Starting phenix.real_space_refine on Sat Nov 18 02:04:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2c_17360/11_2023/8p2c_17360_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2c_17360/11_2023/8p2c_17360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2c_17360/11_2023/8p2c_17360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2c_17360/11_2023/8p2c_17360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2c_17360/11_2023/8p2c_17360_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2c_17360/11_2023/8p2c_17360_updated.pdb" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 4 5.21 5 S 136 5.16 5 C 13258 2.51 5 N 3694 2.21 5 O 4045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 21173 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5203 Classifications: {'peptide': 647} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 626} Chain breaks: 3 Chain: "B" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5202 Classifications: {'peptide': 647} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 626} Chain breaks: 3 Chain: "C" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5202 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 626} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5202 Classifications: {'peptide': 647} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 626} Chain breaks: 3 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 10.93, per 1000 atoms: 0.52 Number of scatterers: 21173 At special positions: 0 Unit cell: (168.434, 104.107, 129.499, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 36 15.00 Mg 4 11.99 O 4045 8.00 N 3694 7.00 C 13258 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: 7.85 Conformation dependent library (CDL) restraints added in 3.7 seconds 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 16 sheets defined 47.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.48 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 4.060A pdb=" N ALA A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 46 removed outlier: 3.541A pdb=" N HIS A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.614A pdb=" N GLN A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 92 removed outlier: 4.137A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 99 No H-bonds generated for 'chain 'A' and resid 96 through 99' Processing helix chain 'A' and resid 122 through 141 removed outlier: 3.699A pdb=" N ALA A 130 " --> pdb=" O MET A 126 " (cutoff:3.500A) Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 198 through 214 removed outlier: 3.949A pdb=" N VAL A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 246 Proline residue: A 230 - end of helix removed outlier: 4.160A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 300 removed outlier: 3.626A pdb=" N GLN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 366 through 381 removed outlier: 4.421A pdb=" N ASP A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 381 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 409 Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 456 through 485 removed outlier: 3.534A pdb=" N ASN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 514 through 519 removed outlier: 3.548A pdb=" N ILE A 517 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN A 518 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS A 519 " --> pdb=" O VAL A 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 514 through 519' Processing helix chain 'A' and resid 529 through 536 Processing helix chain 'A' and resid 545 through 569 removed outlier: 3.813A pdb=" N GLU A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 595 removed outlier: 4.641A pdb=" N LYS A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.746A pdb=" N ASP A 633 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'B' and resid 17 through 28 removed outlier: 3.550A pdb=" N MET B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 48 Processing helix chain 'B' and resid 57 through 70 removed outlier: 3.619A pdb=" N ALA B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B 70 " --> pdb=" O MET B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 94 removed outlier: 4.003A pdb=" N GLN B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.581A pdb=" N ILE B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 122 through 141 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 200 through 213 removed outlier: 3.763A pdb=" N GLN B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 246 Proline residue: B 230 - end of helix removed outlier: 4.020A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 304 removed outlier: 4.844A pdb=" N HIS B 279 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 280 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE B 302 " --> pdb=" O MET B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 removed outlier: 3.512A pdb=" N CYS B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 331 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU B 333 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 381 removed outlier: 3.953A pdb=" N CYS B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.728A pdb=" N CYS B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 463 through 485 removed outlier: 3.731A pdb=" N ASN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 496 through 499 No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 545 through 569 removed outlier: 3.932A pdb=" N GLU B 549 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 595 removed outlier: 3.883A pdb=" N GLN B 594 " --> pdb=" O