Starting phenix.real_space_refine on Fri Nov 17 04:23:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/11_2023/8ghv_40052_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/11_2023/8ghv_40052.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/11_2023/8ghv_40052_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/11_2023/8ghv_40052_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/11_2023/8ghv_40052_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/11_2023/8ghv_40052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/11_2023/8ghv_40052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/11_2023/8ghv_40052_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/11_2023/8ghv_40052_neut_trim_updated.pdb" } resolution = 2.8 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= 0.004 sd= 1.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1971 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 54 5.16 5 C 5308 2.51 5 N 1383 2.21 5 O 1492 1.98 5 H 7637 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "S GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 15874 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3144 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 4847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 4847 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 698 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 3889 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 131 Chain: "S" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3269 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZI5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.45, per 1000 atoms: 0.47 Number of scatterers: 15874 At special positions: 0 Unit cell: (92.8789, 123.555, 132.076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 O 1492 8.00 N 1383 7.00 C 5308 6.00 H 7637 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 264 " 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: 13.60 Conformation dependent library (CDL) restraints added in 1.7 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 12 sheets defined 32.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.477A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.738A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) 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 8 through 23 removed outlier: 3.671A pdb=" N ALA C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.883A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 140 removed outlier: 3.978A pdb=" N LEU D 117 " --> pdb=" O PRO D 113 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 153 through 178 Processing helix chain 'D' and resid 186 through 219 removed outlier: 3.767A pdb=" N ILE D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 230 through 253 Proline residue: D 251 - end of helix Processing helix chain 'D' and resid 275 through 305 removed outlier: 3.887A pdb=" N SER D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL D 285 " --> pdb=" O GLY D 281 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 356 removed outlier: 4.113A pdb=" N LEU D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 367 Processing helix chain 'D' and resid 373 through 399 removed outlier: 3.746A pdb=" N MET D 384 " --> pdb=" O ALA D 380 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 388 " --> pdb=" O MET D 384 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER D 390 " --> pdb=" O CYS D 386 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 391 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Proline residue: D 394 - end of helix removed outlier: 3.869A pdb=" N ALA D 398 " --> pdb=" O PRO D 394 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 411 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.738A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 37 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.012A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.185A 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: 7.083A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.192A 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: 6.863A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.126A 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: 7.122A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.418A 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: 6.863A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.860A 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: 6.710A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.858A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.590A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 3.520A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= L, first strand: chain 'S' and resid 214 through 218 removed outlier: 3.647A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1071 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: 5.54 Time building geometry restraints manager: 13.