Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 15:18:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckx_30393/04_2023/7ckx_30393_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckx_30393/04_2023/7ckx_30393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckx_30393/04_2023/7ckx_30393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckx_30393/04_2023/7ckx_30393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckx_30393/04_2023/7ckx_30393_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckx_30393/04_2023/7ckx_30393_updated.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7230 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5165 2.51 5 N 1406 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R GLU 85": "OE1" <-> "OE2" Residue "R GLU 132": "OE1" <-> "OE2" Residue "R ARG 227": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8112 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1906 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2587 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2211 Unusual residues: {'CLR': 1, 'G3O': 1} Classifications: {'peptide': 273, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 263, None: 2} Not linked: pdbres="LEU R 344 " pdbres="G3O R 501 " Not linked: pdbres="G3O R 501 " pdbres="CLR R 502 " Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 5.22, per 1000 atoms: 0.64 Number of scatterers: 8112 At special positions: 0 Unit cell: (118, 102, 85, 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 53 16.00 O 1488 8.00 N 1406 7.00 C 5165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " 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: 3.66 Conformation dependent library (CDL) restraints added in 1.3 seconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 36.9% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 16 through 38 removed outlier: 4.125A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.959A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 314 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.983A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.740A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 33 removed outlier: 3.526A pdb=" N ILE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'R' and resid 23 through 50 Processing helix chain 'R' and resid 58 through 74 removed outlier: 4.258A pdb=" N PHE R 62 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL R 73 " --> pdb=" O ASP R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 removed outlier: 4.216A pdb=" N ALA R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 126 Processing helix chain 'R' and resid 128 through 134 Processing helix chain 'R' and resid 137 through 161 removed outlier: 4.321A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 194 through 202 Processing helix chain 'R' and resid 204 through 235 removed outlier: 3.857A pdb=" N LYS R 223 " --> pdb=" O ARG R 219 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 282 removed outlier: 3.829A pdb=" N LEU R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 295 removed outlier: 4.090A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 330 removed outlier: 4.097A pdb=" N ASP R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP R 318 " --> pdb=" O ASP R 314 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 335 through 343 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 6.897A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.887A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 115 removed outlier: 6.798A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.824A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.540A 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: 6.946A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.563A 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: 6.839A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.220A 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: 6.444A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.944A 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: 3.946A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 336 through 338 Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.584A pdb=" N CYS N 99 " --> pdb=" O LYS N 33 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS N 33 " --> pdb=" O CYS N 99 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 987 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: 2.39 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2633 1.35 - 1.46: 2039 1.46 - 1.58: 3540 1.58 - 1.70: 1 1.70 - 1.82: 72 Bond restraints: 8285 Sorted by residual: bond pdb=" C05 G3O R 501 " pdb=" C06 G3O R 501 " ideal model delta sigma weight residual 1.398 1.294 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C08 G3O R 501 " pdb=" C13 G3O R 501 " ideal model delta sigma weight residual 1.534 1.613 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C10 G3O R 501 " pdb=" O09 G3O R 501 " ideal model delta sigma weight residual 1.403 1.479 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C17 G3O R 501 " pdb=" C18 G3O R 501 " ideal model delta sigma weight residual 1.531 1.473 0.058 2.00e-02 2.50e+03 8.42e+00 bond pdb=" C02 G3O R 501 " pdb=" O23 G3O R 501 " ideal model delta sigma weight residual 1.351 1.405 -0.054 2.00e-02 2.50e+03 7.36e+00 ... (remaining 8280 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.41: 176 106.41 - 113.31: 4545 113.31 - 120.22: 2992 120.22 - 127.12: 3446 127.12 - 134.02: 87 Bond angle restraints: 11246 Sorted by residual: angle pdb=" N VAL R 22 " pdb=" CA VAL R 22 " pdb=" C VAL R 22 " ideal model delta sigma weight residual 112.96 109.06 3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" C07 G3O R 501 " pdb=" C08 G3O R 501 " pdb=" C13 G3O R 501 " ideal model delta sigma weight residual 115.56 108.88 6.68 3.00e+00 1.11e-01 4.95e+00 angle pdb=" N VAL R 75 " pdb=" CA VAL R 75 " pdb=" C VAL R 75 " ideal model delta sigma weight residual 112.96 110.78 2.18 1.00e+00 1.00e+00 4.74e+00 angle pdb=" CB LYS B 301 " pdb=" CG LYS B 301 " pdb=" CD LYS B 301 " ideal model delta sigma weight residual 111.30 115.67 -4.37 2.30e+00 1.89e-01 3.62e+00 angle pdb=" CA VAL R 22 " pdb=" C VAL R 22 " pdb=" O VAL R 22 " ideal model delta sigma weight residual 119.29 120.85 -1.56 8.40e-01 1.42e+00 3.44e+00 ... (remaining 11241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4445 17.96 - 35.92: 