Starting phenix.real_space_refine on Sat Aug 23 12:25:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g6e_51099/08_2025/9g6e_51099.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g6e_51099/08_2025/9g6e_51099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g6e_51099/08_2025/9g6e_51099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g6e_51099/08_2025/9g6e_51099.map" model { file = "/net/cci-nas-00/data/ceres_data/9g6e_51099/08_2025/9g6e_51099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g6e_51099/08_2025/9g6e_51099.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.022 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 S 86 5.16 5 Cl 6 4.86 5 C 7639 2.51 5 N 1836 2.21 5 O 2086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11653 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 491, 3746 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 19, 'TRANS': 471} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 476, 3621 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 17, 'TRANS': 458} Chain breaks: 1 bond proxies already assigned to first conformer: 3544 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1735 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "C" Number of atoms: 3910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 491, 3746 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 19, 'TRANS': 471} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 476, 3621 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 17, 'TRANS': 458} Chain breaks: 1 bond proxies already assigned to first conformer: 3544 Chain: "D" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1690 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 2 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 108 Unusual residues: {' CL': 3, 'Y01': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Unusual residues: {' CL': 3, 'Y01': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 42 residue: pdb=" N ALEU A 585 " occ=0.46 ... (14 atoms not shown) pdb=" CD2BLEU A 585 " occ=0.54 residue: pdb=" N AVAL A 586 " occ=0.46 ... (12 atoms not shown) pdb=" CG2BVAL A 586 " occ=0.54 residue: pdb=" N ALEU A 587 " occ=0.46 ... (14 atoms not shown) pdb=" CD2BLEU A 587 " occ=0.54 residue: pdb=" N AMET A 588 " occ=0.46 ... (14 atoms not shown) pdb=" CE BMET A 588 " occ=0.54 residue: pdb=" N ATHR A 589 " occ=0.46 ... (12 atoms not shown) pdb=" CG2BTHR A 589 " occ=0.54 residue: pdb=" N AALA A 590 " occ=0.46 ... (8 atoms not shown) pdb=" CB BALA A 590 " occ=0.54 residue: pdb=" N ALYS A 591 " occ=0.46 ... (16 atoms not shown) pdb=" NZ BLYS A 591 " occ=0.54 residue: pdb=" N AILE A 592 " occ=0.46 ... (14 atoms not shown) pdb=" CD1BILE A 592 " occ=0.54 residue: pdb=" N AVAL A 593 " occ=0.46 ... (12 atoms not shown) pdb=" CG2BVAL A 593 " occ=0.54 residue: pdb=" N AGLY A 594 " occ=0.46 ... (6 atoms not shown) pdb=" O BGLY A 594 " occ=0.54 residue: pdb=" N AASP A 595 " occ=0.46 ... (14 atoms not shown) pdb=" OD2BASP A 595 " occ=0.54 residue: pdb=" N AVAL A 596 " occ=0.46 ... (12 atoms not shown) pdb=" CG2BVAL A 596 " occ=0.54 ... (remaining 30 not shown) Time building chain proxies: 3.76, per 1000 atoms: 0.32 Number of scatterers: 11653 At special positions: 0 Unit cell: (112.959, 79.002, 102.564, 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) Cl 6 17.00 S 86 16.00 O 2086 8.00 N 1836 7.00 C 7639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 174 " - pdb=" SG CYS D 255 " distance=2.03 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 224 " distance=2.03 Simple disulfide: pdb=" SG CYS D 221 " - pdb=" SG CYS D 275 " distance=2.03 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 513.