Starting phenix.real_space_refine on Sat Aug 23 10:02:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ylu_39391/08_2025/8ylu_39391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ylu_39391/08_2025/8ylu_39391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ylu_39391/08_2025/8ylu_39391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ylu_39391/08_2025/8ylu_39391.map" model { file = "/net/cci-nas-00/data/ceres_data/8ylu_39391/08_2025/8ylu_39391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ylu_39391/08_2025/8ylu_39391.cif" } resolution = 2.8 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= 0.186 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 44 5.49 5 Mg 1 5.21 5 S 38 5.16 5 C 7175 2.51 5 N 1947 2.21 5 O 2236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 11441 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3554 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Chain: "B" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3554 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1715 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "D" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1715 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "E" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "F" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 450 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.44, per 1000 atoms: 0.21 Number of scatterers: 11441 At special positions: 0 Unit cell: (94.64, 118.56, 126.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 44 15.00 Mg 1 11.99 O 2236 8.00 N 1947 7.00 C 7175 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 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 507.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 14 sheets defined 46.6% alpha, 12.3% beta 22 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.852A pdb=" N ALA A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 27 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 51 Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.738A pdb=" N GLY A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.549A pdb=" N GLY A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.842A pdb=" N ALA A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 156 through 161 removed outlier: 3.760A pdb=" N ASN A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 161' Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.655A pdb=" N LEU A 251 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 removed outlier: 3.660A pdb=" N ARG A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 365 removed outlier: 4.156A pdb=" N LEU A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.569A pdb=" N LEU A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 385 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.704A pdb=" N LYS A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.743A pdb=" N ILE A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 removed outlier: 3.646A pdb=" N ALA B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.848A pdb=" N GLY B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 76 through 88 removed outlier: 4.006A pdb=" N ALA B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 removed outlier: 3.576A pdb=" N TYR B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 319 through 362 removed outlier: 3.873A pdb=" N LEU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 removed outlier: 4.004A pdb=" N SER B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 404 through 426 removed outlier: 3.565A pdb=" N LYS B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 439 Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 448 through 454 Processing helix chain 'C' and resid 455 through 465 Processing helix chain 'C' and resid 488 through 494 Processing helix chain 'C' and resid 494 through 504 Processing helix chain 'C' and resid 536 through 545 removed outlier: 4.613A pdb=" N ASP C 545 " --> pdb=" O GLU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 561 removed outlier: 3.574A pdb=" N LEU C 561 " --> pdb=" O LEU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 572 Processing helix chain 'C' and resid 583 through 592 removed outlier: 3.510A pdb=" N LEU C 587 " --> pdb=" O ASN C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 604 removed outlier: 3.572A pdb=" N TRP C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 455 through 463 removed outlier: 3.707A pdb=" N ILE D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 504 removed outlier: 5.182A pdb=" N TYR D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) Proline residue: D 497 - end of helix Processing helix chain 'D' and resid 506 through 512 removed outlier: 3.950A pdb=" N PHE D 510 " --> pdb=" O TRP D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 