdb=" CG PRO R 355 " ideal model delta sigma weight residual 103.20 74.58 28.62 1.50e+00 4.44e-01 3.64e+02 angle pdb=" CA PRO R 355 " pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " ideal model delta sigma weight residual 104.50 71.73 32.77 1.90e+00 2.77e-01 2.97e+02 angle pdb=" CA PRO R 355 " pdb=" N PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 112.00 102.69 9.31 1.40e+00 5.10e-01 4.42e+01 angle pdb=" N PRO R 355 " pdb=" CA PRO R 355 " pdb=" CB PRO R 355 " ideal model delta sigma weight residual 103.48 97.38 6.10 1.00e+00 1.00e+00 3.73e+01 angle pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 106.10 125.14 -19.04 3.20e+00 9.77e-02 3.54e+01 ... (remaining 13688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 5332 22.39 - 44.78: 585 44.78 - 67.17: 75 67.17 - 89.56: 22 89.56 - 111.95: 2 Dihedral angle restraints: 6016 sinusoidal: 2358 harmonic: 3658 Sorted by residual: dihedral pdb=" N PRO R 355 " pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " pdb=" CB PRO R 355 " ideal model delta sinusoidal sigma weight residual 30.00 91.78 -61.78 1 1.50e+01 4.44e-03 2.25e+01 dihedral pdb=" C2 CLR R 602 " pdb=" C3 CLR R 602 " pdb=" C4 CLR R 602 " pdb=" C5 CLR R 602 " ideal model delta sinusoidal sigma weight residual -55.03 56.92 -111.95 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C5 CLR R 602 " pdb=" C3 CLR R 602 " pdb=" C4 CLR R 602 " pdb=" O1 CLR R 602 " ideal model delta sinusoidal sigma weight residual 175.64 64.31 111.33 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 6013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1275 0.051 - 0.102: 224 0.102 - 0.153: 42 0.153 - 0.204: 1 0.204 - 0.255: 1 Chirality restraints: 1543 Sorted by residual: chirality pdb=" CB THR B 181 " pdb=" CA THR B 181 " pdb=" OG1 THR B 181 " pdb=" CG2 THR B 181 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA TYR C 235 " pdb=" N TYR C 235 " pdb=" C TYR C 235 " pdb=" CB TYR C 235 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CA THR B 181 " pdb=" N THR B 181 " pdb=" C THR B 181 " pdb=" CB THR B 181 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1540 not shown) Planarity restraints: 1731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 354 " 0.037 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO R 355 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 355 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 355 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 40 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO C 41 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 235 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO C 236 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.025 5.00e-02 4.00e+02 ... (remaining 1728 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 692 2.74 - 3.28: 9278 3.28 - 3.82: 16110 3.82 - 4.36: 18974 4.36 - 4.90: 34547 Nonbonded interactions: 79601 Sorted by model distance: nonbonded pdb=" NH1 ARG A 205 " pdb=" OD1 ASP B 186 " model vdw 2.198 2.520 nonbonded pdb=" OG SER B 74 " pdb=" OD2 ASP B 76 " model vdw 2.239 2.440 nonbonded pdb=" NE2 GLN A 52 " pdb=" O ASP A 335 " model vdw 2.273 2.520 nonbonded pdb=" OD1 ASP N 90 " pdb=" OH TYR N 94 " model vdw 2.279 2.440 nonbonded pdb=" NH2 ARG C 180 " pdb=" OE2 GLU C 222 " model vdw 2.297 2.520 ... (remaining 79596 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 7.110 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.220 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 0.371 10097 Z= 0.207 Angle : 0.658 32.766 13693 Z= 0.356 Chirality : 0.040 0.255 1543 Planarity : 0.004 0.054 1731 Dihedral : 18.014 111.951 3645 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.09 % Allowed : 31.36 % Favored : 68.54 % 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: 1.05 (0.24), residues: 1240 helix: 2.54 (0.26), residues: 394 sheet: 0.47 (0.29), residues: 316 loop : -0.57 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 316 HIS 0.003 0.001 HIS B 311 PHE 0.015 0.001 PHE A 189 TYR 0.021 0.001 TYR C 235 ARG 0.013 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.079 Fit side-chains REVERT: B 42 ARG cc_start: 0.7413 (mmp-170) cc_final: 0.7086 (tpp-160) REVERT: R 353 VAL cc_start: 0.6955 (t) cc_final: 0.6711 (p) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 1.1658 time to fit residues: 152.2539 Evaluate side-chains 109 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 349 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0570 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10097 Z= 0.292 Angle : 0.581 11.397 13693 Z= 0.298 Chirality : 0.042 0.234 1543 Planarity : 0.004 0.049 1731 Dihedral : 5.413 40.261 1442 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.38 % Allowed : 28.08 % Favored : 65.54 % 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: 0.76 (0.24), residues: 1240 helix: 2.22 (0.26), residues: 400 sheet: 0.23 (0.28), residues: 321 loop : -0.66 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 324 PHE 0.017 0.001 PHE A 189 TYR 0.031 0.002 TYR C 235 ARG 0.010 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 104 time to evaluate : 1.076 Fit side-chains REVERT: B 13 GLN cc_start: 0.7528 (tp40) cc_final: 0.7302 (tp-100) REVERT: B 59 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: B 197 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6126 (mtp-110) REVERT: B 234 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.7618 (t80) REVERT: B 311 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.5323 (t-90) REVERT: B 336 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8300 (tt) REVERT: C 46 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: C 235 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.7149 (t80) REVERT: R 75 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7538 (t-170) outliers start: 68 outliers final: 28 residues processed: 155 average time/residue: 