Starting phenix.real_space_refine on Fri May 16 17:46:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ev8_28622/05_2025/8ev8_28622_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ev8_28622/05_2025/8ev8_28622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ev8_28622/05_2025/8ev8_28622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ev8_28622/05_2025/8ev8_28622.map" model { file = "/net/cci-nas-00/data/ceres_data/8ev8_28622/05_2025/8ev8_28622_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ev8_28622/05_2025/8ev8_28622_neut.cif" } resolution = 3.11 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= 0.045 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 66 5.16 5 C 9609 2.51 5 N 2401 2.21 5 O 2668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 187 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14748 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3675 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 449, 3664 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 449, 3664 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain breaks: 1 bond proxies already assigned to first conformer: 3733 Chain: "B" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3632 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 14, 'TRANS': 430} Chain breaks: 1 Chain: "C" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3697 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "D" Number of atoms: 3610 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Conformer: "B" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} bond proxies already assigned to first conformer: 3684 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 392 " occ=0.70 ... (20 atoms not shown) pdb=" CZ BPHE A 392 " occ=0.30 Time building chain proxies: 13.70, per 1000 atoms: 0.93 Number of scatterers: 14748 At special positions: 0 Unit cell: (107.9, 112.88, 131.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 4 15.00 O 2668 8.00 N 2401 7.00 C 9609 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 - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 339 " " NAG B 801 " - " ASN B 339 " " NAG C 801 " - " ASN C 339 " Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 2.5 seconds 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3394 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 12 sheets defined 66.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 166 through 193 Proline residue: A 178 - end of helix removed outlier: 3.864A pdb=" N ASP A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.755A pdb=" N TYR A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 222 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.804A pdb=" N LYS A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.753A pdb=" N VAL A 273 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 278 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.109A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 329 Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 374 through 407 Processing helix chain 'A' and resid 407 through 427 Processing helix chain 'A' and resid 430 through 447 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 487 through 497 Processing helix chain 'A' and resid 548 through 554 removed outlier: 3.689A pdb=" N ILE A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 591 through 610 Processing helix chain 'B' and resid 165 through 193 removed outlier: 3.856A pdb=" N TYR B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.815A pdb=" N ASP B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 199 through 223 Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.941A pdb=" N LYS B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.917A pdb=" N VAL B 273 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 278 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.218A pdb=" N LEU B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 329 Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 374 through 407 Processing helix chain 'B' and resid 407 through 427 Processing helix chain 'B' and resid 430 through 447 