LYS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 632 Proline residue: B 630 - end of helix Processing helix chain 'B' and resid 653 through 665 removed outlier: 3.508A pdb=" N VAL B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.728A pdb=" N MET C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 47 removed outlier: 3.589A pdb=" N GLU C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 69 Processing helix chain 'C' and resid 75 through 92 removed outlier: 3.998A pdb=" N LYS C 79 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 92 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 122 through 141 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 145 through 152 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 197 through 214 removed outlier: 3.610A pdb=" N ALA C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 246 Proline residue: C 230 - end of helix removed outlier: 4.021A pdb=" N ARG C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N MET C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 300 removed outlier: 4.563A pdb=" N ALA C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 290 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 338 removed outlier: 3.896A pdb=" N CYS C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 381 removed outlier: 4.386A pdb=" N ASP C 369 " --> pdb=" O ARG C 366 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU C 370 " --> pdb=" O ASN C 367 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 381 " --> pdb=" O THR C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 409 Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 458 through 485 Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 514 through 519 removed outlier: 4.403A pdb=" N ASN C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N HIS C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 514 through 519' Processing helix chain 'C' and resid 529 through 536 Processing helix chain 'C' and resid 545 through 569 Processing helix chain 'C' and resid 586 through 595 removed outlier: 3.857A pdb=" N LYS C 590 " --> pdb=" O LYS C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 628 Processing helix chain 'C' and resid 653 through 665 Processing helix chain 'D' and resid 20 through 28 removed outlier: 3.537A pdb=" N LYS D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 48 removed outlier: 3.920A pdb=" N GLN D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 70 removed outlier: 3.645A pdb=" N ALA D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 70 " --> pdb=" O MET D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 94 removed outlier: 3.970A pdb=" N GLN D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS D 79 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 122 through 141 Proline residue: D 136 - end of helix Processing helix chain 'D' and resid 145 through 152 Processing helix chain 'D' and resid 176 through 182 Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.896A pdb=" N ALA D 201 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 243 removed outlier: 3.543A pdb=" N LEU D 228 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 4.008A pdb=" N ARG D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 254 No H-bonds generated for 'chain 'D' and resid 252 through 254' Processing helix chain 'D' and resid 276 through 303 removed outlier: 3.814A pdb=" N ALA D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS D 303 " --> pdb=" O MET D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 335 removed outlier: 3.546A pdb=" N GLN D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.769A pdb=" N ALA D 379 " --> pdb=" O CYS D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 409 Processing helix chain 'D' and resid 444 through 450 removed outlier: 4.123A pdb=" N CYS D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 485 removed outlier: 3.506A pdb=" N ASN D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 492 No H-bonds generated for 'chain 'D' and resid 490 through 492' Processing helix chain 'D' and resid 496 through 499 No H-bonds generated for 'chain 'D' and resid 496 through 499' Processing helix chain 'D' and resid 513 through 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 530 through 536 Processing helix chain 'D' and resid 545 through 569 Processing helix chain 'D' and resid 589 through 595 removed outlier: 3.967A pdb=" N GLN D 594 " --> pdb=" O LYS D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 634 Proline residue: D 630 - end of helix removed outlier: 4.626A pdb=" N ASP D 633 " --> pdb=" O ALA D 629 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU D 634 " --> pdb=" O PRO D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 665 Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 156 through 158 removed outlier: 7.626A pdb=" N THR A 521 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE A 438 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLY A 523 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR A 440 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY A 525 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASN A 442 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE A 527 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 526 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.496A pdb=" N ILE A 350 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR A 317 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 352 " --> pdb=" O TYR A 317 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN A 385 " --> pdb=" O TRP A 353 