Starting phenix.real_space_refine on Wed Aug 7 23:19:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2c_17360/08_2024/8p2c_17360.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2c_17360/08_2024/8p2c_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_17360/08_2024/8p2c_17360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2c_17360/08_2024/8p2c_17360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2c_17360/08_2024/8p2c_17360.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2c_17360/08_2024/8p2c_17360.cif" } 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 12.76, per 1000 atoms: 0.60 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: 7.92 Conformation dependent library (CDL) restraints added in 3.4 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... Secondary structure from input PDB file: 108 helices and 14 sheets defined 54.0% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 removed outlier: 3.575A pdb=" N ALA A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) 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 36 through 45 removed outlier: 4.207A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 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 74 through 92 removed outlier: 3.854A pdb=" N GLN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) 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 95 through 100 Processing helix chain 'A' and resid 121 through 142 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 144 through 153 Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 175 through 182 removed outlier: 4.064A pdb=" N ILE A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 213 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) Processing helix chain 'A' and resid 223 through 247 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 272 through 301 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 323 through 339 Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.699A pdb=" N LYS A 408 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 455 through 486 removed outlier: 3.534A pdb=" N ASN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 513 through 520 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) Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 544 through 570 removed outlier: 3.728A pdb=" N GLN A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) 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 585 through 596 removed outlier: 3.815A pdb=" N LYS A 589 " --> pdb=" O GLY A 585 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 4.382A pdb=" N LEU A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 Processing helix chain 'B' and resid 17 through 29 removed outlier: 3.550A pdb=" N MET B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 49 removed outlier: 4.027A pdb=" N GLN B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 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) Processing helix chain 'B' and resid 73 through 93 removed outlier: 4.081A pdb=" N ALA B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) 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) Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.922A pdb=" N SER B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 103' Processing helix chain 'B' and resid 121 through 142 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 175 through 182 removed outlier: 4.156A pdb=" N ILE B 179 " --> pdb=" O PRO B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.717A pdb=" N LEU B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 229 through 247 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) removed outlier: 3.763A pdb=" N THR B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 277 through 305 removed outlier: 3.845A pdb=" N ILE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS B 303 " --> pdb=" O MET B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 339 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 368 through 382 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 405 through 410 removed outlier: 3.588A pdb=" N LYS B 408 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 455 through 460 Processing helix chain 'B' and resid 462 through 486 removed outlier: 3.731A pdb=" N ASN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 512 through 520 removed outlier: 4.554A pdb=" N SER B 515 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE B 517 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASN B 518 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS B 519 " --> pdb=" O VAL B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 535 removed outlier: 3.549A pdb=" N CYS B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 570 removed outlier: 4.058A pdb=" N GLN B 548 " --> pdb=" O SER B 544 " (cutoff:3.500A) 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 587 through 596 removed outlier: 3.883A pdb=" N GLN B 594 " --> pdb=" O LYS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 630 through 633 removed outlier: 3.691A pdb=" N ASP B 633 " --> pdb=" O PRO B 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 630 through 633' Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.508A pdb=" N VAL B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 29 