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 461 through 478 removed outlier: 6.164A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 591 through 610 Processing helix chain 'C' and resid 165 through 193 removed outlier: 3.945A pdb=" N TYR C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.816A pdb=" N ASP C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 199 through 222 Processing helix chain 'C' and resid 235 through 245 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.986A pdb=" N LYS C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.957A pdb=" N VAL C 273 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 278 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.957A pdb=" N LEU C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 329 Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 374 through 407 removed outlier: 3.657A pdb=" N ASN C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 427 Processing helix chain 'C' and resid 430 through 447 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 478 removed outlier: 6.088A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 591 through 610 Processing helix chain 'D' and resid 215 through 242 Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 249 through 271 removed outlier: 3.592A pdb=" N TRP D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 297 through 307 removed outlier: 4.156A pdb=" N GLN D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 removed outlier: 3.817A pdb=" N ILE D 312 " --> pdb=" O PRO D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 313 through 318 Processing helix chain 'D' and resid 324 through 329 removed outlier: 3.719A pdb=" N MET D 328 " --> pdb=" O ALA D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 345 removed outlier: 4.178A pdb=" N PHE D 334 " --> pdb=" O LYS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 379 removed outlier: 4.377A pdb=" N TYR D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'D' and resid 416 through 449 Processing helix chain 'D' and resid 449 through 469 Processing helix chain 'D' and resid 472 through 490 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'D' and resid 503 through 521 removed outlier: 3.618A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 592 through 596 Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 631 through 646 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.888A pdb=" N ILE A 568 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL A 539 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228 Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 503 Processing sheet with id=AA6, first strand: chain 'B' and resid 508 through 510 removed outlier: 6.598A pdb=" N TYR B 508 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER B 570 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 510 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 527 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL B 540 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 529 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'C' and resid 499 through 502 Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510 removed outlier: 6.463A pdb=" N TYR C 508 " --> pdb=" O SER C 570 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER C 570 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS C 510 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.034A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 541 through 545 Processing sheet with id=AB3, first strand: chain 'D' and resid 550 through 552 removed outlier: 6.543A pdb=" N PHE D 550 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA D 610 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL D 582 " --> pdb=" O VAL D 571 " (cutoff:3.500A) 938 hydrogen bonds defined for protein. 