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LYS A 355 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 387 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 641 through 643 Processing sheet with id= E, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= F, first strand: chain 'B' and resid 156 through 158 removed outlier: 7.812A pdb=" N THR B 521 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 438 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY B 523 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N THR B 440 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY B 525 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ASN B 442 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE B 527 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B 526 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 184 through 186 removed outlier: 3.575A pdb=" N GLY B 189 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.515A pdb=" N ILE B 350 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYR B 317 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE B 352 " --> pdb=" O TYR B 317 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN B 385 " --> pdb=" O TRP B 353 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LYS B 355 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU B 387 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 4 through 6 Processing sheet with id= J, first strand: chain 'C' and resid 156 through 158 removed outlier: 7.672A pdb=" N THR C 521 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE C 438 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY C 523 " --> pdb=" O PHE C 438 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N THR C 440 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY C 525 " --> pdb=" O THR C 440 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ASN C 442 " --> pdb=" O GLY C 525 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE C 527 " --> pdb=" O ASN C 442 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE C 526 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 219 through 221 removed outlier: 6.544A pdb=" N ILE C 350 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR C 317 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE C 352 " --> pdb=" O TYR C 317 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASN C 385 " --> pdb=" O TRP C 353 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LYS C 355 " --> pdb=" O ASN C 385 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU C 387 " --> pdb=" O LYS C 355 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 641 through 643 Processing sheet with id= M, first strand: chain 'D' and resid 12 through 14 Processing sheet with id= N, first strand: chain 'D' and resid 156 through 158 removed outlier: 7.334A pdb=" N THR D 521 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N PHE D 438 " --> pdb=" O THR D 521 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLY D 523 " --> pdb=" O PHE D 438 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N THR D 440 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY D 525 " --> pdb=" O THR D 440 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN D 442 " --> pdb=" O GLY D 525 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE D 527 " --> pdb=" O ASN D 442 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE D 526 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 184 through 186 removed outlier: 3.557A pdb=" N GLY D 189 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.325A pdb=" N ILE D 350 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N TYR D 317 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE D 352 " --> pdb=" O TYR D 317 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN D 385 " --> pdb=" O TRP D 353 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LYS D 355 " --> pdb=" O ASN D 385 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU D 387 " --> pdb=" O LYS D 355 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 2091 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: 6.90 Time building geometry restraints manager: 8.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6968 1.34 - 1.46: 3841 1.46 - 1.58: 10502 1.58 - 1.69: 58 1.69 - 1.81: 236 Bond restraints: 21605 Sorted by residual: bond pdb=" CA TYR B 607 " pdb=" C TYR B 607 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.08e-02 8.57e+03 9.40e-01 bond pdb=" CA LYS C 135 " pdb=" C LYS C 135 " ideal model delta sigma weight residual 1.520 1.532 -0.012 1.23e-02 6.61e+03 8.82e-01 bond pdb=" CA GLY C 325 " pdb=" C GLY C 325 " ideal model delta sigma weight residual 1.515 1.509 0.006 6.20e-03 2.60e+04 8.79e-01 bond pdb=" CA LYS A 135 " pdb=" C LYS A 135 " ideal model delta sigma weight residual 1.520 1.532 -0.011 1.23e-02 6.61e+03 8.33e-01 bond pdb=" CG PRO D 384 " pdb=" CD PRO D 384 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 7.87e-01 ... (remaining 21600 not shown) Histogram of bond angle deviations from ideal: 99.99 - 107.98: 892 107.98 - 115.97: 13262 115.97 - 123.96: 14511 123.96 - 131.95: 476 131.95 - 139.94: 56 Bond angle restraints: 29197 Sorted by residual: angle pdb=" C ARG D 604 " pdb=" N ASP D 605 " pdb=" CA ASP D 605 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N ILE B 443 " pdb=" CA ILE B 443 " pdb=" C ILE B 443 " ideal model delta sigma weight residual 113.71 110.22 3.49 9.50e-01 1.11e+00 1.35e+01 angle pdb=" C SER C 48 " pdb=" N TYR C 49 " pdb=" CA TYR C 49 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.64e+00 angle pdb=" N