545 removed outlier: 3.583A pdb=" N ALA D 543 " --> pdb=" O GLU D 539 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP D 545 " --> pdb=" O GLU D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 561 removed outlier: 3.526A pdb=" N LEU D 561 " --> pdb=" O LEU D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 583 through 593 Processing helix chain 'D' and resid 595 through 604 removed outlier: 4.125A pdb=" N ARG D 599 " --> pdb=" O ASN D 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 5.559A pdb=" N ILE D 515 " --> pdb=" O VAL D 578 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU D 411 " --> pdb=" O ALA D 482 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET D 484 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU D 413 " --> pdb=" O MET D 484 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 165 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 211 Processing sheet with id=AA5, first strand: chain 'A' and resid 220 through 223 removed outlier: 5.971A pdb=" N THR A 220 " --> pdb=" O THR A 232 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 305 through 308 removed outlier: 4.431A pdb=" N ILE A 305 " --> pdb=" O TYR A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 7 removed outlier: 5.579A pdb=" N ILE C 515 " --> pdb=" O VAL C 578 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE C 481 " --> pdb=" O ARG C 516 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL C 518 " --> pdb=" O ILE C 481 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE C 483 " --> pdb=" O VAL C 518 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU C 411 " --> pdb=" O ALA C 482 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AB1, first strand: chain 'B' and resid 207 through 211 Processing sheet with id=AB2, first strand: chain 'B' and resid 220 through 223 removed outlier: 6.160A pdb=" N THR B 220 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 305 through 308 removed outlier: 4.136A pdb=" N ILE B 305 " --> pdb=" O TYR B 317 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 530 through 534 Processing sheet with id=AB5, first strand: chain 'D' and resid 530 through 534 removed outlier: 3.662A pdb=" N SER D 551 " --> pdb=" O HIS D 526 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2990 1.33 - 1.45: 2315 1.45 - 1.57: 6313 1.57 - 1.69: 86 1.69 - 1.81: 70 Bond restraints: 11774 Sorted by residual: bond pdb=" CB ASN B 253 " pdb=" CG ASN B 253 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.43e+00 bond pdb=" CB ASP C 408 " pdb=" CG ASP C 408 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CB GLU A 285 " pdb=" CG GLU A 285 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" CA ASP C 408 " pdb=" CB ASP C 408 " ideal model delta sigma weight residual 1.528 1.541 -0.013 1.35e-02 5.49e+03 9.54e-01 bond pdb=" CA ASN B 253 " pdb=" CB ASN B 253 " ideal model delta sigma weight residual 1.527 1.537 -0.010 1.15e-02 7.56e+03 7.94e-01 ... (remaining 11769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 15795 1.72 - 3.44: 243 3.44 - 5.16: 20 5.16 - 6.88: 5 6.88 - 8.60: 1 Bond angle restraints: 16064 Sorted by residual: angle pdb=" CA ASN B 253 " pdb=" CB ASN B 253 " pdb=" CG ASN B 253 " ideal model delta sigma weight residual 112.60 115.45 -2.85 1.00e+00 1.00e+00 8.15e+00 angle pdb=" C GLY D 421 " pdb=" N TYR D 422 " pdb=" CA TYR D 422 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.80e+00 angle pdb=" CA LEU D 492 " pdb=" CB LEU D 492 " pdb=" CG LEU D 492 " ideal model delta sigma weight residual 116.30 124.90 -8.60 3.50e+00 8.16e-02 6.04e+00 angle pdb=" CB GLU A 285 " pdb=" CG GLU A 285 " pdb=" CD GLU A 285 " ideal model delta sigma weight residual 112.60 116.70 -4.10 1.70e+00 3.46e-01 5.81e+00 angle pdb=" CA ASP C 408 " pdb=" CB ASP C 408 " pdb=" CG ASP C 408 " ideal model delta sigma weight residual 112.60 115.01 -2.41 1.00e+00 1.00e+00 5.80e+00 ... (remaining 16059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.11: 6244 28.11 - 56.22: 676 56.22 - 84.33: 58 84.33 - 112.44: 3 112.44 - 140.55: 1 Dihedral angle restraints: 6982 sinusoidal: 3170 harmonic: 3812 Sorted by residual: dihedral pdb=" CA PHE A 36 " pdb=" C PHE A 36 " pdb=" N LYS A 37 " pdb=" CA LYS A 37 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA TYR B 238 " pdb=" C TYR B 238 " pdb=" N ASP B 239 " pdb=" CA ASP B 239 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PHE B 36 " pdb=" C PHE B 36 " pdb=" N LYS B 37 " pdb=" CA LYS B 37 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 6979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1080 0.030 - 0.060: 476 0.060 - 0.091: 106 0.091 - 0.121: 63 0.121 - 0.151: 15 Chirality restraints: 1740 Sorted by residual: chirality pdb=" CA ASP C 408 " pdb=" N ASP C 408 " pdb=" C ASP C 408 " pdb=" CB ASP C 408 