removed outlier: 3.728A pdb=" N MET C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 48 removed outlier: 3.935A pdb=" N ILE C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) 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 70 removed outlier: 3.718A pdb=" N LYS C 70 " --> pdb=" O MET C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 92 removed outlier: 3.860A pdb=" N GLN C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) 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 94 through 101 Processing helix chain 'C' and resid 121 through 142 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 175 through 182 removed outlier: 4.208A pdb=" N ILE C 179 " --> pdb=" O PRO C 175 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 211 removed outlier: 3.975A pdb=" N ALA C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) 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) Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 231 through 247 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 274 through 301 removed outlier: 3.605A pdb=" N GLN C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) 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 322 through 339 removed outlier: 3.529A pdb=" N ARG C 326 " --> pdb=" O SER C 322 " (cutoff:3.500A) 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 367 through 382 removed outlier: 3.648A pdb=" N TYR C 371 " --> pdb=" O ASN C 367 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.754A pdb=" N LYS C 408 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 450 Processing helix chain 'C' and resid 457 through 486 removed outlier: 3.651A pdb=" N ASP C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 493 removed outlier: 3.539A pdb=" N GLN C 492 " --> pdb=" O MET C 489 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 493 " --> pdb=" O ALA C 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 489 through 493' Processing helix chain 'C' and resid 513 through 518 removed outlier: 4.403A pdb=" N ASN C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 537 Processing helix chain 'C' and resid 544 through 570 removed outlier: 3.525A pdb=" N GLN C 548 " --> pdb=" O SER C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 596 removed outlier: 3.857A pdb=" N LYS C 590 " --> pdb=" O LYS C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 629 Processing helix chain 'C' and resid 653 through 666 Processing helix chain 'D' and resid 19 through 29 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 36 through 49 removed outlier: 4.570A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) 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 69 removed outlier: 3.645A pdb=" N ALA D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 93 removed outlier: 3.969A pdb=" N ALA D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) 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) Processing helix chain 'D' and resid 97 through 103 Processing helix chain 'D' and resid 121 through 142 Proline residue: D 136 - end of helix Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 175 through 183 removed outlier: 4.174A pdb=" N ILE D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 213 removed outlier: 3.636A pdb=" N ALA D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) 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) removed outlier: 3.760A pdb=" N ASN D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.543A pdb=" N LEU D 228 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 244 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 251 through 255 removed outlier: 3.883A pdb=" N TYR D 255 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 304 removed outlier: 3.534A pdb=" N HIS D 279 " --> pdb=" O ARG D 275 " (cutoff:3.500A) 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 322 through 336 removed outlier: 3.546A pdb=" N GLN D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 378 Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.694A pdb=" N LYS D 408 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 449 Processing helix chain 'D' and resid 455 through 486 removed outlier: 3.506A pdb=" N ASN D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 493 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'D' and resid 512 through 516 removed outlier: 4.420A pdb=" N SER D 515 " --> pdb=" O THR D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 537 Processing helix chain 'D' and resid 544 through 570 Processing helix chain 'D' and resid 588 through 596 removed outlier: 3.967A pdb=" N GLN D 594 " --> pdb=" O LYS D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 629 Processing helix chain 'D' and resid 630 through 635 removed outlier: 4.391A pdb=" N ASP D 633 " --> pdb=" O PRO D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 666 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.455A pdb=" N THR A 4 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 removed outlier: 5.119A pdb=" N ASN A 435 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLY A 523 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER A 437 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N GLY A 525 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER A 439 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE A 527 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 441 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 526 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.525A pdb=" N VAL A 172 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN A 219 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN A 316 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A 221 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER A 313 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE A 352 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 315 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LYS A 354 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N TYR A 317 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE A 641 " --> pdb=" O SER A 672 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AA5, first strand: chain 'B' and resid 156 through 158 removed outlier: 7.883A pdb=" N GLY B 523 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE B 438 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY B 525 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N THR B 440 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE B 527 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASN B 442 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B 526 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 173 removed outlier: 6.497A pdb=" N VAL B 172 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER B 313 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ILE B 352 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 315 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS B 354 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR B 317 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN B 351 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU B 387 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP B 353 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing sheet with id=AA7, 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=AA8, first strand: chain 'C' and resid 12 through 13 removed outlier: 6.352A pdb=" N THR C 4 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 156 through 158 removed outlier: 5.139A pdb=" N ASN C 435 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N GLY C 523 " --> pdb=" O ASN C 435 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER C 437 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLY C 525 " --> pdb=" O SER C 437 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER C 439 " --> pdb=" O GLY C 525 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE C 527 " --> pdb=" O SER C 439 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE C 441 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU C 522 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU C 576 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE C 524 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 172 through 173 removed outlier: 6.609A pdb=" N VAL C 172 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN C 219 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ASN C 316 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE C 221 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER C 313 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE C 352 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 315 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LYS C 354 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR C 317 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.644A pdb=" N SER D 53 " --> pdb=" O ILE D 2 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 156 through 158 removed outlier: 5.021A pdb=" N ASN D 435 " --> pdb=" O THR D 521 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLY D 523 " --> pdb=" O ASN D 435 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER D 437 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLY D 525 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER D 439 " --> pdb=" O GLY D 525 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE D 527 " --> pdb=" O SER D 439 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE D 441 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE D 526 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 172 through 173 removed outlier: 6.463A pdb=" N VAL D 172 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER D 313 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE D 352 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 315 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LYS D 354 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR D 317 " --> pdb=" O LYS D 354 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN D 351 " --> pdb=" O ASN D 385 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU D 387 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP D 353 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing sheet with id=AB5, 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) 878 hydrogen bonds defined for protein. 