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 77.3% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 113 through 170 removed outlier: 3.857A pdb=" N GLU A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 196 removed outlier: 4.119A pdb=" N SER A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.592A pdb=" N LEU A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.987A pdb=" N ILE A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 302 removed outlier: 3.678A pdb=" N ASP A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.515A pdb=" N VAL A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 320 through 346 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 407 Processing helix chain 'A' and resid 409 through 435 Processing helix chain 'A' and resid 461 through 467 removed outlier: 3.597A pdb=" N ALA A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 Processing helix chain 'A' and resid 486 through 505 Processing helix chain 'A' and resid 513 through 536 removed outlier: 3.894A pdb=" N SER A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 558 removed outlier: 3.640A pdb=" N TYR A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 removed outlier: 3.593A pdb=" N MET A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 599 removed outlier: 3.907A pdb=" N ILE A 583 " --> pdb=" O TYR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'B' and resid 81 through 105 removed outlier: 4.031A pdb=" N GLU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 115 through 130 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 184 through 203 removed outlier: 3.574A pdb=" N CYS B 199 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 removed outlier: 4.195A pdb=" N LYS B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N CYS B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.980A pdb=" N TYR B 228 " --> pdb=" O CYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 Processing helix chain 'B' and resid 282 through 310 Proline residue: B 296 - end of helix Processing helix chain 'C' and resid 114 through 170 removed outlier: 3.929A pdb=" N GLU C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 196 removed outlier: 4.194A pdb=" N SER C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 223 through 240 removed outlier: 3.629A pdb=" N LEU C 227 " --> pdb=" O ARG C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.968A pdb=" N ILE C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 302 removed outlier: 3.571A pdb=" N ASP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 316 removed outlier: 3.793A pdb=" N GLU C 314 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 373 through 407 removed outlier: 4.254A pdb=" N VAL C 377 " --> pdb=" O HIS C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 435 Processing helix chain 'C' and resid 461 through 467 removed outlier: 3.735A pdb=" N ALA C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 480 Processing helix chain 'C' and resid 486 through 505 removed outlier: 3.502A pdb=" N PHE C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 536 removed outlier: 4.094A pdb=" N SER C 533 " --> pdb=" O GLY C 529 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR C 534 " --> pdb=" O ILE C 530 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 560 removed outlier: 3.616A pdb=" N TYR C 547 " --> pdb=" O ASP C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 574 Processing helix chain 'C' and resid 579 through 599 removed outlier: 4.077A pdb=" N ILE C 583 " --> pdb=" O TYR C 579 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N BGLU C 599 " --> pdb=" O BASP C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 615 Processing helix chain 'D' and resid 88 through 105 Processing helix chain 'D' and resid 110 through 115 removed outlier: 3.565A pdb=" N CYS D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 131 removed outlier: 3.568A pdb=" N ILE D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 153 through 169 Processing helix chain 'D' and resid 170 through 175 removed outlier: 3.998A pdb=" N CYS D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 175 " --> pdb=" O CYS D 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 170 through 175' Processing helix chain 'D' and resid 183 through 203 removed outlier: 3.792A pdb=" N CYS D 199 " --> pdb=" O HIS D 195 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 200 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 224 removed outlier: 4.061A pdb=" N CYS D 224 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 246 Processing helix chain 'D' and resid 255 through 270 Processing helix chain 'D' and resid 281 through 309 Proline residue: D 296 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 440 Processing sheet with id=AA2, first strand: chain 'C' and resid 438 through 440 821 hydrogen bonds defined for protein. 