VAL B 377 " pdb=" CA VAL B 377 " pdb=" C VAL B 377 " ideal model delta sigma weight residual 111.81 109.58 2.23 8.60e-01 1.35e+00 6.72e+00 angle pdb=" C ALA C 504 " pdb=" N GLU C 505 " pdb=" CA GLU C 505 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.32e+00 ... (remaining 29192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 12105 17.65 - 35.30: 617 35.30 - 52.95: 140 52.95 - 70.59: 25 70.59 - 88.24: 10 Dihedral angle restraints: 12897 sinusoidal: 5341 harmonic: 7556 Sorted by residual: dihedral pdb=" CA ILE B 460 " pdb=" C ILE B 460 " pdb=" N ASP B 461 " pdb=" CA ASP B 461 " ideal model delta harmonic sigma weight residual 180.00 149.51 30.49 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CA GLY B 34 " pdb=" C GLY B 34 " pdb=" N GLU B 35 " pdb=" CA GLU B 35 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA SER D 71 " pdb=" C SER D 71 " pdb=" N ALA D 72 " pdb=" CA ALA D 72 " ideal model delta harmonic sigma weight residual 180.00 157.54 22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 12894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1642 0.027 - 0.053: 901 0.053 - 0.080: 391 0.080 - 0.106: 131 0.106 - 0.133: 69 Chirality restraints: 3134 Sorted by residual: chirality pdb=" CA ILE D 598 " pdb=" N ILE D 598 " pdb=" C ILE D 598 " pdb=" CB ILE D 598 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL D 613 " pdb=" N VAL D 613 " pdb=" C VAL D 613 " pdb=" CB VAL D 613 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE B 598 " pdb=" N ILE B 598 " pdb=" C ILE B 598 " pdb=" CB ILE B 598 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 3131 not shown) Planarity restraints: 3718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 298 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C ASN B 298 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN B 298 " -0.011 2.00e-02 2.50e+03 pdb=" N MET B 299 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 121 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 122 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 121 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO C 122 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 122 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 122 " -0.022 5.00e-02 4.00e+02 ... (remaining 3715 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 102 2.53 - 3.12: 15570 3.12 - 3.71: 31355 3.71 - 4.31: 45571 4.31 - 4.90: 77375 Nonbonded interactions: 169973 Sorted by model distance: nonbonded pdb=" O3B DTP C 801 " pdb="MG MG D 804 " model vdw 1.935 2.170 nonbonded pdb=" O2A DTP A 801 " pdb="MG MG B 804 " model vdw 2.009 2.170 nonbonded pdb="MG MG C 804 " pdb=" O3G DTP D 801 " model vdw 2.025 2.170 nonbonded pdb=" O3B DTP A 801 " pdb="MG MG B 804 " model vdw 2.037 2.170 nonbonded pdb=" O2A DTP C 801 " pdb="MG MG D 804 " model vdw 2.038 2.170 ... (remaining 169968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 305 or resid 311 through 674 or \ resid 801 through 804)) selection = (chain 'B' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 674 or resid 801 through 804)) selection = (chain 'C' and (resid 1 through 305 or resid 311 through 674 or resid 801 throug \ h 804)) selection = (chain 'D' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 674 or resid 801 through 804)) } 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: 5.120 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: 0.020 Extract box with map and model: 19.690 Check model and map are aligned: 0.370 Set scattering table: 0.190 Process input model: 56.120 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 0.036 21605 Z= 0.195 Angle : 0.494 7.340 29197 Z= 0.277 Chirality : 0.042 0.133 3134 Planarity : 0.004 0.042 3718 Dihedral : 11.453 88.243 8033 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.85 % Favored : 93.04 % Rotamer: Outliers : 2.68 % Allowed : 5.81 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.71 (0.17), residues: 2556 helix: 0.71 (0.16), residues: 1230 sheet: 0.72 (0.37), residues: 224 loop : -2.17 (0.17), residues: 1102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 572 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 10 residues processed: 618 average time/residue: 1.4153 time to fit residues: 986.4957 Evaluate side-chains 501 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 491 time to evaluate : 2.457 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.2946 time to fit residues: 5.0937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.4980 chunk 194 optimal weight: 0.0870 chunk 107 optimal weight: 0.0040 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 0.0170 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 232 optimal weight: 0.6980 overall best weight: 0.2608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 213 ASN A 338 GLN A 435 ASN A 455 ASN A 477 GLN A 518 ASN A 639 HIS A 667 ASN A 674 ASN B 78 GLN B 85 ASN B 88 ASN B 219 GLN B 271 GLN B 334 GLN B 342 ASN B 385 ASN B 388 ASN C 42 GLN C 54 GLN C 88 ASN C 154 ASN C 181 ASN C 219 GLN C 237 GLN C 242 ASN C 253 ASN C 338 GLN C 455 ASN C 458 GLN C 477 GLN C 485 GLN C 492 GLN C 541 HIS C 609 ASN C 626 GLN C 639 HIS C 667 ASN D 30 HIS D 54 GLN D 78 GLN D 85 ASN D 213 ASN D 237 GLN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21605 Z= 0.147 Angle : 0.494 10.783 29197 Z= 0.262 Chirality : 0.041 0.170 3134 Planarity : 0.004 0.038 3718 Dihedral : 6.197 79.669 2872 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.75 % Favored : 94.13 % Rotamer: Outliers : 3.84 % Allowed : 13.76 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.42 (0.17), residues: 2556 helix: 0.95 (0.16), residues: 1212 sheet: 1.13 (0.38), residues: 214 loop : -2.02 (0.17), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 492 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 26 residues processed: 538 average time/residue: 1.5110 time to fit residues: 907.7579 Evaluate side-chains 492 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 466 time to evaluate : 2.282 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 17 residues processed: 9 average time/residue: 0.5949 time to fit residues: 10.1378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.0040 chunk 72 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 232 optimal weight: 0.1980 chunk 251 optimal weight: 0.2980 chunk 207 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 186 optimal weight: 0.