Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 07:25:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsc_12564/07_2023/7nsc_12564.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsc_12564/07_2023/7nsc_12564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsc_12564/07_2023/7nsc_12564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsc_12564/07_2023/7nsc_12564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsc_12564/07_2023/7nsc_12564.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsc_12564/07_2023/7nsc_12564.pdb" } resolution = 3.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5955 2.51 5 N 1607 2.21 5 O 1703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "E GLU 295": "OE1" <-> "OE2" Residue "E GLU 299": "OE1" <-> "OE2" Residue "E ASP 373": "OD1" <-> "OD2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E ARG 392": "NH1" <-> "NH2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E GLU 551": "OE1" <-> "OE2" Residue "E GLU 560": "OE1" <-> "OE2" Residue "E ARG 627": "NH1" <-> "NH2" Residue "E TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 40": "OE1" <-> "OE2" Residue "H PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H ARG 169": "NH1" <-> "NH2" Residue "H GLU 184": "OE1" <-> "OE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ASP 218": "OD1" <-> "OD2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 9327 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2065 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 17, 'TRANS': 258} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 4631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4631 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 18, 'TRANS': 596} Chain breaks: 2 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 20, 'ASN:plan1': 5, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 127 Chain: "H" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1178 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "D" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1453 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain breaks: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 4.74, per 1000 atoms: 0.51 Number of scatterers: 9327 At special positions: 0 Unit cell: (83.3, 136.85, 118.15, 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 62 16.00 O 1703 8.00 N 1607 7.00 C 5955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.6 seconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2324 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 3 sheets defined 55.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 338 through 356 removed outlier: 3.903A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 696 through 713 removed outlier: 3.668A pdb=" N ALA A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 721 No H-bonds generated for 'chain 'A' and resid 718 through 721' Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'E' and resid 21 through 33 Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 81 through 90 removed outlier: 3.648A pdb=" N CYS E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 100 Processing helix chain 'E' and resid 105 through 120 Processing helix chain 'E' and resid 127 through 131 removed outlier: 4.272A pdb=" N THR E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 127 through 131' Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 147 through 161 Processing helix chain 'E' and resid 164 through 173 removed outlier: 3.556A pdb=" N HIS E 173 " --> pdb=" O ILE E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 4.669A pdb=" N HIS E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU E 182 " --> pdb=" O ASN E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 206 through 214 removed outlier: 3.817A pdb=" N THR E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASN E 214 " --> pdb=" O MET E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 removed outlier: 3.815A pdb=" N VAL E 227 " --> pdb=" O PRO E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 252 Processing helix chain 'E' and resid 262 through 274 removed outlier: 3.911A pdb=" N THR E 266 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU E 267 " --> pdb=" O VAL E 263 " (cutoff:3.500A) Proline residue: E 268 - end of helix removed outlier: 3.965A pdb=" N CYS E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 293 removed outlier: 3.825A pdb=" N GLU E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 287 " --> pdb=" O ARG E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 306 removed outlier: 3.766A pdb=" N ILE E 306 " --> pdb=" O ARG E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 334 through 338 Processing helix chain 'E' and resid 340 through 355 removed outlier: 4.102A pdb=" N ARG E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 367 Processing helix chain 'E' and resid 371 through 379 Processing helix chain 'E' and resid 384 through 398 removed outlier: 4.347A pdb=" N ALA E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 411 removed outlier: 4.608A pdb=" N PHE E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN E 409 " --> pdb=" O ARG E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.794A pdb=" N MET E 418 " --> pdb=" O TRP E 414 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS E 419 " --> pdb=" O LYS E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 439 removed outlier: 4.066A pdb=" N VAL E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET E 435 " --> pdb=" O VAL E 431 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS E 437 " --> pdb=" O SER E 433 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASN E 438 " --> pdb=" O SER E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 452 removed outlier: 4.512A pdb=" N ILE E 450 