2724 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: 4.52 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4546 1.34 - 1.46: 3082 1.46 - 1.58: 7369 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 15102 Sorted by residual: bond pdb=" O5' PCG A 802 " pdb=" PA PCG A 802 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" O5' PCG D 901 " pdb=" PA PCG D 901 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" O5' PCG C 802 " pdb=" PA PCG C 802 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.39e+01 bond pdb=" O5' PCG B 802 " pdb=" PA PCG B 802 " ideal model delta sigma weight residual 1.606 1.490 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" O3' PCG D 901 " pdb=" PA PCG D 901 " ideal model delta sigma weight residual 1.617 1.513 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 15097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 20371 3.66 - 7.32: 84 7.32 - 10.98: 34 10.98 - 14.64: 4 14.64 - 18.30: 12 Bond angle restraints: 20505 Sorted by residual: angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 109.85 128.15 -18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 109.85 128.11 -18.26 3.00e+00 1.11e-01 3.70e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 109.85 128.10 -18.25 3.00e+00 1.11e-01 3.70e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 109.85 128.06 -18.21 3.00e+00 1.11e-01 3.69e+01 angle pdb=" O1A PCG A 802 " pdb=" PA PCG A 802 " pdb=" O5' PCG A 802 " ideal model delta sigma weight residual 102.28 118.01 -15.73 3.00e+00 1.11e-01 2.75e+01 ... (remaining 20500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 8477 25.94 - 51.87: 504 51.87 - 77.81: 43 77.81 - 103.75: 10 103.75 - 129.68: 16 Dihedral angle restraints: 9050 sinusoidal: 3767 harmonic: 5283 Sorted by residual: dihedral pdb=" C3' PCG B 802 " pdb=" O3' PCG B 802 " pdb=" PA PCG B 802 " pdb=" O2A PCG B 802 " ideal model delta sinusoidal sigma weight residual 279.09 149.41 129.68 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C3' PCG C 802 " pdb=" O3' PCG C 802 " pdb=" PA PCG C 802 " pdb=" O2A PCG C 802 " ideal model delta sinusoidal sigma weight residual 279.09 149.46 129.63 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C3' PCG D 901 " pdb=" O3' PCG D 901 " pdb=" PA PCG D 901 " pdb=" O2A PCG D 901 " ideal model delta sinusoidal sigma weight residual 279.09 149.46 129.63 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 9047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 2329 0.356 - 0.712: 0 0.712 - 1.069: 0 1.069 - 1.425: 0 1.425 - 1.781: 4 Chirality restraints: 2333 Sorted by residual: chirality pdb=" C4' PCG C 802 " pdb=" C3' PCG C 802 " pdb=" C5' PCG C 802 " pdb=" O4' PCG C 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.93e+01 chirality pdb=" C4' PCG B 802 " pdb=" C3' PCG B 802 " pdb=" C5' PCG B 802 " pdb=" O4' PCG B 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.92e+01 chirality pdb=" C4' PCG A 802 " pdb=" C3' PCG A 802 " pdb=" C5' PCG A 802 " pdb=" O4' PCG A 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.91e+01 ... (remaining 2330 not shown) Planarity restraints: 2526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO D 273 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 502 " 0.040 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO D 503 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 503 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 503 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 411 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO D 412 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 412 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 412 " -0.033 5.00e-02 4.00e+02 ... (remaining 2523 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3552 2.79 - 3.31: 13288 3.31 - 3.84: 25514 3.84 - 4.37: 29262 4.37 - 4.90: 50796 Nonbonded interactions: 122412 Sorted by model distance: nonbonded pdb=" O THR C 360 " pdb=" OG1 THR C 364 " model vdw 2.257 3.040 nonbonded pdb=" O SER B 551 " pdb=" OD1 ASN B 562 " model vdw 2.308 3.040 nonbonded pdb=" O THR B 360 " pdb=" OG1 THR B 364 " model vdw 2.313 3.040 nonbonded pdb=" O LEU C 195 " pdb=" NE1 TRP C 203 " model vdw 2.331 3.120 nonbonded pdb=" ND2 ASN B 317 " pdb=" OD1 ASP B 384 " model vdw 2.333 3.120 ... (remaining 122407 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 159 through 260 or resid 270 through 391 or resid 393 thro \ ugh 611 or resid 801 through 802)) selection = (chain 'B' and (resid 159 