2544 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: 6.38 Time building geometry restraints manager: 8.74 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: 12218 17.65 - 35.30: 723 35.30 - 52.95: 207 52.95 - 70.59: 50 70.59 - 88.24: 23 Dihedral angle restraints: 13221 sinusoidal: 5665 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 13218 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: 101 2.53 - 3.12: 15481 3.12 - 3.71: 31294 3.71 - 4.31: 45268 4.31 - 4.90: 77305 Nonbonded interactions: 169449 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 169444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 9.870 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: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 55.760 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.540 ------------------------------------------------------------------------------- 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= 0.192 Angle : 0.494 7.340 29197 Z= 0.277 Chirality : 0.042 0.133 3134 Planarity : 0.004 0.042 3718 Dihedral : 13.175 88.243 8357 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 409 HIS 0.003 0.001 HIS D 279 PHE 0.015 0.001 PHE D 438 TYR 0.015 0.001 TYR B 163 ARG 0.003 0.000 ARG C 330 *********************** 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 : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6747 (mm-30) REVERT: A 604 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.8037 (mtt-85) REVERT: A 628 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 645 ILE cc_start: 0.8613 (tt) cc_final: 0.8325 (pt) REVERT: B 96 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7725 (mtp180) REVERT: B 497 MET cc_start: 0.8725 (mmt) cc_final: 0.8185 (mmt) REVERT: C 206 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8084 (mm) REVERT: D 17 GLU cc_start: 0.7272 (tp30) cc_final: 0.7041 (tp30) REVERT: D 152 MET cc_start: 0.6358 (ttm) cc_final: 0.6065 (ttm) REVERT: D 160 ASP cc_start: 0.6753 (p0) cc_final: 0.6385 (p0) REVERT: D 273 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7431 (ttt-90) REVERT: D 405 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7137 (pp20) REVERT: D 587 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.7206 (m-80) outliers start: 60 outliers final: 10 residues processed: 618 average time/residue: 1.3445 time to fit residues: 941.1342 Evaluate side-chains 503 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 490 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 232 optimal weight: 0.0070 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 338 GLN A 435 ASN A 455 ASN A 477 GLN A 518 ASN B 85 ASN B 88 ASN B 219 GLN B 271 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 342 ASN B 385 ASN B 388 ASN B 541 HIS 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 492 GLN C 541 HIS C 609 ASN C 626 GLN 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** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21605 Z= 0.167 Angle : 0.530 10.735 29197 Z= 0.282 Chirality : 0.043 0.180 3134 Planarity : 0.004 0.038 3718 Dihedral : 11.159 87.470 3223 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 3.71 % Allowed : 13.53 % Favored : 82.76 % 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: -0.44 (0.17), residues: 2556 helix: 0.85 (0.16), residues: 1264 sheet: 1.12 (0.37), residues: 212 loop : -2.04 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 409 HIS 0.006 0.001 HIS B 297 PHE 0.024 0.001 PHE B 641 TYR 0.019 0.001 TYR D 337 ARG 0.009 0.000 ARG D 400 *********************** 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 568 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 485 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7462 (mtm) cc_final: 0.7167 (mmm) REVERT: A 489 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7494 (mtp) REVERT: A 594 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: B 50 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7911 (mtt-85) REVERT: B 96 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7692 (mtp180) REVERT: B 397 GLU cc_start: 0.7708 (pp20) cc_final: 0.7489 (pp20) REVERT: C 39 LEU cc_start: 0.8498 (tp) cc_final: 0.8196 (tt) REVERT: C 66 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7737 (tpt) REVERT: C 489 MET cc_start: 0.7456 (mtp) cc_final: 0.7133 (mtp) REVERT: D 41 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: D 44 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.8033 (t) REVERT: D 148 ARG cc_start: 0.6908 (ttt-90) cc_final: 0.6662 (ttt-90) REVERT: D 548 GLN cc_start: 0.6234 (OUTLIER) cc_final: 0.5904 (tt0) outliers start: 83 outliers final: 22 residues processed: 528 average time/residue: 1.4123 time to fit residues: 837.4235 Evaluate side-chains 482 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 453 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 548 GLN Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 620 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 193 optimal weight: 0.0980 chunk 158 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 251 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 230 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 186 optimal weight: 0.0050 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 518 ASN B 297 HIS B 541 HIS C 237 GLN C 253 ASN C 609 ASN D 154 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 455 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21605 Z= 0.196 Angle : 0.522 7.056 29197 Z= 0.279 Chirality : 0.043 0.178 3134 Planarity : 0.004 0.037 3718 Dihedral : 10.750 88.013 3208 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.91 % Favored : 93.97 % Rotamer: Outliers : 3.75 % Allowed : 15.27 % Favored : 80.97 % 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: -0.35 (0.17), residues: 2556 helix: 0.96 (0.16), residues: 1264 sheet: 1.02 (0.37), residues: 212 loop : -2.02 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 409 HIS 0.004 0.001 HIS B 297 PHE 0.023 0.002 PHE D 184 TYR 0.019 0.001 TYR D 337 ARG 0.010 0.000 ARG D 400 *********************** 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 565 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 481 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7498 (mtm) cc_final: 0.7201 (mmm) REVERT: A 132 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7912 (mp0) REVERT: A 195 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6955 (mtpp) REVERT: A 487 THR cc_start: 0.7618 (p) cc_final: 0.7279 (p) REVERT: A 508 LYS cc_start: 0.8265 (mppt) cc_final: 0.8051 (mmtt) REVERT: A 594 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: B 50 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7920 (mtt-85) REVERT: B 96 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7758 (mtp180) REVERT: B 236 TYR cc_start: 0.8081 (t80) cc_final: 0.7873 (t80) REVERT: B 397 GLU cc_start: 0.7812 (pp20) cc_final: 0.7561 (OUTLIER) REVERT: C 39 LEU cc_start: 0.8463 (tp) cc_final: 0.8222 (tt) REVERT: C 49 TYR cc_start: 0.7292 (t80) cc_final: 0.6931 (t80) REVERT: C 66 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7804 (tpt) REVERT: C 628 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7971 (mt-10) REVERT: D 41 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: D 254 LEU cc_start: 0.7215 (mt) cc_final: 0.6928 (mp) REVERT: D 468 ASP cc_start: 0.6521 (OUTLIER) cc_final: 0.6254 (t0) outliers start: 84 outliers final: 27 residues processed: 520 average time/residue: 1.4819 time to fit residues: 867.3430 Evaluate side-chains 495 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 463 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 620 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 B 541 HIS C 253 ASN C 289 HIS C 338 GLN C 609 ASN D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 GLN D 626 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21605 Z= 0.293 Angle : 0.585 7.220 29197 Z= 0.312 Chirality : 0.046 0.164 3134 Planarity : 0.004 0.040 3718 Dihedral : 10.898 85.927 3204 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.85 % Favored : 93.04 % Rotamer: Outliers : 3.89 % Allowed : 15.81 % Favored : 80.30 % 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: 0.86 (0.15), residues: 1264 sheet: 0.44 (0.35), residues: 236 loop : -2.10 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 501 HIS 0.005 0.001 HIS A 541 PHE 0.024 0.002 PHE D 184 TYR 0.027 0.002 TYR B 371 ARG 0.008 0.001 ARG D 148 *********************** 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 575 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 488 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 THR cc_start: 0.8337 (t) cc_final: 0.8019 (m) REVERT: A 508 LYS cc_start: 0.8415 (mppt) cc_final: 0.8203 (mmtt) REVERT: A 576 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8274 (tp) REVERT: A 586 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8308 (mttm) REVERT: A 603 ASP cc_start: 0.7011 (m-30) cc_final: 0.6786 (m-30) REVERT: B 50 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7917 (mtt-85) REVERT: B 96 ARG cc_start: 0.7984 (mtp180) cc_final: 0.7774 (mtp180) REVERT: B 397 GLU cc_start: 0.7848 (pp20) cc_final: 0.7551 (pp20) REVERT: B 663 MET cc_start: 0.5161 (mmm) cc_final: 0.4530 (mmm) REVERT: C 39 LEU cc_start: 0.8484 (tp) cc_final: 0.8095 (tt) REVERT: C 49 TYR cc_start: 0.7255 (t80) cc_final: 0.6886 (t80) REVERT: C 66 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7845 (tpt) REVERT: C 100 MET cc_start: 0.7557 (mpp) cc_final: 0.7125 (mpp) REVERT: C 380 ARG cc_start: 0.7903 (tpt-90) cc_final: 0.7511 (tpt-90) REVERT: C 628 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8009 (mt-10) REVERT: D 41 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: D 254 LEU cc_start: 0.7321 (mt) cc_final: 0.7034 (mp) REVERT: D 449 GLU cc_start: 0.7551 (tt0) cc_final: 0.7312 (tm-30) REVERT: D 468 ASP cc_start: 0.6565 (OUTLIER) cc_final: 0.6302 (t0) outliers start: 87 outliers final: 33 residues processed: 531 average time/residue: 1.4487 time to fit residues: 863.0044 Evaluate side-chains 513 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 475 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 620 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.0980 chunk 140 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 0.0050 chunk 211 optimal weight: 0.0770 chunk 171 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 126 optimal weight: 0.0170 chunk 222 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 overall best weight: 0.