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 464 removed outlier: 3.679A pdb=" N THR E 463 " --> pdb=" O LEU E 459 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN E 464 " --> pdb=" O CYS E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 482 removed outlier: 4.774A pdb=" N ASN E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU E 478 " --> pdb=" O GLY E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 496 removed outlier: 4.847A pdb=" N ASP E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 506 Processing helix chain 'E' and resid 511 through 525 removed outlier: 3.804A pdb=" N LEU E 525 " --> pdb=" O LEU E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 538 removed outlier: 3.604A pdb=" N ASP E 532 " --> pdb=" O ARG E 528 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR E 537 " --> pdb=" O LYS E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 551 removed outlier: 3.816A pdb=" N GLN E 544 " --> pdb=" O LYS E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 571 Processing helix chain 'E' and resid 575 through 581 removed outlier: 3.767A pdb=" N ILE E 579 " --> pdb=" O ALA E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 592 Processing helix chain 'E' and resid 598 through 611 removed outlier: 3.763A pdb=" N CYS E 607 " --> pdb=" O ALA E 603 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 608 " --> pdb=" O ALA E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 629 removed outlier: 3.967A pdb=" N MET E 629 " --> pdb=" O LYS E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 639 Processing helix chain 'E' and resid 645 through 656 Processing helix chain 'H' and resid 27 through 38 Processing helix chain 'H' and resid 44 through 52 removed outlier: 3.871A pdb=" N LYS H 48 " --> pdb=" O GLU H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 87 Processing helix chain 'H' and resid 92 through 96 removed outlier: 5.089A pdb=" N THR H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 92 through 96' Processing helix chain 'H' and resid 98 through 114 Processing helix chain 'H' and resid 166 through 183 Processing helix chain 'H' and resid 191 through 209 removed outlier: 4.164A pdb=" N LYS H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 219 No H-bonds generated for 'chain 'H' and resid 216 through 219' Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.888A pdb=" N LYS D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.935A pdb=" N ASN D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175 removed outlier: 5.760A pdb=" N ASP A 173 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER A 201 " --> pdb=" O PHE A 175 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 200 through 203 current: chain 'A' and resid 314 through 319 removed outlier: 6.714A pdb=" N TYR A 229 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N HIS A 250 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER A 251 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 181 removed outlier: 4.696A pdb=" N ARG A 186 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU A 323 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A 279 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 280 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASN A 290 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 126 through 133 removed outlier: 3.801A pdb=" N SER D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS D 156 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N THR D 172 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU D 240 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE D 174 " --> pdb=" O GLN D 238 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG D 234 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASP D 229 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU D 237 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY D 256 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 268 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA D 267 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN D 282 " --> pdb=" O TYR D 273 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1383 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: 2.70 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1519 1.30 - 1.43: 2422 1.43 - 1.56: 5480 1.56 - 1.68: 0 1.68 - 1.81: 97 Bond restraints: 9518 Sorted by residual: bond pdb=" C TYR A 254 " pdb=" O TYR A 254 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.14e-02 7.69e+03 2.82e+01 bond pdb=" N TYR A 727 " pdb=" CA TYR A 727 " ideal model delta sigma weight residual 1.457 1.389 0.068 1.29e-02 6.01e+03 2.81e+01 bond pdb=" CA TYR A 727 " pdb=" C TYR A 727 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.34e-02 5.57e+03 9.28e+00 bond pdb=" CG TYR A 254 " pdb=" CD1 TYR A 254 " ideal model delta sigma weight residual 1.389 1.338 0.051 2.10e-02 2.27e+03 5.96e+00 bond pdb=" CE2 TYR A 254 " pdb=" CZ TYR A 254 " ideal model delta sigma weight residual 1.378 1.321 0.057 2.40e-02 1.74e+03 5.72e+00 ... (remaining 9513 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.61: 197 105.61 - 112.74: 5139 112.74 - 119.87: 3117 119.87 - 127.01: 4368 127.01 - 134.14: 112 Bond angle restraints: 12933 Sorted by residual: angle pdb=" N HIS E 181 " pdb=" CA HIS E 181 " pdb=" C HIS E 181 " ideal model delta sigma weight residual 114.56 106.20 8.36 1.27e+00 6.20e-01 4.33e+01 angle pdb=" CA ASP A 726 " pdb=" C ASP A 726 " pdb=" N TYR A 727 " ideal model delta sigma weight residual 118.08 112.46 5.62 1.30e+00 5.92e-01 1.87e+01 angle pdb=" O GLY A 253 " pdb=" C GLY A 253 " pdb=" N TYR A 254 " ideal model delta sigma weight residual 123.54 126.90 -3.36 9.20e-01 1.18e+00 1.33e+01 angle pdb=" CA HIS E 181 " pdb=" C HIS E 181 " pdb=" N LEU E 182 " ideal model delta