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA ASN B 253 " pdb=" N ASN B 253 " pdb=" C ASN B 253 " pdb=" CB ASN B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 217 " pdb=" N ILE A 217 " pdb=" C ILE A 217 " pdb=" CB ILE A 217 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1737 not shown) Planarity restraints: 1904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 253 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.81e+00 pdb=" C ASN B 253 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN B 253 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS B 254 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 14 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C ASN B 14 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN B 14 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU B 15 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 88 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.37e+00 pdb=" C ALA B 88 " -0.032 2.00e-02 2.50e+03 pdb=" O ALA B 88 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN B 89 " 0.011 2.00e-02 2.50e+03 ... (remaining 1901 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 345 2.70 - 3.25: 10397 3.25 - 3.80: 18907 3.80 - 4.35: 25437 4.35 - 4.90: 41735 Nonbonded interactions: 96821 Sorted by model distance: nonbonded pdb=" OD1 ASP A 7 " pdb=" OG SER A 10 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR A 117 " pdb=" OP1 DA E 10 " model vdw 2.190 3.040 nonbonded pdb=" N GLU B 284 " pdb=" OE1 GLU B 284 " model vdw 2.212 3.120 nonbonded pdb=" O VAL B 369 " pdb=" NZ LYS B 373 " model vdw 2.219 3.120 nonbonded pdb=" OH TYR B 73 " pdb=" OP2 DA E 8 " model vdw 2.223 3.040 ... (remaining 96816 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 393 through 605) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.890 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:8.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11774 Z= 0.140 Angle : 0.511 8.602 16064 Z= 0.285 Chirality : 0.040 0.151 1740 Planarity : 0.003 0.039 1904 Dihedral : 20.360 140.552 4538 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.89 % Allowed : 29.70 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.23), residues: 1300 helix: 0.97 (0.23), residues: 548 sheet: -0.44 (0.42), residues: 154 loop : -0.79 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 351 TYR 0.013 0.001 TYR D 575 PHE 0.013 0.001 PHE A 401 TRP 0.011 0.001 TRP C 602 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00316 (11774) covalent geometry : angle 0.51124 (16064) hydrogen bonds : bond 0.12905 ( 517) hydrogen bonds : angle 5.76202 ( 1424) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.385 Fit side-chains REVERT: B 387 MET cc_start: 0.6910 (ttt) cc_final: 0.6666 (tmm) REVERT: D 569 MET cc_start: 0.8847 (ptt) cc_final: 0.8542 (ptt) outliers start: 10 outliers final: 8 residues processed: 130 average time/residue: 0.6967 time to fit residues: 96.7705 Evaluate side-chains 123 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 486 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN B 81 GLN B 89 ASN C 605 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116653 restraints weight = 13304.820| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.52 r_work: 0.3317 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.0551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11774 Z= 0.139 Angle : 0.503 7.884 16064 Z= 0.280 Chirality : 0.040 0.148 1740 Planarity : 0.003 0.039 1904 Dihedral : 16.488 143.124 1937 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.19 % Allowed : 26.51 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.23), residues: 1300 helix: 1.03 (0.23), residues: 556 sheet: -0.65 (0.40), residues: 164 loop : -0.86 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 351 TYR 0.011 0.001 TYR D 575 PHE 0.019 0.001 PHE B 401 TRP 0.009 0.001 TRP D 602 HIS 0.002 0.001 HIS D 489 Details of bonding type rmsd covalent geometry : bond 0.00315 (11774) covalent geometry : angle 0.50322 (16064) hydrogen bonds : bond 0.03878 ( 517) hydrogen bonds : angle 4.68383 ( 1424) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.336 Fit side-chains REVERT: A 241 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: A 338 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6276 (ttm170) REVERT: B 373 LYS cc_start: 0.7456 (mttt) cc_final: 0.7255 (mttp) REVERT: B 416 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.5907 (tptp) REVERT: C 601 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7795 (mp0) REVERT: D 512 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8265 (mp10) outliers start: 36 outliers final: 14 residues processed: 155 average time/residue: 0.6311 time to fit residues: 104.6329 Evaluate side-chains 135 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN B 89 