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 395 GLN A 639 HIS B 46 HIS B 61 GLN B 78 GLN B 342 ASN B 541 HIS C 237 GLN C 253 ASN C 485 GLN C 609 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21605 Z= 0.159 Angle : 0.484 6.889 29197 Z= 0.257 Chirality : 0.041 0.174 3134 Planarity : 0.004 0.037 3718 Dihedral : 6.048 79.104 2872 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.90 % Rotamer: Outliers : 3.84 % Allowed : 15.54 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.36 (0.17), residues: 2556 helix: 0.97 (0.16), residues: 1230 sheet: 1.17 (0.38), residues: 214 loop : -1.99 (0.17), residues: 1112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 487 time to evaluate : 2.317 Fit side-chains revert: symmetry clash outliers start: 86 outliers final: 32 residues processed: 530 average time/residue: 1.4672 time to fit residues: 871.2802 Evaluate side-chains 500 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 468 time to evaluate : 2.406 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 16 residues processed: 16 average time/residue: 0.4413 time to fit residues: 13.3049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 233 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN A 278 GLN A 639 HIS B 342 ASN B 541 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN C 289 HIS C 609 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21605 Z= 0.278 Angle : 0.547 7.748 29197 Z= 0.291 Chirality : 0.044 0.159 3134 Planarity : 0.004 0.041 3718 Dihedral : 6.406 82.873 2872 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.16 % Favored : 92.72 % Rotamer: Outliers : 4.06 % Allowed : 15.90 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.17), residues: 2556 helix: 0.87 (0.16), residues: 1216 sheet: 0.71 (0.36), residues: 234 loop : -2.09 (0.17), residues: 1106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 481 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 43 residues processed: 519 average time/residue: 1.5303 time to fit residues: 887.2314 Evaluate side-chains 515 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 472 time to evaluate : 2.478 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 20 residues processed: 23 average time/residue: 0.5688 time to fit residues: 20.8009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.4980 chunk 140 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 222 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN A 278 GLN A 639 HIS B 342 ASN B 541 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN D 18 GLN D 54 GLN D 61 GLN D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21605 Z= 0.260 Angle : 0.544 7.181 29197 Z= 0.289 Chirality : 0.044 0.212 3134 Planarity : 0.004 0.047 3718 Dihedral : 6.447 87.361 2872 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.92 % Favored : 92.96 % Rotamer: Outliers : 3.97 % Allowed : 17.60 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.58 (0.17), residues: 2556 helix: 0.85 (0.16), residues: 1220 sheet: 0.63 (0.36), residues: 234 loop : -2.11 (0.17), residues: 1102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 475 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 45 residues processed: 527 average time/residue: 1.5033 time to fit residues: 886.8036 Evaluate side-chains 516 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 471 time to evaluate : 2.679 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 25 residues processed: 20 average time/residue: 0.5686 time to fit residues: 18.2437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.5980 chunk 222 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 61 optimal weight: 0.0270 chunk 247 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 338 GLN A 639 HIS B 342 ASN B 541 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN D 18 GLN D 54 GLN D 61 GLN D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21605 Z= 0.259 Angle : 0.549 8.375 29197 Z= 0.291 Chirality : 0.044 0.149 3134 Planarity : 0.004 0.042 3718 Dihedral : 6.441 89.134 2872 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.36 % Favored : 92.57 % Rotamer: Outliers : 3.80 % Allowed : 18.54 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.58 (0.17), residues: 2556 helix: 0.86 (0.15), residues: 1220 sheet: 0.59 (0.36), residues: 234 loop : -2.12 (0.17), residues: 1102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 466 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 45 residues processed: 509 average time/residue: 1.5818 time to fit residues: 900.7243 Evaluate side-chains 511 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 466 time to evaluate : 2.480 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 26 residues processed: 19 average time/residue: 0.7397 time to fit residues: 