2451 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: 1.44 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2014 1.33 - 1.45: 3066 1.45 - 1.57: 6720 1.57 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 11932 Sorted by residual: bond pdb=" C ILE A 432 " pdb=" O ILE A 432 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.35e-02 5.49e+03 6.10e+00 bond pdb=" C3 BMA E 3 " pdb=" O3 BMA E 3 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" C3 BMA H 3 " pdb=" O3 BMA H 3 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" C ILE A 432 " pdb=" N TYR A 433 " ideal model delta sigma weight residual 1.334 1.360 -0.026 1.27e-02 6.20e+03 4.08e+00 bond pdb=" C1 MAN E 5 " pdb=" C2 MAN E 5 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.11e+00 ... (remaining 11927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 16024 2.20 - 4.40: 184 4.40 - 6.60: 48 6.60 - 8.80: 4 8.80 - 11.00: 1 Bond angle restraints: 16261 Sorted by residual: angle pdb=" CA ILE A 432 " pdb=" C ILE A 432 " pdb=" O ILE A 432 " ideal model delta sigma weight residual 120.25 125.15 -4.90 1.08e+00 8.57e-01 2.06e+01 angle pdb=" CB MET A 562 " pdb=" CG MET A 562 " pdb=" SD MET A 562 " ideal model delta sigma weight residual 112.70 123.70 -11.00 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C LEU A 431 " pdb=" N ILE A 432 " pdb=" CA ILE A 432 " ideal model delta sigma weight residual 120.29 114.68 5.61 1.72e+00 3.38e-01 1.06e+01 angle pdb=" O LEU A 431 " pdb=" C LEU A 431 " pdb=" N ILE A 432 " ideal model delta sigma weight residual 122.12 125.32 -3.20 1.06e+00 8.90e-01 9.10e+00 angle pdb=" CG ARG D 271 " pdb=" CD ARG D 271 " pdb=" NE ARG D 271 " ideal model delta sigma weight residual 112.00 118.52 -6.52 2.20e+00 2.07e-01 8.80e+00 ... (remaining 16256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.39: 6598 20.39 - 40.78: 716 40.78 - 61.17: 170 61.17 - 81.56: 39 81.56 - 101.96: 9 Dihedral angle restraints: 7532 sinusoidal: 3344 harmonic: 4188 Sorted by residual: dihedral pdb=" CB CYS A 438 " pdb=" SG CYS A 438 " pdb=" SG CYS A 454 " pdb=" CB CYS A 454 " ideal model delta sinusoidal sigma weight residual 93.00 171.12 -78.12 1 1.00e+01 1.00e-02 7.62e+01 dihedral pdb=" CB CYS B 199 " pdb=" SG CYS B 199 " pdb=" SG CYS B 224 " pdb=" CB CYS B 224 " ideal model delta sinusoidal sigma weight residual -86.00 -159.49 73.49 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS D 84 " pdb=" SG CYS D 84 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual -86.00 -159.45 73.45 1 1.00e+01 1.00e-02 6.86e+01 ... (remaining 7529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1593 0.051 - 0.103: 313 0.103 - 0.154: 34 0.154 - 0.206: 0 0.206 - 0.257: 2 Chirality restraints: 1942 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ILE A 218 " pdb=" N ILE A 218 " pdb=" C ILE A 218 " pdb=" CB ILE A 218 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1939 not shown) Planarity restraints: 1970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 431 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C LEU A 431 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 431 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 432 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 248 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 249 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 249 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 249 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 248 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 249 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 249 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 249 " 0.021 5.00e-02 4.00e+02 ... (remaining 1967 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 472 2.72 - 3.26: 12493 3.26 - 3.81: 20225 3.81 - 4.35: 25116 4.35 - 4.90: 41981 Nonbonded interactions: 100287 Sorted by model distance: nonbonded pdb=" O ALEU C 585 " pdb=" OG1ATHR C 589 " model vdw 2.173 3.040 nonbonded pdb=" O VAL A 228 " pdb=" OG SER A 232 " model vdw 2.195 3.040 nonbonded pdb=" O ALEU A 585 " pdb=" OG1ATHR A 589 " model vdw 2.201 3.040 nonbonded pdb=" O ASN B 177 " pdb=" ND2 ASN B 178 " model vdw 2.204 3.120 nonbonded pdb=" O VAL C 228 " pdb=" OG SER C 232 " model vdw 2.205 3.040 ... (remaining 100282 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 113 through 584 or resid 902 through 903 or resid 905 thro \ ugh 906)) selection = (chain 