ASN C 505 ASN C 605 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113947 restraints weight = 13559.906| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.53 r_work: 0.3275 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11774 Z= 0.195 Angle : 0.539 8.105 16064 Z= 0.298 Chirality : 0.042 0.150 1740 Planarity : 0.004 0.043 1904 Dihedral : 16.518 141.500 1927 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.84 % Allowed : 26.77 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.23), residues: 1300 helix: 0.87 (0.22), residues: 558 sheet: -0.67 (0.41), residues: 164 loop : -0.93 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.015 0.001 TYR D 575 PHE 0.016 0.002 PHE B 401 TRP 0.012 0.002 TRP D 602 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00458 (11774) covalent geometry : angle 0.53915 (16064) hydrogen bonds : bond 0.04108 ( 517) hydrogen bonds : angle 4.65435 ( 1424) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.315 Fit side-chains REVERT: A 92 ASN cc_start: 0.8134 (t0) cc_final: 0.7888 (t0) REVERT: A 241 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: A 338 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6282 (ttm170) REVERT: A 384 LYS cc_start: 0.6983 (tptt) cc_final: 0.6714 (ttmt) REVERT: B 124 LYS cc_start: 0.8148 (pttt) cc_final: 0.7882 (pttp) REVERT: B 361 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5527 (tptp) REVERT: C 417 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: D 512 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8244 (mt0) outliers start: 32 outliers final: 15 residues processed: 147 average time/residue: 0.6131 time to fit residues: 96.4296 Evaluate side-chains 142 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 530 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 41 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 123 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN C 605 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117171 restraints weight = 13465.828| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.52 r_work: 0.3328 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11774 Z= 0.123 Angle : 0.484 7.381 16064 Z= 0.270 Chirality : 0.040 0.145 1740 Planarity : 0.003 0.042 1904 Dihedral : 16.384 143.994 1927 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.30 % Allowed : 26.95 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.23), residues: 1300 helix: 1.11 (0.23), residues: 558 sheet: -0.37 (0.43), residues: 154 loop : -0.96 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 205 TYR 0.014 0.001 TYR D 575 PHE 0.015 0.001 PHE A 401 TRP 0.011 0.001 TRP C 602 HIS 0.002 0.000 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00277 (11774) covalent geometry : angle 0.48377 (16064) hydrogen bonds : bond 0.03380 ( 517) hydrogen bonds : angle 4.45331 ( 1424) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.310 Fit side-chains REVERT: A 241 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: A 338 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6282 (ttm170) REVERT: A 384 LYS cc_start: 0.6898 (tptt) cc_final: 0.6694 (ttmt) REVERT: B 124 LYS cc_start: 0.8085 (pttt) cc_final: 0.7808 (pttp) REVERT: B 361 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5686 (tmtt) REVERT: B 416 LYS cc_start: 0.6413 (OUTLIER) cc_final: 0.5821 (tptp) REVERT: C 417 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: C 601 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7828 (mp0) REVERT: D 512 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8173 (mp10) outliers start: 26 outliers final: 8 residues processed: 145 average time/residue: 0.6402 time to fit residues: 99.2279 Evaluate side-chains 133 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 80 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN C 605 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.137417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113621 restraints weight = 13450.400| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.52 r_work: 0.3269 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11774 Z= 0.194 Angle : 0.538 6.990 16064 Z= 0.298 Chirality : 0.042 0.149 1740 Planarity : 0.004 0.045 1904 Dihedral : 16.474 140.916 1926 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.10 % Allowed : 26.95 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.23), residues: 1300 helix: 0.94 (0.22), residues: 558 sheet: -0.46 (0.43), residues: 154 loop : -1.02 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 351 TYR 0.019 0.001 TYR D 575 PHE 0.014 0.001 PHE A 149 TRP 0.012 0.002 TRP D 602 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00455 (11774) covalent geometry : angle 0.53847 (16064) hydrogen bonds : bond 0.03993 ( 517) hydrogen bonds : angle 4.55446 ( 1424) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.386 