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 612 HIS B 289 HIS B 342 ASN B 541 HIS ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN C 609 ASN D 242 ASN D 300 ASN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21605 Z= 0.139 Angle : 0.501 6.454 29197 Z= 0.266 Chirality : 0.041 0.162 3134 Planarity : 0.004 0.047 3718 Dihedral : 9.794 88.752 3200 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 2.68 % Allowed : 18.45 % Favored : 78.87 % 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: -0.07 (0.17), residues: 2556 helix: 1.27 (0.16), residues: 1250 sheet: 0.86 (0.36), residues: 214 loop : -1.89 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 409 HIS 0.003 0.001 HIS A 46 PHE 0.021 0.001 PHE D 184 TYR 0.024 0.001 TYR D 337 ARG 0.013 0.000 ARG D 400 *********************** 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 539 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 479 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.6931 (tp30) cc_final: 0.6695 (mm-30) REVERT: A 21 MET cc_start: 0.7521 (mmm) cc_final: 0.7246 (mmm) REVERT: A 41 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6674 (mp0) REVERT: A 45 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7008 (m-30) REVERT: A 132 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: A 301 THR cc_start: 0.8167 (t) cc_final: 0.7949 (t) REVERT: A 489 MET cc_start: 0.7677 (mtp) cc_final: 0.7338 (mtp) REVERT: A 508 LYS cc_start: 0.8320 (mppt) cc_final: 0.8104 (mmtt) REVERT: A 586 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8295 (mttm) REVERT: B 50 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7899 (mtt-85) REVERT: B 96 ARG cc_start: 0.7966 (mtp180) cc_final: 0.7764 (mtp180) REVERT: B 382 PHE cc_start: 0.6854 (m-80) cc_final: 0.6636 (m-80) REVERT: B 388 ASN cc_start: 0.7089 (m-40) cc_final: 0.6831 (t0) REVERT: B 397 GLU cc_start: 0.7804 (pp20) cc_final: 0.7544 (pp20) REVERT: C 39 LEU cc_start: 0.8364 (tp) cc_final: 0.8111 (tt) REVERT: C 47 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6575 (mm) REVERT: C 49 TYR cc_start: 0.7193 (t80) cc_final: 0.6834 (t80) REVERT: C 188 HIS cc_start: 0.8356 (p90) cc_final: 0.8090 (p90) REVERT: C 380 ARG cc_start: 0.7732 (tpt-90) cc_final: 0.7387 (tpt-90) REVERT: D 3 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: D 41 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: D 254 LEU cc_start: 0.7188 (mt) cc_final: 0.6923 (mp) REVERT: D 370 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5806 (mt) REVERT: D 405 GLU cc_start: 0.7188 (pp20) cc_final: 0.6976 (pp20) REVERT: D 468 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.6226 (t0) outliers start: 60 outliers final: 16 residues processed: 509 average time/residue: 1.3962 time to fit residues: 798.5176 Evaluate side-chains 486 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 462 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 468 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN B 541 HIS C 181 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN C 338 GLN C 609 ASN D 18 GLN D 242 ASN D 626 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21605 Z= 0.299 Angle : 0.597 8.761 29197 Z= 0.316 Chirality : 0.046 0.157 3134 Planarity : 0.004 0.038 3718 Dihedral : 10.520 85.609 3200 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 3.13 % Allowed : 18.76 % Favored : 78.12 % 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: -0.29 (0.17), residues: 2556 helix: 1.07 (0.15), residues: 1262 sheet: 0.57 (0.35), residues: 232 loop : -2.00 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 425 HIS 0.005 0.001 HIS A 541 PHE 0.025 0.002 PHE D 184 TYR 0.023 0.002 TYR D 337 ARG 0.009 0.001 ARG D 148 *********************** 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 544 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 474 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7915 (t) REVERT: A 42 GLN cc_start: 0.8423 (mt0) cc_final: 0.8023 (mp10) REVERT: A 301 THR cc_start: 0.8376 (t) cc_final: 0.8160 (t) REVERT: A 576 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8245 (tp) REVERT: A 586 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8324 (mttm) REVERT: B 50 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7908 (mtt-85) REVERT: B 96 ARG cc_start: 0.7995 (mtp180) cc_final: 0.7789 (mtp180) REVERT: B 397 GLU cc_start: 0.7868 (pp20) cc_final: 0.7554 (pp20) REVERT: C 39 LEU cc_start: 0.8446 (tp) cc_final: 0.8079 (tt) REVERT: C 47 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6764 (mm) REVERT: C 49 TYR cc_start: 0.7239 (t80) cc_final: 0.6898 (t80) REVERT: C 66 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7807 (tpt) REVERT: C 360 ASN cc_start: 0.8172 (p0) cc_final: 0.7933 (p0) REVERT: C 380 ARG cc_start: 0.7915 (tpt-90) cc_final: 0.7522 (tpt-90) REVERT: D 41 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: D 254 LEU cc_start: 0.7331 (mt) cc_final: 0.7015 (mp) REVERT: D 405 GLU cc_start: 0.7218 (pp20) cc_final: 0.6924 (pp20) REVERT: D 449 GLU cc_start: 0.7597 (tt0) cc_final: 0.7385 (pp20) REVERT: D 468 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6297 (t0) outliers start: 70 outliers final: 26 residues processed: 507 average time/residue: 1.4659 time to fit residues: 832.9914 Evaluate side-chains 499 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 466 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 468 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 180 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 208 optimal weight: 0.2980 chunk 138 optimal weight: 2.9990 chunk 246 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 