through 260 or resid 270 through 391 or resid 393 thro \ ugh 611 or resid 801 through 802)) selection = (chain 'C' and (resid 159 through 260 or resid 270 through 391 or resid 393 thro \ ugh 611 or resid 801 through 802)) } 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=0.30 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: 0.010 Normalize map: mean=0, sd=1: 1.660 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.730 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 15105 Z= 0.260 Angle : 0.871 18.302 20514 Z= 0.420 Chirality : 0.088 1.781 2333 Planarity : 0.006 0.066 2523 Dihedral : 16.901 129.682 5656 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.93 % Allowed : 12.00 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.16), residues: 1781 helix: -1.60 (0.11), residues: 1152 sheet: -2.06 (0.59), residues: 55 loop : -1.36 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 171 HIS 0.004 0.001 HIS A 473 PHE 0.016 0.002 PHE B 426 TYR 0.016 0.002 TYR C 263 ARG 0.005 0.000 ARG C 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 3) link_NAG-ASN : angle 1.92624 ( 9) hydrogen bonds : bond 0.10848 ( 938) hydrogen bonds : angle 5.34039 ( 2724) covalent geometry : bond 0.00540 (15102) covalent geometry : angle 0.87040 (20505) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 1.613 Fit side-chains REVERT: C 418 ASP cc_start: 0.8157 (m-30) cc_final: 0.7942 (m-30) REVERT: C 515 ILE cc_start: 0.8906 (mm) cc_final: 0.8671 (mm) REVERT: D 249 ASN cc_start: 0.7504 (t0) cc_final: 0.7070 (t0) outliers start: 15 outliers final: 5 residues processed: 223 average time/residue: 0.3095 time to fit residues: 97.2388 Evaluate side-chains 151 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 448 LYS Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain C residue 563 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 296 ASN A 562 ASN A 610 ASN B 196 GLN B 229 GLN B 242 HIS B 276 ASN B 407 ASN C 241 GLN C 248 GLN C 317 ASN C 398 ASN C 471 ASN C 473 HIS C 554 ASN D 232 ASN D 340 HIS D 365 HIS D 367 ASN D 423 GLN D 426 ASN D 440 GLN D 531 GLN D 602 ASN D 630 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.154463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.121021 restraints weight = 23395.052| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.30 r_work: 0.2803 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15105 Z= 0.139 Angle : 0.512 7.956 20514 Z= 0.271 Chirality : 0.041 0.193 2333 Planarity : 0.004 0.054 2523 Dihedral : 13.009 147.500 2183 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.43 % Allowed : 14.61 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.19), residues: 1781 helix: 0.51 (0.14), residues: 1132 sheet: -1.63 (0.60), residues: 55 loop : -0.76 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 445 HIS 0.003 0.001 HIS B 473 PHE 0.016 0.001 PHE D 310 TYR 0.014 0.001 TYR C 508 ARG 0.008 0.000 ARG D 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 3) link_NAG-ASN : angle 1.81727 ( 9) hydrogen bonds : bond 0.04111 ( 938) hydrogen bonds : angle 4.33235 ( 2724) covalent geometry : bond 0.00319 (15102) covalent geometry : angle 0.51041 (20505) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.608 Fit side-chains REVERT: A 481 ARG cc_start: 0.7387 (ptt180) cc_final: 0.7080 (ptt180) REVERT: A 501 THR cc_start: 0.7656 (m) cc_final: 0.7347 (p) REVERT: A 504 SER cc_start: 0.8748 (m) cc_final: 0.8544 (m) REVERT: A 546 TYR cc_start: 0.8394 (p90) cc_final: 0.8056 (p90) REVERT: B 162 ASP cc_start: 0.8058 (p0) cc_final: 0.7838 (p0) REVERT: B 274 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7705 (mtp85) REVERT: B 296 ASN cc_start: 0.6800 (p0) cc_final: 0.6347 (p0) REVERT: B 402 MET cc_start: 0.8619 (ttp) cc_final: 0.8374 (ttm) REVERT: B 497 LYS cc_start: 0.8108 (mttp) cc_final: 0.7693 (mttp) REVERT: B 546 TYR cc_start: 0.8501 (p90) cc_final: 0.8251 (p90) REVERT: C 344 GLU cc_start: 0.7625 (tp30) cc_final: 0.7339 (tp30) REVERT: C 418 ASP cc_start: 0.8635 (m-30) cc_final: 0.8370 (m-30) REVERT: D 249 ASN cc_start: 0.7527 (t0) cc_final: 0.6800 (t0) REVERT: D 252 TYR cc_start: 0.6256 (t80) cc_final: 