381 35.92 - 53.88: 62 53.88 - 71.84: 7 71.84 - 89.80: 7 Dihedral angle restraints: 4902 sinusoidal: 1886 harmonic: 3016 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -32.80 -53.20 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ASP R 120 " pdb=" CB ASP R 120 " pdb=" CG ASP R 120 " pdb=" OD1 ASP R 120 " ideal model delta sinusoidal sigma weight residual -30.00 -86.23 56.23 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 4899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 969 0.042 - 0.085: 245 0.085 - 0.127: 65 0.127 - 0.169: 2 0.169 - 0.212: 2 Chirality restraints: 1283 Sorted by residual: chirality pdb=" C08 G3O R 501 " pdb=" C07 G3O R 501 " pdb=" C13 G3O R 501 " pdb=" O09 G3O R 501 " both_signs ideal model delta sigma weight residual False -2.38 -2.59 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C20 G3O R 501 " pdb=" C19 G3O R 501 " pdb=" C21 G3O R 501 " pdb=" C22 G3O R 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.95 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C10 G3O R 501 " pdb=" C05 G3O R 501 " pdb=" C11 G3O R 501 " pdb=" O09 G3O R 501 " both_signs ideal model delta sigma weight residual False 2.41 2.54 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1280 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 205 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO R 206 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO R 206 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 206 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET R 78 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO R 79 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 79 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 79 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP R 103 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" CG ASP R 103 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASP R 103 " 0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP R 103 " 0.007 2.00e-02 2.50e+03 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 280 2.71 - 3.26: 8425 3.26 - 3.80: 13819 3.80 - 4.35: 17810 4.35 - 4.90: 29030 Nonbonded interactions: 69364 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.160 2.440 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.178 2.440 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.208 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" OD1 ASP B 290 " model vdw 2.234 2.440 ... (remaining 69359 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 2.960 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 26.300 Find NCS groups from input model: 0.230 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: 0.020 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.003 0.104 8285 Z= 0.189 Angle : 0.498 8.733 11246 Z= 0.281 Chirality : 0.039 0.212 1283 Planarity : 0.003 0.036 1418 Dihedral : 13.483 89.798 2930 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 2.09 % 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: -3.07 (0.24), residues: 1015 helix: -1.25 (0.23), residues: 384 sheet: -2.74 (0.30), residues: 218 loop : -2.23 (0.29), residues: 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 345 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 354 average time/residue: 0.2522 time to fit residues: 114.2704 Evaluate side-chains 271 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 260 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0807 time to fit residues: 2.8562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.0010 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN A 271 ASN A 278 ASN A 371 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 230 ASN B 237 ASN B 311 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS N 31 ASN R 164 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 8285 Z= 0.217 Angle : 0.577 10.893 11246 Z= 0.292 Chirality : 0.042 0.208 1283 Planarity : 0.004 0.043 1418 Dihedral : 3.973 53.705 1133 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 3.60 % 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: -2.10 (0.25), residues: 1015 helix: -0.31 (0.26), residues: 389 sheet: -2.26 (0.32), residues: 204 loop : -1.85 (0.29), residues: 422 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 292 time to evaluate : 1.009 Fit side-chains outliers start: 31 outliers final: 18 residues processed: 305 average time/residue: 0.2135 time to fit residues: 86.9948 Evaluate side-chains 275 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 257 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0780 time to fit residues: 3.9162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 0.1980 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN N 5 GLN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8285 Z= 0.196 Angle : 0.577 12.278 11246 Z= 0.289 Chirality : 0.041 0.136 1283 Planarity : 0.004 0.030 1418 Dihedral : 4.196 52.780 1133 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 2.32 % 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: -1.74 (0.26), residues: 1015 helix: -0.09 (0.27), residues: 390 sheet: -2.11 (0.33), residues: 204 loop : -1.55 (0.30), residues: 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 268 time to evaluate : 1.021 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 277 average time/residue: 0.2136 time to fit residues: 78.6312 Evaluate side-chains 258 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 250 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0899 time to fit residues: 2.7069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 8285 Z= 0.391 Angle : 0.666 14.396 11246 Z= 0.337 Chirality : 0.044 0.219 1283 Planarity : 0.004 0.032 1418 Dihedral : 4.425 51.012 1133 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 4.