sigma weight residual 119.26 115.12 4.14 1.14e+00 7.69e-01 1.32e+01 angle pdb=" O ASP A 726 " pdb=" C ASP A 726 " pdb=" N TYR A 727 " ideal model delta sigma weight residual 122.39 127.03 -4.64 1.30e+00 5.92e-01 1.27e+01 ... (remaining 12928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5079 17.59 - 35.17: 495 35.17 - 52.76: 102 52.76 - 70.34: 15 70.34 - 87.93: 4 Dihedral angle restraints: 5695 sinusoidal: 2107 harmonic: 3588 Sorted by residual: dihedral pdb=" CA ASP E 316 " pdb=" C ASP E 316 " pdb=" N TYR E 317 " pdb=" CA TYR E 317 " ideal model delta harmonic sigma weight residual 180.00 154.11 25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA MET H 73 " pdb=" C MET H 73 " pdb=" N ILE H 74 " pdb=" CA ILE H 74 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA LEU H 89 " pdb=" C LEU H 89 " pdb=" N HIS H 90 " pdb=" CA HIS H 90 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 5692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 984 0.038 - 0.076: 411 0.076 - 0.113: 91 0.113 - 0.151: 19 0.151 - 0.189: 1 Chirality restraints: 1506 Sorted by residual: chirality pdb=" CG LEU H 164 " pdb=" CB LEU H 164 " pdb=" CD1 LEU H 164 " pdb=" CD2 LEU H 164 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CG LEU A 318 " pdb=" CB LEU A 318 " pdb=" CD1 LEU A 318 " pdb=" CD2 LEU A 318 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CB ILE A 232 " pdb=" CA ILE A 232 " pdb=" CG1 ILE A 232 " pdb=" CG2 ILE A 232 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 1503 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 317 " 0.023 2.00e-02 2.50e+03 1.71e-02 5.82e+00 pdb=" CG TYR E 317 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR E 317 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 317 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 317 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 317 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 317 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 317 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 695 " 0.037 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 696 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 696 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 696 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 726 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C ASP A 726 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP A 726 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 727 " -0.013 2.00e-02 2.50e+03 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 22 2.37 - 3.00: 5071 3.00 - 3.63: 13713 3.63 - 4.27: 20345 4.27 - 4.90: 34848 Nonbonded interactions: 73999 Sorted by model distance: nonbonded pdb=" NE2 GLN A 350 " pdb=" OH TYR A 727 " model vdw 1.732 2.520 nonbonded pdb=" OE1 GLU A 344 " pdb=" NH1 ARG E 232 " model vdw 2.212 2.520 nonbonded pdb=" O SER E 526 " pdb=" OG1 THR E 527 " model vdw 2.228 2.440 nonbonded pdb=" O ALA E 352 " pdb=" OG SER E 396 " model vdw 2.231 2.440 nonbonded pdb=" O HIS E 595 " pdb=" NE2 GLN E 601 " model vdw 2.231 2.520 ... (remaining 73994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.220 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.290 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 0.068 9518 Z= 0.317 Angle : 0.705 8.786 12933 Z= 0.383 Chirality : 0.042 0.189 1506 Planarity : 0.004 0.057 1648 Dihedral : 14.497 87.927 3371 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 1206 helix: 0.05 (0.20), residues: 677 sheet: -0.78 (0.46), residues: 140 loop : -2.83 (0.28), residues: 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.046 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1884 time to fit residues: 39.4698 Evaluate side-chains 121 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.0030 chunk 91 optimal weight: 0.0870 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 0.0020 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 overall best weight: 0.1576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 350 GLN A 380 HIS ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 9518 Z= 0.140 Angle : 0.544 7.524 12933 Z= 0.278 Chirality : 0.038 0.135 1506 Planarity : 0.003 0.050 1648 Dihedral : 4.452 20.637 1309 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.25), residues: 1206 helix: 0.58 (0.21), residues: 675 sheet: -0.41 (0.46), residues: 138 loop : -2.72 (0.28), residues: 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.071 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 141 average time/residue: 0.1930 time to fit residues: 39.8871 Evaluate side-chains 130 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0921 time to fit residues: 2.6602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 chunk 118 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9518 Z= 0.212 Angle : 0.557 8.502 12933 Z= 0.283 Chirality : 0.039 0.176 1506 Planarity : 0.004 0.048 1648 Dihedral : 4.380 19.776 1309 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.25), residues: 1206 helix: 0.68 (0.21), residues: 680 sheet: -0.36 (0.46), residues: 138 loop : -2.72 (0.28), residues: 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 1.071 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 133 average time/residue: 0.1863 time to fit residues: 36.9583 Evaluate side-chains 126 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0885 time to fit residues: 2.1496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 0.1980 chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 0.0670 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS E 167 GLN ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9518 Z= 0.222 Angle : 0.569 11.803 12933 Z= 0.287 Chirality : 0.039 0.154 1506 Planarity : 0.004 0.048 1648 Dihedral : 4.368 19.351 1309 