Fit side-chains REVERT: A 92 ASN cc_start: 0.8176 (t0) cc_final: 0.7917 (t0) REVERT: A 226 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6083 (mpp-170) REVERT: A 241 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: A 338 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6359 (ttm170) REVERT: A 384 LYS cc_start: 0.6888 (tptt) cc_final: 0.6624 (ttmt) REVERT: A 440 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7217 (mp0) REVERT: B 124 LYS cc_start: 0.8152 (pttt) cc_final: 0.7902 (pttp) REVERT: B 361 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5531 (tptp) REVERT: B 416 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.5928 (tptp) REVERT: C 408 ASP cc_start: 0.8007 (p0) cc_final: 0.7679 (m-30) REVERT: C 417 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: D 512 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: D 544 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7522 (ttmt) outliers start: 35 outliers final: 17 residues processed: 149 average time/residue: 0.6138 time to fit residues: 97.9909 Evaluate side-chains 144 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 530 LYS Chi-restraints excluded: chain D residue 544 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 131 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 108 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN B 402 HIS C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115945 restraints weight = 13357.915| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.52 r_work: 0.3308 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11774 Z= 0.131 Angle : 0.496 7.188 16064 Z= 0.275 Chirality : 0.040 0.145 1740 Planarity : 0.003 0.042 1904 Dihedral : 16.381 143.201 1926 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.48 % Allowed : 27.48 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.06 (0.23), residues: 1300 helix: 1.10 (0.23), residues: 558 sheet: -0.70 (0.42), residues: 164 loop : -0.94 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.015 0.001 TYR D 575 PHE 0.010 0.001 PHE A 149 TRP 0.012 0.001 TRP C 602 HIS 0.006 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00296 (11774) covalent geometry : angle 0.49558 (16064) hydrogen bonds : bond 0.03432 ( 517) hydrogen bonds : angle 4.44466 ( 1424) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.393 Fit side-chains REVERT: A 92 ASN cc_start: 0.8120 (t0) cc_final: 0.7877 (t0) REVERT: A 226 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6103 (mpp-170) REVERT: A 241 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: A 338 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6301 (ttm170) REVERT: A 384 LYS cc_start: 0.6887 (tptt) cc_final: 0.6670 (ttmt) REVERT: B 124 LYS cc_start: 0.8115 (pttt) cc_final: 0.7862 (pttp) REVERT: B 361 LYS cc_start: 0.5959 (OUTLIER) cc_final: 0.5648 (tmtt) REVERT: B 416 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.5903 (tptp) REVERT: C 417 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: C 601 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7823 (mp0) REVERT: D 512 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8159 (mt0) outliers start: 28 outliers final: 14 residues processed: 146 average time/residue: 0.6451 time to fit residues: 100.7246 Evaluate side-chains 141 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN C 605 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.138718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114920 restraints weight = 13326.345| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.52 r_work: 0.3282 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11774 Z= 0.158 Angle : 0.521 6.961 16064 Z= 0.288 Chirality : 0.041 0.147 1740 Planarity : 0.003 0.043 1904 Dihedral : 16.392 142.095 1926 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.75 % Allowed : 27.84 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.23), residues: 1300 helix: 1.07 (0.23), residues: 558 sheet: -0.72 (0.42), residues: 164 loop : -0.95 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 351 TYR 0.018 0.001 TYR D 575 PHE 0.013 0.001 PHE A 149 TRP 0.012 0.001 TRP C 602 HIS 0.003 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00367 (11774) covalent geometry : angle 0.52091 (16064) hydrogen bonds : bond 0.03633 ( 517) hydrogen bonds : angle 4.46030 ( 1424) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.403 Fit side-chains REVERT: A 92 ASN cc_start: 0.8156 (t0) cc_final: 0.7896 (t0) REVERT: A 226 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6074 (mpp-170) REVERT: A 241 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: A 338 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6351 (ttm170) REVERT: A 384 LYS cc_start: 0.6971 (tptt) cc_final: 0.6722 (ttmt) REVERT: B 124 LYS cc_start: 0.8193 (pttt) cc_final: 0.7926 (pttp) REVERT: B 361 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5680 (tmtt) REVERT: B 416 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.5920 (tptp) REVERT: C 417 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: C 601 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7830 (mp0) REVERT: D 512 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8182 (mt0) outliers start: 31 outliers final: 16 residues processed: 149 average time/residue: 0.6125 time to fit residues: 98.0697 Evaluate side-chains 146 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 0.0670 chunk 133 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN B 81 GLN C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118358 restraints weight = 13322.242| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.51 r_work: 0.3342 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11774 Z= 0.114 Angle : 0.489 7.206 16064 Z= 0.272 Chirality : 0.039 0.143 1740 Planarity : 0.003 0.040 1904 Dihedral : 16.269 144.265 1926 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.68 % Allowed : 29.26 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.23), residues: 1300 helix: 1.30 (0.23), residues: 556 sheet: -0.71 (0.42), residues: 164 loop : -0.90 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 351 TYR 0.014 0.001 TYR D 575 PHE 0.012 0.001 PHE B 401 TRP 0.012 0.001 TRP C 602 HIS 0.002 0.000 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00255 (11774) covalent geometry : angle 0.48902 (16064) hydrogen bonds : bond 0.03147 ( 517) hydrogen bonds : angle 4.31945 ( 1424) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.262 Fit side-chains REVERT: A 226 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6633 (mtt180) REVERT: A 228 GLN cc_start: 0.7843 (mt0) cc_final: 0.7549 (mt0) REVERT: A 338 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6357 (ttm170) REVERT: B 124 LYS cc_start: 0.8135 (pttt) cc_final: 0.7873 (pttp) REVERT: B 293 LYS cc_start: 0.8458 (tptp) cc_final: 0.8232 (tptp) REVERT: B 361 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5716 (tmtt) REVERT: B 416 LYS cc_start: 0.6406 (OUTLIER) cc_final: 0.5813 (tptp) REVERT: C 417 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: C 601 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7816 (mp0) REVERT: D 512 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8123 (mp10) outliers start: 19 outliers final: 9 residues processed: 139 average time/residue: 0.5999 time to fit residues: 89.2678 Evaluate side-chains 138 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 70.2195 > 50: distance: 51 - 56: 15.233 distance: 56 - 57: 21.680 distance: 57 - 58: 3.097 distance: 57 - 60: 21.295 distance: 58 - 59: 10.144 distance: 58 - 65: 15.447 distance: 60 - 61: 15.591 distance: 61 - 62: 26.796 distance: 62 - 63: 31.740 distance: 62 - 64: 31.912 distance: 65 - 66: 39.845 distance: 66 - 67: 20.617 distance: 66 - 69: 10.007 distance: 67 - 68: 39.940 distance: 67 - 76: 21.263 distance: 69 - 70: 9.870 distance: 70 - 71: 5.782 distance: 70 - 72: 43.942 distance: 72 - 74: 24.093 distance: 73 - 75: 14.484 distance: 74 - 75: 27.179 distance: 77 - 78: 13.915 distance: 78 - 79: 31.224 distance: 78 - 83: 27.201 distance: 83 - 84: 23.776 distance: 84 - 85: 10.098 distance: 84 - 87: 9.661 distance: 85 - 86: 46.331 distance: 85 - 92: 24.144 distance: 87 - 88: 11.667 distance: 88 - 89: 17.574 distance: 89 - 90: 6.074 distance: 89 - 91: 4.017 distance: 93 - 96: 4.078 distance: 94 - 95: 4.394 distance: 94 - 103: 23.235 distance: 96 - 97: 5.942 distance: 97 - 98: 9.167 distance: 97 - 99: 21.887 distance: 98 - 100: 22.517 distance: 99 - 101: 34.539 distance: 101 - 102: 21.871 distance: 103 - 104: 28.879 distance: 104 - 105: 3.789 distance: 104 - 107: 19.176 distance: 105 - 106: 5.102 distance: 105 - 114: 9.782 distance: 107 - 108: 23.639 distance: 108 - 109: 22.010 distance: 109 - 110: 17.415 distance: 110 - 111: 10.533 distance: 111 - 112: 8.164 distance: 111 - 113: 21.746 distance: 114 - 115: 19.836 distance: 115 - 116: 31.153 distance: 116 - 117: 6.692 distance: 116 - 118: 42.418 distance: 118 - 119: 56.823 distance: 118 - 177: 36.487 distance: 119 - 120: 37.089 distance: 119 - 122: 13.357 distance: 120 - 121: 46.754 distance: 120 - 127: 3.443 distance: 121 - 174: 28.473 distance: 122 - 123: 14.768 distance: 123 - 124: 7.975 distance: 124 - 125: 62.361 distance: 124 - 126: 8.905 distance: 127 - 128: 4.309 distance: 128 - 129: 10.274 distance: 128 - 131: 34.870 distance: 129 - 130: 47.414 distance: 131 - 132: 40.822 distance: 131 - 133: 39.857 distance: 134 - 135: 5.104 distance: 134 - 163: 25.446 distance: 135 - 136: 18.154 distance: 135 - 138: 21.161 distance: 136 - 137: 20.263 distance: 136 - 141: 10.034 distance: 137 - 160: 16.687 distance: 138 - 140: 5.943