0.5335 (m-80) REVERT: D 344 ILE cc_start: 0.8175 (tp) cc_final: 0.7959 (pt) REVERT: D 443 ASP cc_start: 0.8497 (t70) cc_final: 0.8256 (t70) REVERT: D 536 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7487 (ptp) outliers start: 23 outliers final: 15 residues processed: 183 average time/residue: 0.2361 time to fit residues: 65.9989 Evaluate side-chains 162 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 173 optimal weight: 0.0270 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 ASN C 554 ASN D 230 ASN D 440 GLN D 630 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.154771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.113320 restraints weight = 29497.908| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.06 r_work: 0.2916 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15105 Z= 0.126 Angle : 0.484 8.487 20514 Z= 0.256 Chirality : 0.040 0.178 2333 Planarity : 0.004 0.055 2523 Dihedral : 12.685 151.114 2175 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.62 % Allowed : 15.41 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1781 helix: 1.29 (0.15), residues: 1128 sheet: -0.88 (0.60), residues: 59 loop : -0.47 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 171 HIS 0.004 0.001 HIS D 365 PHE 0.014 0.001 PHE A 192 TYR 0.011 0.001 TYR C 263 ARG 0.007 0.000 ARG D 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 3) link_NAG-ASN : angle 1.83808 ( 9) hydrogen bonds : bond 0.03954 ( 938) hydrogen bonds : angle 4.10415 ( 2724) covalent geometry : bond 0.00290 (15102) covalent geometry : angle 0.48222 (20505) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.515 Fit side-chains REVERT: A 481 ARG cc_start: 0.7394 (ptt180) cc_final: 0.7077 (ptt180) REVERT: A 543 ASP cc_start: 0.7646 (t70) cc_final: 0.7364 (t0) REVERT: A 546 TYR cc_start: 0.8315 (p90) cc_final: 0.8052 (p90) REVERT: B 162 ASP cc_start: 0.8008 (p0) cc_final: 0.7663 (p0) REVERT: B 296 ASN cc_start: 0.6816 (p0) cc_final: 0.6269 (p0) REVERT: B 402 MET cc_start: 0.8649 (ttp) cc_final: 0.8429 (ttm) REVERT: B 497 LYS cc_start: 0.8129 (mttp) cc_final: 0.7692 (mttp) REVERT: B 546 TYR cc_start: 0.8495 (p90) cc_final: 0.8080 (p90) REVERT: C 292 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7670 (tt0) REVERT: C 344 GLU cc_start: 0.7663 (tp30) cc_final: 0.7338 (tp30) REVERT: C 418 ASP cc_start: 0.8663 (m-30) cc_final: 0.8413 (m-30) REVERT: D 213 TYR cc_start: 0.7412 (t80) cc_final: 0.7199 (t80) REVERT: D 249 ASN cc_start: 0.7341 (t0) cc_final: 0.6650 (t0) REVERT: D 252 TYR cc_start: 0.6273 (t80) cc_final: 0.5291 (m-80) REVERT: D 344 ILE cc_start: 0.8268 (tp) cc_final: 0.8018 (pt) REVERT: D 424 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8491 (tp) REVERT: D 443 ASP cc_start: 0.8521 (t70) cc_final: 0.8307 (t70) REVERT: D 536 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7449 (ptp) REVERT: D 559 LYS cc_start: 0.8244 (ptmt) cc_final: 0.7699 (ptmm) outliers start: 26 outliers final: 16 residues processed: 175 average time/residue: 0.2358 time to fit residues: 63.0356 Evaluate side-chains 165 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 109 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 HIS A 610 ASN B 473 HIS D 630 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.152536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.119271 restraints weight = 34963.560| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 4.56 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15105 Z= 0.157 Angle : 0.500 8.722 20514 Z= 0.265 Chirality : 0.041 0.188 2333 Planarity : 0.004 0.053 2523 Dihedral : 12.547 152.915 2171 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.80 % Allowed : 15.91 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.20), residues: 1781 helix: 1.53 (0.15), residues: 1134 sheet: -0.68 (0.60), residues: 59 loop : -0.26 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 171 HIS 0.004 0.001 HIS D 365 PHE 0.017 0.001 PHE A 192 TYR 0.014 0.001 TYR C 354 ARG 0.005 0.000 ARG D 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 3) link_NAG-ASN : angle 1.84450 ( 9) hydrogen bonds : bond 0.04137 ( 938) hydrogen bonds : angle 4.07245 ( 2724) covalent geometry : bond 0.00376 (15102) covalent geometry : angle 0.49836 (20505) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 1.696 Fit side-chains REVERT: A 231 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7281 (tp) REVERT: A 543 ASP cc_start: 0.7566 (t70) cc_final: 0.7209 (t0) REVERT: A 546 TYR cc_start: 0.8217 (p90) cc_final: 0.8005 (p90) REVERT: B 455 GLU cc_start: 0.7485 (tp30) cc_final: 0.7251 (tp30) REVERT: B 497 LYS cc_start: 0.8351 (mttp) cc_final: 0.7992 (mttp) REVERT: B 546 TYR cc_start: 0.8205 (p90) cc_final: 0.7872 (p90) REVERT: C 418 ASP cc_start: 0.8193 (m-30) cc_final: 0.7989 (m-30) REVERT: C 515 ILE cc_start: 0.8794 (mm) cc_final: 0.8514 (mm) REVERT: D 249 ASN cc_start: 0.7473 (t0) cc_final: 0.6875 (t0) REVERT: D 252 TYR cc_start: 0.6539 (t80) cc_final: 0.5779 (m-80) REVERT: D 424 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8079 (tp) REVERT: D 536 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7487 (ptp) REVERT: D 559 LYS cc_start: 0.8236 (ptmt) cc_final: 0.7694 (ptmm) outliers start: 29 outliers final: 18 residues processed: 185 average time/residue: 0.2431 time to fit residues: 69.1576 Evaluate side-chains 179 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 136 optimal weight: 0.0570 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 630 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.155816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121279 restraints weight = 30588.993| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 4.42 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15105 Z= 0.106 Angle : 0.456 9.457 20514 Z= 0.243 Chirality : 0.039 0.178 2333 Planarity : 0.003 0.053 2523 Dihedral : 12.396 153.378 2171 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.86 % Allowed : 15.97 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1781 helix: 1.84 (0.15), residues: 1133 sheet: -0.64 (0.59), residues: 61 loop : -0.08 (0.28), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 171 HIS 0.003 0.001 HIS D 630 PHE 0.012 0.001 PHE C 301 TYR 0.010 0.001 TYR C 357 ARG 0.005 0.000 ARG D 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 3) link_NAG-ASN : angle 1.78461 ( 9) hydrogen bonds : bond 0.03699 ( 938) hydrogen bonds : angle 3.86109 ( 2724) covalent geometry : bond 0.00232 (15102) covalent geometry : angle 0.45462 (20505) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 1.441 Fit side-chains REVERT: A 184 TYR cc_start: 0.7119 (m-80) cc_final: 0.6862 (m-80) REVERT: A 231 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7126 (tp) REVERT: A 543 ASP cc_start: 0.7542 (t70) cc_final: 0.7207 (t0) REVERT: B 455 GLU cc_start: 0.7452 (tp30) cc_final: 0.7214 (tp30) REVERT: B 546 TYR cc_start: 0.8168 (p90) cc_final: 0.7728 (p90) REVERT: C 418 ASP cc_start: 0.8151 (m-30) cc_final: 0.7934 (m-30) REVERT: C 515 ILE cc_start: 0.8751 (mm) cc_final: 0.8481 (mm) REVERT: D 213 TYR cc_start: 0.7557 (t80) cc_final: 0.7340 (t80) REVERT: D 249 ASN cc_start: 0.7281 (t0) cc_final: 0.6798 (t0) REVERT: D 252 TYR cc_start: 0.6396 (t80) cc_final: 0.5524 (m-80) REVERT: D 424 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7822 (tp) REVERT: D 536 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7332 (ptp) REVERT: D 559 LYS cc_start: 0.8195 (ptmt) cc_final: 0.7547 (ptmm) outliers start: 30 outliers final: 19 residues processed: 195 average time/residue: 0.2263 time to fit residues: 68.0641 Evaluate side-chains 178 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 301 GLN D 440 GLN D 630 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.152894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.116675 restraints weight = 25111.102| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.92 r_work: 0.2746 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15105 Z= 0.157 Angle : 0.504 9.803 20514 Z= 0.265 Chirality : 0.041 0.203 2333 Planarity : 0.004 0.050 2523 Dihedral : 12.406 153.449 2171 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.74 % Allowed : 16.22 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.20), residues: 1781 helix: 1.78 (0.15), residues: 1134 sheet: -0.42 (0.60), residues: 59 loop : -0.06 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 171 HIS 0.004 0.001 HIS D 365 PHE 0.018 0.001 PHE A 192 TYR 0.014 0.001 TYR C 354 ARG 0.004 0.000 ARG D 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00089 ( 3) link_NAG-ASN : angle 1.75383 ( 9) hydrogen bonds : bond 0.04079 ( 938) hydrogen bonds : angle 3.95276 ( 2724) covalent geometry : bond 0.00375 (15102) covalent geometry : angle 0.50303 (20505) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 1.563 Fit side-chains REVERT: A 231 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7038 (tp) REVERT: A 543 ASP cc_start: 0.7739 (t70) cc_final: 0.7423 (t0) REVERT: A 546 TYR cc_start: 0.8436 (p90) cc_final: 0.8191 (p90) REVERT: B 162 ASP cc_start: 0.7887 (p0) cc_final: 0.7685 (p0) REVERT: B 296 ASN cc_start: 0.6932 (p0) cc_final: 0.6409 (p0) REVERT: B 402 MET cc_start: 0.8598 (ttm) cc_final: 0.8364 (ttt) REVERT: B 497 LYS cc_start: 0.8165 (mmtm) cc_final: 0.7945 (mmtm) REVERT: B 546 TYR cc_start: 0.8452 (p90) cc_final: 0.7971 (p90) REVERT: C 418 ASP cc_start: 0.8697 (m-30) cc_final: 0.8442 (m-30) REVERT: C 515 ILE cc_start: 0.8377 (mm) cc_final: 0.8114 (mm) REVERT: D 249 ASN cc_start: 0.7346 (t0) cc_final: 0.6755 (t0) REVERT: D 252 TYR cc_start: 0.6390 (t80) cc_final: 0.5294 (m-80) REVERT: D 424 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8485 (tp) REVERT: D 523 ASP cc_start: 0.7351 (t0) cc_final: 0.6990 (p0) REVERT: D 536 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7509 (ptp) REVERT: D 559 LYS cc_start: 0.8237 (ptmt) cc_final: 0.7438 (ptmm) outliers start: 28 outliers final: 21 residues processed: 183 average time/residue: 0.2385 time to fit residues: 67.4347 Evaluate side-chains 178 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9365 > 50: distance: 42 - 200: 33.868 distance: 45 - 197: 31.506 distance: 57 - 184: 33.873 distance: 60 - 181: 28.412 distance: 96 - 207: 27.996 distance: 99 - 204: 35.374 distance: 111 - 192: 36.216 distance: 114 - 189: 36.689 distance: 170 - 173: 33.691 distance: 173 - 174: 37.387 distance: 174 - 175: 49.856 distance: 174 - 177: 33.613 distance: 175 - 176: 56.384 distance: 175 - 181: 27.913 distance: 177 - 178: 28.521 distance: 178 - 179: 40.558 distance: 181 - 182: 13.118 distance: 182 - 183: 29.018 distance: 182 - 185: 56.862 distance: 183 - 184: 49.700 distance: 183 - 189: 8.594 distance: 185 - 186: 38.698 distance: 186 - 187: 55.972 distance: 186 - 188: 41.363 distance: 190 - 193: 56.667 distance: 191 - 192: 40.624 distance: 193 - 194: 38.858 distance: 194 - 195: 56.490 distance: 194 - 196: 43.124 distance: 197 - 198: 57.032 distance: 198 - 199: 27.532 distance: 198 - 201: 40.087 distance: 199 - 200: 12.497 distance: 199 - 204: 42.918 distance: 201 - 202: 40.086 distance: 201 - 203: 38.680 distance: 204 - 205: 47.683 distance: 205 - 206: 59.181 distance: 205 - 208: 27.155 distance: 206 - 207: 43.083 distance: 206 - 212: 39.496 distance: 208 - 209: 31.326 distance: 209 - 210: 47.555 distance: 209 - 211: 38.351 distance: 212 - 213: 6.456 distance: 213 - 214: 53.313 distance: 213 - 216: 4.017 distance: 214 - 215: 56.435 distance: 214 - 220: 38.030 distance: 216 - 217: 41.189 distance: 217 - 218: 49.821 distance: 217 - 219: 30.210 distance: 220 - 221: 37.276 distance: 221 - 222: 54.562 distance: 221 - 224: 43.462 distance: 222 - 223: 57.676 distance: 222 - 229: 64.387 distance: 223 - 253: 32.476 distance: 224 - 225: 21.729 distance: 226 - 227: 19.216 distance: 227 - 228: 47.124 distance: 229 - 230: 62.756 distance: 230 - 231: 69.163 distance: 230 - 233: 40.137 distance: 231 - 238: 41.287 distance: 232 - 262: 33.431 distance: 233 - 234: 55.919 distance: 234 - 235: 30.259 distance: 235 - 236: 19.612 distance: 236 - 237: 12.091 distance: 238 - 239: 40.721 distance: 239 - 240: 38.990 distance: 239 - 242: 56.594 distance: 240 - 241: 57.374 distance: 240 - 245: 39.811 distance: 241 - 269: 33.261 distance: 242 - 243: 9.465 distance: 245 - 246: 39.336 distance: 247 - 248: 14.798 distance: 247 - 253: 35.526 distance: 248 - 277: 31.264 distance: 250 - 251: 37.619 distance: 250 - 252: 37.715