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 278 GLN B 342 ASN B 541 HIS C 181 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN C 609 ASN D 18 GLN D 54 GLN D 242 ASN D 626 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3056 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= 0.264 Angle : 0.576 8.096 29197 Z= 0.306 Chirality : 0.045 0.162 3134 Planarity : 0.004 0.040 3718 Dihedral : 10.445 86.696 3200 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.65 % Favored : 93.31 % Rotamer: Outliers : 3.04 % Allowed : 18.98 % Favored : 77.98 % 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: -0.33 (0.17), residues: 2556 helix: 1.06 (0.15), residues: 1246 sheet: 0.57 (0.35), residues: 232 loop : -2.01 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 409 HIS 0.005 0.001 HIS A 541 PHE 0.025 0.002 PHE D 184 TYR 0.024 0.002 TYR D 337 ARG 0.009 0.000 ARG D 148 *********************** 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 540 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 472 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.8015 (t) REVERT: A 70 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8364 (mtmm) REVERT: A 195 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.6870 (mtpp) REVERT: A 301 THR cc_start: 0.8365 (t) cc_final: 0.8157 (t) REVERT: A 576 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8237 (tp) REVERT: A 586 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8329 (mttm) REVERT: B 1 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7801 (tmm) REVERT: B 50 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7902 (mtt-85) REVERT: B 96 ARG cc_start: 0.7996 (mtp180) cc_final: 0.7792 (mtp180) REVERT: B 270 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6303 (tt) REVERT: B 382 PHE cc_start: 0.6894 (m-80) cc_final: 0.6681 (m-80) REVERT: B 397 GLU cc_start: 0.7852 (pp20) cc_final: 0.7542 (pp20) REVERT: C 39 LEU cc_start: 0.8439 (tp) cc_final: 0.8139 (tt) REVERT: C 47 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6747 (mm) REVERT: C 49 TYR cc_start: 0.7197 (t80) cc_final: 0.6866 (t80) REVERT: C 66 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7892 (tpt) REVERT: C 67 GLU cc_start: 0.7825 (tp30) cc_final: 0.7516 (tp30) REVERT: C 100 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7307 (mpt) REVERT: C 380 ARG cc_start: 0.7891 (tpt-90) cc_final: 0.7502 (tpt-90) REVERT: D 18 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7871 (mp-120) REVERT: D 41 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: D 254 LEU cc_start: 0.7335 (mt) cc_final: 0.7073 (mp) REVERT: D 405 GLU cc_start: 0.7259 (pp20) cc_final: 0.6961 (pp20) REVERT: D 449 GLU cc_start: 0.7617 (tt0) cc_final: 0.7396 (tm-30) REVERT: D 468 ASP cc_start: 0.6551 (OUTLIER) cc_final: 0.6279 (t0) outliers start: 68 outliers final: 26 residues processed: 501 average time/residue: 1.4387 time to fit residues: 808.6807 Evaluate side-chains 502 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 464 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 468 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.86 > 50: distance: 57 - 61: 7.892 distance: 61 - 62: 8.710 distance: 62 - 63: 19.839 distance: 62 - 65: 10.432 distance: 63 - 64: 10.989 distance: 63 - 75: 38.866 distance: 65 - 66: 11.710 distance: 66 - 67: 15.221 distance: 66 - 68: 7.185 distance: 67 - 69: 9.158 distance: 68 - 70: 5.100 distance: 68 - 71: 8.242 distance: 69 - 70: 10.427 distance: 70 - 72: 6.900 distance: 71 - 73: 5.433 distance: 72 - 74: 8.214 distance: 73 - 74: 6.576 distance: 75 - 76: 36.011 distance: 76 - 77: 13.486 distance: 76 - 79: 7.953 distance: 77 - 78: 16.103 distance: 77 - 82: 17.694 distance: 79 - 80: 9.582 distance: 79 - 81: 15.024 distance: 82 - 83: 17.601 distance: 83 - 84: 17.377 distance: 84 - 85: 6.432 distance: 84 - 86: 10.289 distance: 86 - 87: 15.913 distance: 87 - 88: 8.690 distance: 87 - 90: 21.696 distance: 88 - 89: 16.054 distance: 88 - 91: 11.909 distance: 91 - 92: 12.419 distance: 92 - 93: 15.987 distance: 92 - 95: 11.515 distance: 93 - 94: 13.351 distance: 93 - 100: 16.601 distance: 95 - 96: 14.210 distance: 96 - 97: 13.660 distance: 97 - 98: 8.836 distance: 97 - 99: 6.375 distance: 100 - 101: 3.212 distance: 101 - 102: 5.695 distance: 101 - 104: 3.918 distance: 102 - 103: 7.500 distance: 102 - 108: 4.116 distance: 104 - 105: 7.042 distance: 105 - 106: 6.808 distance: 105 - 107: 6.711 distance: 109 - 112: 6.388 distance: 110 - 111: 17.892 distance: 110 - 116: 13.186 distance: 112 - 113: 12.661 distance: 113 - 114: 8.942 distance: 113 - 115: 12.829 distance: 116 - 117: 7.287 distance: 117 - 118: 6.058 distance: 117 - 120: 8.705 distance: 118 - 119: 9.947 distance: 118 - 125: 10.078 distance: 120 - 121: 12.891 distance: 121 - 122: 8.044 distance: 122 - 123: 4.503 distance: 123 - 124: 9.613 distance: 125 - 126: 16.282 distance: 125 - 131: 23.935 distance: 126 - 127: 16.460 distance: 126 - 129: 29.357 distance: 127 - 128: 10.270 distance: 127 - 132: 7.413 distance: 129 - 130: 28.707 distance: 130 - 131: 8.124 distance: 132 - 133: 8.936 distance: 133 - 134: 11.597 distance: 133 - 136: 8.714 distance: 134 - 135: 9.347 distance: 134 - 141: 5.114 distance: 136 - 137: 4.431 distance: 137 - 138: 9.830 distance: 138 - 139: 6.395 distance: 138 - 140: 7.638