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7608 1.03 - 1.23: 136 1.23 - 1.43: 3448 1.43 - 1.62: 4778 1.62 - 1.82: 77 Bond restraints: 16047 Sorted by residual: bond pdb=" N VAL D 392 " pdb=" CA VAL D 392 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.08e-02 8.57e+03 1.58e+01 bond pdb=" C LEU B 79 " pdb=" O LEU B 79 " ideal model delta sigma weight residual 1.236 1.192 0.043 1.14e-02 7.69e+03 1.45e+01 bond pdb=" N ILE D 395 " pdb=" CA ILE D 395 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.08e-02 8.57e+03 1.42e+01 bond pdb=" N VAL D 110 " pdb=" H VAL D 110 " ideal model delta sigma weight residual 0.860 0.931 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" N TRP B 332 " pdb=" CA TRP B 332 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.32e-02 5.74e+03 9.39e+00 ... (remaining 16042 not shown) Histogram of bond angle deviations from ideal: 96.87 - 104.33: 91 104.33 - 111.79: 17696 111.79 - 119.25: 3959 119.25 - 126.71: 6919 126.71 - 134.18: 119 Bond angle restraints: 28784 Sorted by residual: angle pdb=" C12 ZI5 D 501 " pdb=" C10 ZI5 D 501 " pdb=" C9 ZI5 D 501 " ideal model delta sigma weight residual 85.91 123.03 -37.12 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C1 ZI5 D 501 " pdb=" C2 ZI5 D 501 " pdb=" C4 ZI5 D 501 " ideal model delta sigma weight residual 152.66 124.12 28.54 3.00e+00 1.11e-01 9.05e+01 angle pdb=" C13 ZI5 D 501 " pdb=" C11 ZI5 D 501 " pdb=" C8 ZI5 D 501 " ideal model delta sigma weight residual 152.65 124.53 28.12 3.00e+00 1.11e-01 8.79e+01 angle pdb=" C11 ZI5 D 501 " pdb=" C8 ZI5 D 501 " pdb=" C7 ZI5 D 501 " ideal model delta sigma weight residual 112.27 124.49 -12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C3 ZI5 D 501 " pdb=" C5 ZI5 D 501 " pdb=" C7 ZI5 D 501 " ideal model delta sigma weight residual 112.83 124.89 -12.06 3.00e+00 1.11e-01 1.62e+01 ... (remaining 28779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 6286 26.04 - 52.07: 207 52.07 - 78.11: 14 78.11 - 104.14: 4 104.14 - 130.18: 1 Dihedral angle restraints: 6512 sinusoidal: 2643 harmonic: 3869 Sorted by residual: dihedral pdb=" C2 ZI5 D 501 " pdb=" C4 ZI5 D 501 " pdb=" C6 ZI5 D 501 " pdb=" C9 ZI5 D 501 " ideal model delta sinusoidal sigma weight residual 273.52 143.34 130.18 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" CB CYS D 257 " pdb=" SG CYS D 257 " pdb=" SG CYS D 264 " pdb=" CB CYS D 264 " ideal model delta sinusoidal sigma weight residual -86.00 -120.33 34.33 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" SG CYS D 257 " pdb=" CB CYS D 264 " pdb=" SG CYS D 264 " pdb=" CA CYS D 264 " ideal model delta sinusoidal sigma weight residual -73.00 -13.90 -59.10 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 6509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 947 0.039 - 0.078: 254 0.078 - 0.117: 95 0.117 - 0.156: 57 0.156 - 0.195: 10 Chirality restraints: 1363 Sorted by residual: chirality pdb=" CA ILE D 396 " pdb=" N ILE D 396 " pdb=" C ILE D 396 " pdb=" CB ILE D 396 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA ILE D 375 " pdb=" N ILE D 375 " pdb=" C ILE D 375 " pdb=" CB ILE D 375 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 1360 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 176 " 0.218 2.00e-02 2.50e+03 2.53e-01 9.63e+02 pdb=" CD GLN B 176 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN B 176 " -0.211 2.00e-02 2.50e+03 pdb=" NE2 GLN B 176 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 176 " 0.387 2.00e-02 2.50e+03 pdb="HE22 GLN B 176 " -0.378 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 304 " -0.550 9.50e-02 1.11e+02 2.36e-01 5.29e+02 pdb=" NE ARG B 304 " -0.154 2.00e-02 2.50e+03 pdb=" CZ ARG B 304 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG B 304 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 304 " 0.029 2.00e-02 2.50e+03 pdb="HH11 ARG B 304 " 0.306 2.00e-02 2.50e+03 pdb="HH12 ARG B 304 " -0.239 2.00e-02 2.50e+03 pdb="HH21 ARG B 304 " 0.142 2.00e-02 2.50e+03 pdb="HH22 ARG B 304 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 291 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C VAL D 291 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL D 291 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR D 292 " -0.017 2.00e-02 2.50e+03 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 882 2.22 - 2.81: 31646 2.81 - 3.41: 37648 3.41 - 4.00: 51753 4.00 - 4.60: 80548 Nonbonded interactions: 202477 Sorted by model distance: nonbonded pdb=" O PHE S 32 " pdb="HH22 ARG S 72 " model vdw 1.623 1.850 nonbonded pdb=" H SER D 265 " pdb=" O ILE D 271 " model vdw 1.650 1.850 nonbonded pdb=" O LYS B 280 " pdb=" HG SER B 281 " model vdw 1.679 1.850 nonbonded pdb="HD22 ASN A 347 " pdb=" O PRO D 221 " model vdw 1.683 1.850 nonbonded pdb="HH22 ARG B 256 " pdb=" OD2 ASP C 36 " model vdw 1.726 1.850 ... (remaining 202472 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.280 Extract box with map and model: 10.330 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 53.000 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 0.061 8410 Z= 0.333 Angle : 0.919 37.125 11461 Z= 0.536 Chirality : 0.049 0.195 1363 Planarity : 0.005 0.126 1444 Dihedral : 14.037 130.178 2779 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.76 % Allowed : 9.24 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.26 (0.25), residues: 1107 helix: 1.99 (0.28), residues: 372 sheet: 0.44 (0.31), residues: 267 loop : -1.56 (0.25), residues: 468 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.279 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 1.6193 time to fit residues: 190.4581 Evaluate side-chains 82 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.4797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 13 GLN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8410 Z= 0.189 Angle : 0.507 6.054 11461 Z= 0.270 Chirality : 0.040 0.134 1363 Planarity : 0.003 0.036 1444 Dihedral : 6.041 76.301 1205 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.77 % Allowed : 12.41 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.56 (0.25), residues: 1107 helix: 2.29 (0.28), residues: 382 sheet: 0.58 (0.32), residues: 270 loop : -1.52 (0.25), residues: 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 1.361 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 