'C' and (resid 113 through 584 or resid 902 through 903 or resid 905 thro \ ugh 906)) } ncs_group { reference = (chain 'B' and resid 79 through 310) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } 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=0.46 max=1.00 mean=0.97 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: 11.550 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.350 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 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 : 0.004 0.047 11953 Z= 0.187 Angle : 0.620 11.001 16311 Z= 0.298 Chirality : 0.040 0.257 1942 Planarity : 0.004 0.042 1970 Dihedral : 17.561 101.956 4793 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.48 % Allowed : 23.53 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.22), residues: 1434 helix: 1.22 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -1.47 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 271 TYR 0.012 0.001 TYR A 448 PHE 0.014 0.001 PHE D 294 TRP 0.018 0.002 ATRP A 616 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00437 (11932) covalent geometry : angle 0.61189 (16261) SS BOND : bond 0.00230 ( 13) SS BOND : angle 1.64310 ( 26) hydrogen bonds : bond 0.20882 ( 821) hydrogen bonds : angle 6.81491 ( 2451) link_ALPHA1-3 : bond 0.00609 ( 2) link_ALPHA1-3 : angle 3.78047 ( 6) link_ALPHA1-6 : bond 0.00454 ( 2) link_ALPHA1-6 : angle 1.60307 ( 6) link_BETA1-4 : bond 0.00260 ( 4) link_BETA1-4 : angle 1.20379 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: B 148 MET cc_start: 0.7784 (pmt) cc_final: 0.7535 (pmm) outliers start: 39 outliers final: 32 residues processed: 155 average time/residue: 0.5267 time to fit residues: 87.9564 Evaluate side-chains 145 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 199 CYS Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 265 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN B 170 ASN C 208 GLN C 321 GLN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.120786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.085148 restraints weight = 133238.788| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 5.69 r_work: 0.2954 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11953 Z= 0.163 Angle : 0.630 9.191 16311 Z= 0.320 Chirality : 0.042 0.250 1942 Planarity : 0.004 0.040 1970 Dihedral : 10.556 77.710 2344 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.62 % Allowed : 20.85 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.22), residues: 1434 helix: 2.05 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : -1.92 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 131 TYR 0.013 0.001 TYR A 448 PHE 0.017 0.001 PHE A 392 TRP 0.015 0.002 TRP C 325 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00363 (11932) covalent geometry : angle 0.62211 (16261) SS BOND : bond 0.00302 ( 13) SS BOND : angle 1.28856 ( 26) hydrogen bonds : bond 0.05176 ( 821) hydrogen bonds : angle 4.46369 ( 2451) link_ALPHA1-3 : bond 0.00088 ( 2) link_ALPHA1-3 : angle 3.76343 ( 6) link_ALPHA1-6 : bond 0.01301 ( 2) link_ALPHA1-6 : angle 1.78134 ( 6) link_BETA1-4 : bond 0.00295 ( 4) link_BETA1-4 : angle 1.48494 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 0.283 Fit side-chains REVERT: A 398 TRP cc_start: 0.8251 (m-10) cc_final: 0.7048 (t60) REVERT: B 144 ARG cc_start: 0.7558 (mpp-170) cc_final: 0.7336 (mpp-170) REVERT: B 148 MET cc_start: 0.7879 (pmt) cc_final: 0.7216 (ptp) REVERT: B 281 ASP cc_start: 0.8007 (t0) cc_final: 0.7571 (t0) REVERT: B 310 LYS cc_start: 0.7970 (pttt) cc_final: 0.7577 (mptt) REVERT: C 398 TRP cc_start: 0.8287 (m-10) cc_final: 0.7079 (t60) REVERT: C 534 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6842 (p90) REVERT: C 616 TRP cc_start: 0.5721 (OUTLIER) cc_final: 0.4035 (m-10) REVERT: D 148 MET cc_start: 0.7943 (pmt) cc_final: 0.7616 (pmm) REVERT: D 174 CYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7849 (m) REVERT: D 281 ASP cc_start: 0.8085 (p0) cc_final: 0.7775 (p0) outliers start: 54 outliers final: 18 residues processed: 163 average time/residue: 0.4928 time to fit residues: 87.0878 Evaluate side-chains 138 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 534 TYR Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 616 TRP Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 175 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 