21.0267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 208 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 113 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 639 HIS B 342 ASN B 541 HIS ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 54 GLN D 61 GLN D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21605 Z= 0.234 Angle : 0.544 7.918 29197 Z= 0.287 Chirality : 0.044 0.157 3134 Planarity : 0.004 0.060 3718 Dihedral : 6.388 89.520 2872 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.89 % Favored : 93.04 % Rotamer: Outliers : 3.22 % Allowed : 19.38 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.54 (0.17), residues: 2556 helix: 0.89 (0.15), residues: 1226 sheet: 0.62 (0.36), residues: 234 loop : -2.12 (0.17), residues: 1096 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 470 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 45 residues processed: 511 average time/residue: 1.4926 time to fit residues: 854.0165 Evaluate side-chains 512 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 467 time to evaluate : 2.375 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 29 residues processed: 16 average time/residue: 0.5294 time to fit residues: 14.6312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.0570 chunk 98 optimal weight: 0.0770 chunk 147 optimal weight: 2.9990 chunk 74 optimal weight: 0.0570 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 639 HIS B 242 ASN B 541 HIS ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 242 ASN D 300 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21605 Z= 0.164 Angle : 0.526 9.515 29197 Z= 0.276 Chirality : 0.042 0.144 3134 Planarity : 0.004 0.052 3718 Dihedral : 6.167 84.716 2872 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.77 % Favored : 93.19 % Rotamer: Outliers : 2.90 % Allowed : 20.01 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.17), residues: 2556 helix: 0.99 (0.16), residues: 1232 sheet: 0.99 (0.38), residues: 214 loop : -2.02 (0.17), residues: 1110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 460 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 43 residues processed: 502 average time/residue: 1.5117 time to fit residues: 851.4539 Evaluate side-chains 488 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 445 time to evaluate : 2.508 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 29 residues processed: 15 average time/residue: 0.8309 time to fit residues: 18.5953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 215 optimal weight: 0.0870 chunk 229 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 639 HIS B 242 ASN C 181 ASN C 242 ASN D 61 GLN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN D 300 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21605 Z= 0.253 Angle : 0.564 9.968 29197 Z= 0.297 Chirality : 0.044 0.198 3134 Planarity : 0.004 0.044 3718 Dihedral : 6.313 86.042 2872 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.68 % Allowed : 20.63 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.46 (0.17), residues: 2556 helix: 0.94 (0.15), residues: 1230 sheet: 0.63 (0.36), residues: 234 loop : -2.06 (0.17), residues: 1092 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 447 time to evaluate : 2.559 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 38 residues processed: 482 average time/residue: 1.5208 time to fit residues: 820.2749 Evaluate side-chains 481 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 443 time to evaluate : 2.135 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 28 residues processed: 10 average time/residue: 0.7722 time to fit residues: 12.5672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 278 GLN A 639 HIS B 242 ASN C 181 ASN ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21605 Z= 0.253 Angle : 0.569 10.134 29197 Z= 0.299 Chirality : 0.044 0.175 3134 Planarity : 0.004 0.057 3718 Dihedral : 6.378 87.876 2872 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.97 % Allowed : 21.66 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.51 (0.17), residues: 2556 helix: 0.89 (0.15), residues: 1232 sheet: 0.64 (0.36), residues: 234 loop : -2.08 (0.17), residues: 1090 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 456 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 33 residues processed: 490 average time/residue: 1.5443 time to fit residues: 849.9479 Evaluate side-chains 490 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 457 time to evaluate : 2.397 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 28 residues processed: 6 average time/residue: 0.4421 time to fit residues: 7.1349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 208 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 278 GLN A 639 HIS B 242 ASN B 626 GLN C 181 ASN ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.135777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.123370 restraints weight = 30080.202| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.67 r_work: 0.3626 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21605 Z= 0.244 Angle : 0.573 13.420 29197 Z= 0.299 Chirality : 0.044 0.188 3134 Planarity : 0.004 0.048 3718 Dihedral : 6.383 88.470 2872 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.05 % Allowed : 21.88 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.52 (0.17), residues: 2556 helix: 0.90 (0.15), residues: 1230 sheet: 0.65 (0.36), residues: 234 loop : -2.11 (0.17), residues: 1092 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11963.42 seconds wall clock time: 212 minutes 32.30 seconds (12752.30 seconds total)