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.26), residues: 1015 helix: -0.10 (0.26), residues: 395 sheet: -2.14 (0.34), residues: 203 loop : -1.35 (0.31), residues: 417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 259 time to evaluate : 0.988 Fit side-chains outliers start: 42 outliers final: 27 residues processed: 280 average time/residue: 0.2179 time to fit residues: 81.0658 Evaluate side-chains 277 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 250 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0771 time to fit residues: 5.1114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 390 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8285 Z= 0.258 Angle : 0.636 14.573 11246 Z= 0.313 Chirality : 0.043 0.150 1283 Planarity : 0.004 0.037 1418 Dihedral : 4.514 50.878 1133 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 2.90 % 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: -1.57 (0.27), residues: 1015 helix: -0.11 (0.26), residues: 394 sheet: -2.30 (0.33), residues: 213 loop : -1.05 (0.32), residues: 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 270 time to evaluate : 1.002 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 281 average time/residue: 0.2199 time to fit residues: 81.4741 Evaluate side-chains 265 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 255 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0826 time to fit residues: 2.7970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 5 GLN N 31 ASN N 84 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8285 Z= 0.220 Angle : 0.652 12.951 11246 Z= 0.320 Chirality : 0.043 0.154 1283 Planarity : 0.004 0.033 1418 Dihedral : 4.586 51.683 1133 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 2.67 % 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: -1.48 (0.27), residues: 1015 helix: -0.03 (0.26), residues: 389 sheet: -2.19 (0.33), residues: 207 loop : -1.05 (0.32), residues: 419 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 273 time to evaluate : 0.937 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 282 average time/residue: 0.2240 time to fit residues: 83.8163 Evaluate side-chains 265 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 250 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0792 time to fit residues: 3.5309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 0.0060 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 371 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 31 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8285 Z= 0.236 Angle : 0.691 12.727 11246 Z= 0.338 Chirality : 0.044 0.236 1283 Planarity : 0.004 0.032 1418 Dihedral : 4.626 51.837 1133 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 1.51 % 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: -1.48 (0.26), residues: 1015 helix: 0.00 (0.26), residues: 388 sheet: -2.17 (0.33), residues: 207 loop : -1.10 (0.31), residues: 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 249 time to evaluate : 0.970 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 255 average time/residue: 0.2166 time to fit residues: 73.4106 Evaluate side-chains 248 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 242 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0814 time to fit residues: 2.2851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN G 18 GLN N 5 GLN N 31 ASN N 84 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8285 Z= 0.252 Angle : 0.697 12.356 11246 Z= 0.341 Chirality : 0.044 0.219 1283 Planarity : 0.004 0.031 1418 Dihedral : 4.626 51.173 1133 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 2.21 % 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: -1.42 (0.27), residues: 1015 helix: -0.01 (0.26), residues: 395 sheet: -2.08 (0.33), residues: 212 loop : -1.04 (0.32), residues: 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 1.005 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 246 average time/residue: 0.2045 time to fit residues: 68.2228 Evaluate side-chains 251 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 239 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0848 time to fit residues: 3.1103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 95 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 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 220 HIS A 371 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS G 18 GLN N 5 GLN N 31 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 8285 Z= 0.244 Angle : 0.706 14.045 11246 Z= 0.345 Chirality : 0.045 0.258 1283 Planarity : 0.004 0.033 1418 Dihedral : 4.651 52.403 1133 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 1.16 % 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: -1.38 (0.27), residues: 1015 helix: 0.06 (0.27), residues: 389 sheet: -2.16 (0.33), residues: 213 loop : -0.98 (0.32), residues: 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 242 time to evaluate : 1.008 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 245 average time/residue: 0.2018 time to fit residues: 67.4371 Evaluate side-chains 241 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1350 time to fit residues: 2.6303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 5 GLN N 31 ASN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 8285 Z= 0.240 Angle : 0.716 13.933 11246 Z= 0.349 Chirality : 0.045 0.351 1283 Planarity : 0.004 0.031 1418 Dihedral : 4.664 52.342 1133 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 0.58 % 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: -1.33 (0.27), residues: 1015 helix: 0.14 (0.27), residues: 389 sheet: -2.16 (0.33), residues: 213 loop : -0.98 (0.32), residues: 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 243 time to evaluate : 1.051 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 243 average time/residue: 0.1968 time to fit residues: 65.7573 Evaluate side-chains 240 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 237 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0838 time to fit residues: 1.8646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 5 GLN N 31 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.162432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130907 restraints weight = 11609.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135812 restraints weight = 6454.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139058 restraints weight = 4428.727| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 8285 Z= 0.266 Angle : 0.733 13.955 11246 Z= 0.358 Chirality : 0.046 0.355 1283 Planarity : 0.004 0.032 1418 Dihedral : 4.725 50.907 1133 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 1.16 % 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: -1.32 (0.27), residues: 1015 helix: 0.13 (0.27), residues: 389 sheet: -2.16 (0.33), residues: 213 loop : -0.94 (0.32), residues: 413 =============================================================================== Job complete usr+sys time: 2129.76 seconds wall clock time: 39 minutes 23.07 seconds (2363.07 seconds total)