108 optimal weight: 0.0970 chunk 135 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN B 170 ASN B 306 HIS C 439 GLN D 274 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085309 restraints weight = 131940.713| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 5.58 r_work: 0.2971 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11953 Z= 0.148 Angle : 0.595 9.217 16311 Z= 0.299 Chirality : 0.041 0.229 1942 Planarity : 0.004 0.042 1970 Dihedral : 9.285 66.044 2321 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.89 % Allowed : 21.17 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.22), residues: 1434 helix: 2.30 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -1.85 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 271 TYR 0.012 0.001 TYR A 448 PHE 0.015 0.001 PHE A 392 TRP 0.015 0.002 TRP A 350 HIS 0.005 0.000 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00336 (11932) covalent geometry : angle 0.58704 (16261) SS BOND : bond 0.00328 ( 13) SS BOND : angle 1.16289 ( 26) hydrogen bonds : bond 0.04718 ( 821) hydrogen bonds : angle 4.22861 ( 2451) link_ALPHA1-3 : bond 0.00241 ( 2) link_ALPHA1-3 : angle 3.57269 ( 6) link_ALPHA1-6 : bond 0.00991 ( 2) link_ALPHA1-6 : angle 2.23589 ( 6) link_BETA1-4 : bond 0.00420 ( 4) link_BETA1-4 : angle 1.38946 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 398 TRP cc_start: 0.8230 (m-10) cc_final: 0.7107 (t60) REVERT: B 148 MET cc_start: 0.7851 (pmt) cc_final: 0.7527 (pmm) REVERT: B 167 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7237 (mt0) REVERT: B 168 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: B 281 ASP cc_start: 0.8107 (t0) cc_final: 0.7636 (t0) REVERT: B 310 LYS cc_start: 0.7838 (pttt) cc_final: 0.7460 (mptt) REVERT: C 313 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: C 398 TRP cc_start: 0.8224 (m-10) cc_final: 0.7096 (t60) REVERT: C 534 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6761 (p90) REVERT: C 616 TRP cc_start: 0.5694 (OUTLIER) cc_final: 0.3935 (m-10) REVERT: D 148 MET cc_start: 0.7896 (pmt) cc_final: 0.7567 (pmm) REVERT: D 174 CYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7912 (m) REVERT: D 281 ASP cc_start: 0.8126 (p0) cc_final: 0.7896 (p0) outliers start: 45 outliers final: 16 residues processed: 154 average time/residue: 0.5792 time to fit residues: 95.8608 Evaluate side-chains 140 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 534 TYR Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 616 TRP Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 175 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 18 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 439 GLN B 170 ASN B 306 HIS D 242 ASN D 274 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.119645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.084915 restraints weight = 133444.261| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 5.34 r_work: 0.2978 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11953 Z= 0.149 Angle : 0.598 9.777 16311 Z= 0.298 Chirality : 0.041 0.244 1942 Planarity : 0.004 0.042 1970 Dihedral : 8.414 59.914 2318 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.46 % Allowed : 20.36 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.22), residues: 1434 helix: 2.35 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -1.78 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 271 TYR 0.012 0.001 TYR A 448 PHE 0.016 0.001 PHE B 294 TRP 0.015 0.001 TRP A 524 HIS 0.004 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00341 (11932) covalent geometry : angle 0.59053 (16261) SS BOND : bond 0.00245 ( 13) SS BOND : angle 1.19294 ( 26) hydrogen bonds : bond 0.04376 ( 821) hydrogen bonds : angle 4.11752 ( 2451) link_ALPHA1-3 : bond 0.00218 ( 2) link_ALPHA1-3 : angle 3.65812 ( 6) link_ALPHA1-6 : bond 0.00720 ( 2) link_ALPHA1-6 : angle 1.56660 ( 6) link_BETA1-4 : bond 0.00466 ( 4) link_BETA1-4 : angle 1.48278 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 117 time to evaluate : 0.462 Fit side-chains REVERT: A 398 TRP cc_start: 0.8219 (m-10) cc_final: 0.7119 (t60) REVERT: A 405 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8298 (mtm-85) REVERT: B 144 ARG cc_start: 0.7793 (mpp-170) cc_final: 0.7527 (mpp-170) REVERT: B 148 MET cc_start: 0.7928 (pmt) cc_final: 0.7647 (pmm) REVERT: B 167 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7222 (mt0) REVERT: B 168 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: B 222 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8412 (pmmt) REVERT: B 281 ASP cc_start: 0.8111 (t0) cc_final: 0.7677 (t0) REVERT: C 398 TRP cc_start: 0.8213 (m-10) cc_final: 0.7145 (t60) REVERT: C 616 TRP cc_start: 0.5670 (OUTLIER) cc_final: 0.3854 (m-10) REVERT: D 174 CYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7884 (m) outliers start: 52 outliers final: 17 residues processed: 154 average time/residue: 0.5543 time to fit residues: 92.0271 Evaluate side-chains 137 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 616 TRP Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 274 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 45 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN B 170 ASN B 306 HIS D 242 ASN D 274 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.119181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.084676 restraints weight = 130213.327| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 5.51 r_work: 0.2972 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11953 Z= 0.149 Angle : 0.607 9.561 16311 Z= 0.303 Chirality : 0.041 0.227 1942 Planarity : 0.004 0.042 1970 Dihedral : 8.181 59.910 2316 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.48 % Allowed : 21.09 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.22), residues: 1434 helix: 2.39 (0.15), residues: 1041 sheet: None (None), residues: 0 loop : -1.78 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 271 TYR 0.012 0.001 TYR A 448 PHE 0.023 0.001 PHE D 294 TRP 0.016 0.001 TRP A 524 HIS 0.005 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00343 (11932) covalent geometry : angle 0.59686 (16261) SS BOND : bond 0.00273 ( 13) SS BOND : angle 1.93661 ( 26) hydrogen bonds : bond 0.04324 ( 821) hydrogen bonds : angle 4.09009 ( 2451) link_ALPHA1-3 : bond 0.00100 ( 2) link_ALPHA1-3 : angle 3.62961 ( 6) link_ALPHA1-6 : bond 0.00420 ( 2) link_ALPHA1-6 : angle 1.50422 ( 6) link_BETA1-4 : bond 0.00339 ( 4) link_BETA1-4 : angle 1.52568 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 165 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8659 (ttmt) REVERT: A 398 TRP cc_start: 0.8215 (m-10) cc_final: 0.7111 (t60) REVERT: A 405 ARG cc_start: 0.8578 (mtt180) cc_final: 0.8244 (mtm-85) REVERT: A 584 MET cc_start: 0.8702 (mmt) cc_final: 0.8374 (mmt) REVERT: B 144 ARG cc_start: 0.7856 (mpp-170) cc_final: 0.7595 (mpp-170) REVERT: B 167 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7169 (mt0) REVERT: B 168 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: B 222 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8453 (pmmt) REVERT: B 281 ASP cc_start: 0.8134 (t0) cc_final: 0.7728 (t0) REVERT: C 398 TRP cc_start: 0.8212 (m-10) cc_final: 0.7131 (t60) REVERT: C 608 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.4185 (pp) REVERT: C 616 TRP cc_start: 0.5596 (OUTLIER) cc_final: 0.3818 (m-10) REVERT: D 148 MET cc_start: 0.7909 (pmt) cc_final: 0.7594 (pmm) REVERT: D 174 CYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7928 (m) outliers start: 41 outliers final: 15 residues processed: 147 average time/residue: 0.5899 time to fit residues: 93.2663 Evaluate side-chains 139 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 616 TRP Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 175 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 123 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN B 170 ASN B 306 HIS C 439 GLN D 242 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.119821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.085278 restraints weight = 142243.799| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 5.49 r_work: 0.2986 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11953 Z= 0.141 Angle : 0.604 10.534 16311 Z= 0.300 Chirality : 0.040 0.207 1942 Planarity : 0.004 0.042 1970 Dihedral : 8.040 59.705 2316 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.48 % Allowed : 21.09 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.22), residues: 1434 helix: 2.46 (0.15), residues: 1041 sheet: None (None), residues: 0 loop : -1.73 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 271 TYR 0.011 0.001 TYR A 448 