1.0508 time to fit residues: 176.9655 Evaluate side-chains 138 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 102 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 127 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 111 optimal weight: 0.0050 chunk 120 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.4492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10097 Z= 0.131 Angle : 0.469 8.747 13693 Z= 0.244 Chirality : 0.040 0.190 1543 Planarity : 0.003 0.045 1731 Dihedral : 4.654 39.354 1440 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.23 % Allowed : 30.61 % Favored : 65.16 % 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: 1.01 (0.24), residues: 1240 helix: 2.50 (0.26), residues: 398 sheet: 0.38 (0.29), residues: 316 loop : -0.56 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS C 35 PHE 0.035 0.001 PHE R 349 TYR 0.027 0.001 TYR C 235 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 110 time to evaluate : 1.131 Fit side-chains REVERT: B 59 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: B 146 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8200 (mp) REVERT: B 197 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6148 (mtp-110) REVERT: B 215 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: B 234 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.7528 (t80) REVERT: B 311 HIS cc_start: 0.7218 (OUTLIER) cc_final: 0.5294 (t-90) REVERT: B 336 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8000 (tt) REVERT: C 46 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: N 90 ASP cc_start: 0.7263 (t0) cc_final: 0.7051 (t0) REVERT: R 75 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7531 (t-170) REVERT: R 349 PHE cc_start: 0.7383 (t80) cc_final: 0.7149 (t80) outliers start: 45 outliers final: 19 residues processed: 142 average time/residue: 1.0567 time to fit residues: 163.2974 Evaluate side-chains 136 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 123 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 112 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10097 Z= 0.202 Angle : 0.505 9.601 13693 Z= 0.260 Chirality : 0.041 0.209 1543 Planarity : 0.004 0.047 1731 Dihedral : 4.734 37.941 1440 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.01 % Allowed : 29.48 % Favored : 64.51 % 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: 0.94 (0.24), residues: 1240 helix: 2.46 (0.26), residues: 397 sheet: 0.30 (0.28), residues: 321 loop : -0.60 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS C 35 PHE 0.016 0.001 PHE A 189 TYR 0.028 0.001 TYR C 235 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 107 time to evaluate : 0.854 Fit side-chains REVERT: A 294 GLU cc_start: 0.6320 (tm-30) cc_final: 0.6077 (tm-30) REVERT: A 310 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7146 (tptt) REVERT: B 13 GLN cc_start: 0.7485 (tp40) cc_final: 0.7244 (tp-100) REVERT: B 59 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: B 146 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8219 (mp) REVERT: B 197 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6216 (mtp-110) REVERT: B 215 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: B 234 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.7497 (t80) REVERT: B 311 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.5245 (t-90) REVERT: B 336 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8145 (tt) REVERT: C 38 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7418 (ttp-170) REVERT: C 46 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: R 75 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7544 (t-170) REVERT: R 301 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5790 (tt) outliers start: 64 outliers final: 33 residues processed: 155 average time/residue: 1.0375 time to fit residues: 174.1517 Evaluate side-chains 151 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 106 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 301 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 72.5567 > 50: distance: 56 - 107: 32.649 distance: 85 - 91: 27.339 distance: 91 - 92: 20.738 distance: 92 - 93: 39.639 distance: 95 - 96: 42.434 distance: 98 - 99: 9.322 distance: 98 - 156: 58.775 distance: 99 - 100: 8.649 distance: 99 - 102: 32.489 distance: 100 - 101: 8.117 distance: 101 - 153: 41.479 distance: 102 - 103: 40.813 distance: 104 - 105: 35.959 distance: 105 - 106: 15.269 distance: 105 - 108: 40.953 distance: 106 - 107: 58.951 distance: 106 - 109: 43.246 distance: 109 - 110: 39.777 distance: 109 - 139: 58.306 distance: 110 - 111: 57.471 distance: 110 - 113: 65.815 distance: 111 - 112: 68.325 distance: 111 - 115: 41.201 distance: 112 - 136: 39.777 distance: 113 - 114: 56.594 distance: 115 - 116: 39.368 distance: 116 - 119: 38.710 distance: 117 - 118: 40.953 distance: 119 - 120: 64.555 distance: 120 - 121: 11.028 distance: 121 - 122: 39.080 distance: 124 - 125: 56.711 distance: 125 - 126: 24.576 distance: 125 - 128: 39.144 distance: 126 - 127: 16.172 distance: 126 - 132: 26.061 distance: 128 - 129: 56.688 distance: 129 - 131: 36.619 distance: 132 - 133: 39.541 distance: 133 - 134: 34.964 distance: 134 - 135: 56.992 distance: 134 - 136: 51.928 distance: 136 - 137: 61.442 distance: 137 - 138: 27.516 distance: 137 - 140: 10.547 distance: 138 - 139: 26.982 distance: 138 - 145: 57.348 distance: 140 - 141: 30.782 distance: 141 - 142: 26.455 distance: 142 - 143: 22.731 distance: 143 - 144: 59.259 distance: 145 - 146: 41.137 distance: 145 - 192: 37.522 distance: 146 - 147: 57.836 distance: 146 - 149: 53.208 distance: 147 - 148: 39.025 distance: 147 - 153: 39.859 distance: 148 - 189: 36.167 distance: 149 - 150: 37.302 distance: 150 - 151: 47.805 distance: 150 - 152: 15.582 distance: 154 - 155: 13.638 distance: 154 - 157: 5.242 distance: 155 - 156: 26.722 distance: 155 - 161: 28.350 distance: 157 - 159: 6.620 distance: 158 - 160: 34.403