98 average time/residue: 1.5105 time to fit residues: 164.3794 Evaluate side-chains 87 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.2165 time to fit residues: 2.6569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.0020 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8410 Z= 0.126 Angle : 0.441 6.523 11461 Z= 0.234 Chirality : 0.039 0.138 1363 Planarity : 0.002 0.030 1444 Dihedral : 5.487 67.576 1205 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.65 % Allowed : 13.29 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.84 (0.25), residues: 1107 helix: 2.66 (0.28), residues: 382 sheet: 0.65 (0.31), residues: 271 loop : -1.43 (0.25), residues: 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.294 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 91 average time/residue: 1.5976 time to fit residues: 160.6331 Evaluate side-chains 83 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1727 time to fit residues: 2.2251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN D 181 HIS ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8410 Z= 0.263 Angle : 0.552 6.855 11461 Z= 0.294 Chirality : 0.041 0.155 1363 Planarity : 0.003 0.038 1444 Dihedral : 5.422 58.844 1205 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.28 % Allowed : 13.92 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.65 (0.25), residues: 1107 helix: 2.49 (0.28), residues: 380 sheet: 0.60 (0.31), residues: 268 loop : -1.55 (0.25), residues: 459 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.246 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 93 average time/residue: 1.6448 time to fit residues: 169.1120 Evaluate side-chains 89 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.2517 time to fit residues: 3.3338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8410 Z= 0.171 Angle : 0.490 6.583 11461 Z= 0.260 Chirality : 0.039 0.142 1363 Planarity : 0.003 0.035 1444 Dihedral : 5.001 53.679 1205 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.65 % Allowed : 15.06 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.79 (0.25), residues: 1107 helix: 2.64 (0.27), residues: 381 sheet: 0.78 (0.31), residues: 267 loop : -1.58 (0.25), residues: 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.228 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 1.6200 time to fit residues: 166.4345 Evaluate side-chains 86 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.2696 time to fit residues: 2.4552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.0060 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8410 Z= 0.166 Angle : 0.484 6.698 11461 Z= 0.257 Chirality : 0.039 0.138 1363 Planarity : 0.003 0.035 1444 Dihedral : 4.773 49.080 1205 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.03 % Allowed : 15.19 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.87 (0.25), residues: 1107 helix: 2.72 (0.27), residues: 382 sheet: 0.82 (0.31), residues: 267 loop : -1.55 (0.25), residues: 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.374 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 94 average time/residue: 1.5796 time to fit residues: 163.7936 Evaluate side-chains 91 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.2157 time to fit residues: 2.6647 ------------------------------------------------------------------------------- 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-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 50.202 > 50: distance: 151 - 159: 7.598 distance: 152 - 153: 3.560 distance: 152 - 160: 4.052 distance: 153 - 154: 10.367 distance: 153 - 163: 3.627 distance: 155 - 162: 3.898 distance: 156 - 158: 3.504 distance: 163 - 164: 4.515 distance: 163 - 170: 5.472 distance: 164 - 165: 4.603 distance: 165 - 166: 9.320 distance: 165 - 179: 5.753 distance: 167 - 168: 3.512 distance: 167 - 169: 3.398 distance: 168 - 173: 3.705 distance: 168 - 175: 3.107 distance: 169 - 177: 3.409 distance: 169 - 178: 3.894 distance: 179 - 180: 7.266 distance: 180 - 183: 5.305 distance: 186 - 191: 6.359 distance: 187 - 190: 3.003 distance: 187 - 192: 4.114 distance: 188 - 189: 6.533 distance: 188 - 193: 6.394 distance: 193 - 194: 7.512 distance: 193 - 197: 4.458 distance: 194 - 195: 11.311 distance: 194 - 198: 4.610 distance: 194 - 199: 6.357 distance: 195 - 196: 5.847 distance: 195 - 200: 8.495 distance: 200 - 201: 18.764 distance: 200 - 205: 13.567 distance: 201 - 202: 7.266 distance: 201 - 204: 21.199 distance: 201 - 206: 16.214 distance: 202 - 203: 7.052 distance: 202 - 207: 8.571 distance: 207 - 208: 9.539 distance: 207 - 213: 6.705 distance: 208 - 209: 12.250 distance: 208 - 211: 9.935 distance: 208 - 214: 8.107 distance: 209 - 210: 13.676 distance: 209 - 218: 7.110 distance: 211 - 212: 12.346 distance: 211 - 215: 10.839 distance: 211 - 216: 14.305 distance: 212 - 217: 3.625 distance: 218 - 219: 8.706 distance: 218 - 229: 28.880 distance: 219 - 220: 6.723 distance: 219 - 222: 5.744 distance: 219 - 230: 6.718 distance: 220 - 221: 7.187 distance: 220 - 242: 8.396 distance: 222 - 223: 5.168 distance: 222 - 231: 3.489 distance: 222 - 232: 6.092 distance: 223 - 224: 4.020 distance: 223 - 233: 5.617 distance: 223 - 234: 5.154 distance: 224 - 235: 3.560 distance: 225 - 226: 3.235 distance: 242 - 251: 5.561 distance: 243 - 246: 3.128 distance: 246 - 253: 7.633 distance: 246 - 254: 4.468 distance: 247 - 248: 3.421 distance: 248 - 249: 3.599 distance: 259 - 266: 6.809 distance: 260 - 261: 3.687 distance: 261 - 262: 3.105 distance: 261 - 273: 3.714 distance: 263 - 265: 3.124 distance: 264 - 269: 4.065 distance: 265 - 271: 4.406 distance: 265 - 272: 3.940