PHE 0.023 0.001 PHE B 294 TRP 0.017 0.001 TRP A 524 HIS 0.006 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00323 (11932) covalent geometry : angle 0.59540 (16261) SS BOND : bond 0.00234 ( 13) SS BOND : angle 1.67554 ( 26) hydrogen bonds : bond 0.04175 ( 821) hydrogen bonds : angle 4.04405 ( 2451) link_ALPHA1-3 : bond 0.00031 ( 2) link_ALPHA1-3 : angle 3.51863 ( 6) link_ALPHA1-6 : bond 0.00407 ( 2) link_ALPHA1-6 : angle 1.44663 ( 6) link_BETA1-4 : bond 0.00332 ( 4) link_BETA1-4 : angle 1.52482 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 165 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8685 (ttmt) REVERT: A 398 TRP cc_start: 0.8220 (m-10) cc_final: 0.7130 (t60) REVERT: A 405 ARG cc_start: 0.8565 (mtt180) cc_final: 0.8264 (mtm-85) REVERT: B 148 MET cc_start: 0.7752 (pmt) cc_final: 0.7502 (pmm) REVERT: B 167 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7155 (mt0) REVERT: B 168 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8570 (mp0) REVERT: B 222 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8506 (pmmt) REVERT: B 281 ASP cc_start: 0.8155 (t0) cc_final: 0.7809 (t0) REVERT: C 169 LYS cc_start: 0.8512 (mtpp) cc_final: 0.7762 (ttpp) REVERT: C 398 TRP cc_start: 0.8198 (m-10) cc_final: 0.7134 (t60) REVERT: C 562 MET cc_start: 0.9042 (tpp) cc_final: 0.8796 (mmm) REVERT: C 608 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.5086 (mt) REVERT: C 616 TRP cc_start: 0.5612 (OUTLIER) cc_final: 0.3774 (m-10) REVERT: D 144 ARG cc_start: 0.7867 (mpp-170) cc_final: 0.7659 (mpp-170) REVERT: D 148 MET cc_start: 0.7926 (pmt) cc_final: 0.7615 (pmm) REVERT: D 174 CYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8028 (m) outliers start: 41 outliers final: 19 residues processed: 149 average time/residue: 0.4987 time to fit residues: 80.3934 Evaluate side-chains 140 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 543 ASP Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 616 TRP Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.5527 > 50: distance: 9 - 40: 5.315 distance: 14 - 21: 12.345 distance: 21 - 22: 25.573 distance: 22 - 23: 20.943 distance: 22 - 25: 10.491 distance: 23 - 24: 7.986 distance: 23 - 30: 14.377 distance: 25 - 26: 14.653 distance: 26 - 27: 10.144 distance: 27 - 28: 16.850 distance: 27 - 29: 25.422 distance: 30 - 31: 9.120 distance: 31 - 32: 13.821 distance: 31 - 34: 16.423 distance: 32 - 33: 31.530 distance: 32 - 40: 15.586 distance: 34 - 35: 26.500 distance: 35 - 36: 10.783 distance: 35 - 37: 21.822 distance: 36 - 38: 12.809 distance: 37 - 39: 5.766 distance: 38 - 39: 18.837 distance: 40 - 41: 11.272 distance: 41 - 42: 24.950 distance: 41 - 44: 22.550 distance: 42 - 43: 22.127 distance: 42 - 48: 15.072 distance: 44 - 45: 18.319 distance: 45 - 46: 21.512 distance: 45 - 47: 18.157 distance: 48 - 49: 15.060 distance: 49 - 50: 47.834 distance: 49 - 52: 22.003 distance: 50 - 51: 48.161 distance: 50 - 56: 36.085 distance: 52 - 53: 7.686 distance: 53 - 54: 20.359 distance: 53 - 55: 21.243 distance: 56 - 57: 6.044 distance: 57 - 58: 31.411 distance: 57 - 60: 20.942 distance: 58 - 59: 11.681 distance: 60 - 61: 23.901 distance: 61 - 62: 25.135 distance: 62 - 63: 17.445 distance: 62 - 64: 34.125 distance: 65 - 66: 13.468 distance: 66 - 67: 8.986 distance: 66 - 69: 16.198 distance: 67 - 68: 10.027 distance: 67 - 77: 17.480 distance: 69 - 70: 6.676 distance: 70 - 71: 14.862 distance: 70 - 72: 7.606 distance: 71 - 73: 6.203 distance: 72 - 74: 6.618 distance: 73 - 75: 9.561 distance: 74 - 75: 8.696 distance: 75 - 76: 12.819 distance: 77 - 78: 11.040 distance: 78 - 79: 17.874 distance: 78 - 81: 10.434 distance: 79 - 80: 14.860 distance: 79 - 83: 9.064 distance: 81 - 82: 13.610 distance: 83 - 84: 13.125 distance: 84 - 85: 28.395 distance: 84 - 87: 13.387 distance: 85 - 86: 29.651 distance: 85 - 92: 29.400 distance: 86 - 114: 22.049 distance: 87 - 88: 9.068 distance: 88 - 89: 10.747 distance: 89 - 90: 5.111 distance: 89 - 91: 9.605 distance: 92 - 93: 19.033 distance: 93 - 94: 13.490 distance: 93 - 96: 13.073 distance: 94 - 95: 15.844 distance: 94 - 99: 19.877 distance: 96 - 97: 34.623 distance: 96 - 98: 9.508 distance: 99 - 100: 8.062 distance: 100 - 101: 22.241 distance: 100 - 103: 5.898 distance: 101 - 102: 17.775 distance: 101 - 105: 11.138 distance: 103 - 104: 27.261 distance: 104 - 160: 12.657