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1206 helix: 0.73 (0.21), residues: 679 sheet: -0.42 (0.46), residues: 140 loop : -2.67 (0.28), residues: 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.125 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 134 average time/residue: 0.1870 time to fit residues: 37.3519 Evaluate side-chains 127 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0882 time to fit residues: 2.3539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 GLN D 152 ASN D 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 9518 Z= 0.236 Angle : 0.579 9.604 12933 Z= 0.289 Chirality : 0.039 0.164 1506 Planarity : 0.004 0.046 1648 Dihedral : 4.389 21.836 1309 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1206 helix: 0.71 (0.21), residues: 681 sheet: -0.43 (0.46), residues: 140 loop : -2.64 (0.28), residues: 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.088 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 131 average time/residue: 0.1870 time to fit residues: 36.4669 Evaluate side-chains 128 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0893 time to fit residues: 2.4495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN D 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9518 Z= 0.220 Angle : 0.563 9.986 12933 Z= 0.283 Chirality : 0.039 0.161 1506 Planarity : 0.003 0.045 1648 Dihedral : 4.348 21.531 1309 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1206 helix: 0.79 (0.21), residues: 678 sheet: -0.37 (0.46), residues: 140 loop : -2.64 (0.28), residues: 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.065 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 136 average time/residue: 0.1844 time to fit residues: 37.5307 Evaluate side-chains 127 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0914 time to fit residues: 2.9440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 240 ASN ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN D 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9518 Z= 0.245 Angle : 0.579 9.699 12933 Z= 0.292 Chirality : 0.040 0.178 1506 Planarity : 0.004 0.045 1648 Dihedral : 4.383 20.873 1309 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1206 helix: 0.74 (0.21), residues: 680 sheet: -0.31 (0.46), residues: 140 loop : -2.60 (0.29), residues: 386 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.093 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 127 average time/residue: 0.1928 time to fit residues: 36.6558 Evaluate side-chains 127 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0994 time to fit residues: 2.7634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 91 optimal weight: 0.0010 chunk 106 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 380 HIS ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9518 Z= 0.191 Angle : 0.558 11.089 12933 Z= 0.281 Chirality : 0.039 0.192 1506 Planarity : 0.003 0.044 1648 Dihedral : 4.264 20.568 1309 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1206 helix: 0.82 (0.21), residues: 679 sheet: -0.15 (0.47), residues: 139 loop : -2.62 (0.29), residues: 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.083 Fit side-chains outliers start: 14 outliers final: 3 residues processed: 134 average time/residue: 0.1904 time to fit residues: 38.0291 Evaluate side-chains 123 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0863 time to fit residues: 1.9259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 0.0170 chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 0.0970 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS D 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9518 Z= 0.154 Angle : 0.528 8.631 12933 Z= 0.265 Chirality : 0.038 0.134 1506 Planarity : 0.003 0.043 1648 Dihedral : 4.091 19.502 1309 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1206 helix: 0.95 (0.21), residues: 684 sheet: 0.09 (0.47), residues: 138 loop : -2.64 (0.29), residues: 384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.380 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 133 average time/residue: 0.2000 time to fit residues: 38.5977 Evaluate side-chains 121 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1101 time to fit residues: 1.9297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9518 Z= 0.219 Angle : 0.565 9.618 12933 Z= 0.283 Chirality : 0.039 0.189 1506 Planarity : 0.003 0.043 1648 Dihedral : 4.185 19.442 1309 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1206 helix: 0.87 (0.21), residues: 682 sheet: 0.02 (0.47), residues: 137 loop : -2.66 (0.28), residues: 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.082 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 126 average time/residue: 0.1895 time to fit residues: 35.4820 Evaluate side-chains 123 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0886 time to fit residues: 2.1678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.0170 chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 0.0010 chunk 17 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 69 optimal weight: 0.0030 overall best weight: 0.0632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.121469 restraints weight = 14106.211| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.88 r_work: 0.3404 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 9518 Z= 0.138 Angle : 0.531 9.170 12933 Z= 0.264 Chirality : 0.038 0.179 1506 Planarity : 0.003 0.040 1648 Dihedral : 3.927 18.488 1309 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1206 helix: 1.07 (0.21), residues: 684 sheet: 0.25 (0.47), residues: 138 loop : -2.58 (0.29), residues: 384 =============================================================================== Job complete usr+sys time: 2167.75 seconds wall clock time: 39 minutes 58.52 seconds (2398.52 seconds total)