Starting phenix.real_space_refine on Thu Jul 2 04:10:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vx5_32169/07_2026/7vx5_32169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vx5_32169/07_2026/7vx5_32169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vx5_32169/07_2026/7vx5_32169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vx5_32169/07_2026/7vx5_32169.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vx5_32169/07_2026/7vx5_32169.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vx5_32169/07_2026/7vx5_32169.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vx5_32169/07_2026/7vx5_32169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vx5_32169/07_2026/7vx5_32169.map" } resolution = 3.8 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= -0.002 sd= 0.066 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 Zn 1 6.06 5 S 37 5.16 5 C 4144 2.51 5 N 1073 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6487 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1539 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.75, per 1000 atoms: 0.27 Number of scatterers: 6487 At special positions: 0 Unit cell: (77.603, 100.556, 118.044, 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) Zn 1 29.99 S 37 16.00 O 1232 8.00 N 1073 7.00 C 4144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 NAG-ASN " NAG A 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 53 " " NAG E1301 " - " ASN E 343 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 447.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 57.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.644A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.682A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.524A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.903A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.610A pdb=" N LYS A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.527A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.767A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 4.010A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.588A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.754A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.905A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.649A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.647A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.912A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.561A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.106A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.504A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.471A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.583A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.038A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.604A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.821A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.575A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.880A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.849A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.592A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 383 through 389 removed outlier: 3.579A pdb=" N ASN E 388 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 4.220A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.009A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.917A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.920A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 283 hydrogen bonds defined for protein. 797 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: 0.78 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2080 1.34 - 1.46: 1694 1.46 - 1.58: 2836 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6668 Sorted by residual: bond pdb=" C LYS E 424 " pdb=" N LEU E 425 " ideal model delta sigma weight residual 1.331 1.374 -0.043 2.07e-02 2.33e+03 4.35e+00 bond pdb=" CA CYS E 336 " pdb=" C CYS E 336 " ideal model delta sigma weight residual 1.526 1.505 0.021 1.14e-02 7.69e+03 3.41e+00 bond pdb=" CA GLN E 484 " pdb=" C GLN E 484 " ideal model delta sigma weight residual 1.528 1.506 0.022 1.38e-02 5.25e+03 2.57e+00 bond pdb=" C ALA A 36 " pdb=" N GLU A 37 " ideal model delta sigma weight residual 1.335 1.315 0.020 1.31e-02 5.83e+03 2.35e+00 bond pdb=" CA VAL E 445 " pdb=" C VAL E 445 " ideal model delta sigma weight residual 1.522 1.502 0.020 1.35e-02 5.49e+03 2.27e+00 ... (remaining 6663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 8677 1.49 - 2.99: 347 2.99 - 4.48: 34 4.48 - 5.97: 5 5.97 - 7.46: 1 Bond angle restraints: 9064 Sorted by residual: angle pdb=" N GLY E 446 " pdb=" CA GLY E 446 " pdb=" C GLY E 446 " ideal model delta sigma weight residual 115.36 107.90 7.46 1.33e+00 5.65e-01 3.15e+01 angle pdb=" N GLY A 147 " pdb=" CA GLY A 147 " pdb=" C GLY A 147 " ideal model delta sigma weight residual 112.64 117.74 -5.10 1.21e+00 6.83e-01 1.78e+01 angle pdb=" C VAL E 445 " pdb=" CA VAL E 445 " pdb=" CB VAL E 445 " ideal model delta sigma weight residual 111.32 105.41 5.91 1.63e+00 3.76e-01 1.31e+01 angle pdb=" C TYR E 495 " pdb=" N GLY E 496 " pdb=" CA GLY E 496 " ideal model delta sigma weight residual 120.98 117.78 3.20 9.00e-01 1.23e+00 1.27e+01 angle pdb=" C ALA A 36 " pdb=" N GLU A 37 " pdb=" CA GLU A 37 " ideal model delta sigma weight residual 120.28 116.09 4.19 1.34e+00 5.57e-01 9.78e+00 ... (remaining 9059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 3778 15.98 - 31.96: 85 31.96 - 47.95: 23 47.95 - 63.93: 6 63.93 - 79.91: 3 Dihedral angle restraints: 3895 sinusoidal: 1571 harmonic: 2324 Sorted by residual: dihedral pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" N GLY A 147 " pdb=" CA GLY A 147 " ideal model delta harmonic sigma weight residual 180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ALA E 352 " pdb=" C ALA E 352 " pdb=" N TRP E 353 " pdb=" CA TRP E 353 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA TYR A 497 " pdb=" C TYR A 497 " pdb=" N CYS A 498 " pdb=" CA CYS A 498 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 3892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 760 0.050 - 0.100: 167 0.100 - 0.150: 30 0.150 - 0.200: 3 0.200 - 0.250: 1 Chirality restraints: 961 Sorted by residual: chirality pdb=" CA VAL E 445 " pdb=" N VAL E 445 " pdb=" C VAL E 445 " pdb=" CB VAL E 445 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA GLN E 498 " pdb=" N GLN E 498 " pdb=" C GLN E 498 " pdb=" CB GLN E 498 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA GLU A 37 " pdb=" N GLU A 37 " pdb=" C GLU A 37 " pdb=" CB GLU A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 958 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 498 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO E 499 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 499 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 499 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 583 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 484 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C GLN E 484 " -0.025 2.00e-02 2.50e+03 pdb=" O GLN E 484 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY E 485 " 0.008 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1458 2.78 - 3.31: 6109 3.31 - 3.84: 10401 3.84 - 4.37: 12459 4.37 - 4.90: 21156 Nonbonded interactions: 51583 Sorted by model distance: nonbonded pdb=" OH TYR A 83 " pdb=" OD1 ASN E 487 " model vdw 2.246 3.040 nonbonded pdb=" N SER A 19 " pdb=" OE1 GLU A 23 " model vdw 2.264 3.120 nonbonded pdb=" O MET A 152 " pdb=" NH1 ARG A 161 " model vdw 2.270 3.120 nonbonded pdb=" OD1 ASN A 394 " pdb=" N GLY A 395 " model vdw 2.275 3.120 nonbonded pdb=" O MET A 190 " pdb=" ND2 ASN A 194 " model vdw 2.279 3.120 ... (remaining 51578 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.310 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.820 Find NCS groups from input model: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 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 0.090 6682 Z= 0.181 Angle : 0.655 7.463 9093 Z= 0.422 Chirality : 0.044 0.250 961 Planarity : 0.004 0.065 1171 Dihedral : 8.618 79.909 2384 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: -2.69 (0.25), residues: 788 helix: -2.96 (0.19), residues: 375 sheet: -0.42 (0.60), residues: 60 loop : -0.37 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.025 0.001 TYR E 495 PHE 0.020 0.002 PHE E 497 TRP 0.017 0.001 TRP A 302 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.18 ( 6668) covalent geometry : angle 0.65192 / 0.42 ( 9064) SS BOND : bond 0.00229 / 0.12 ( 7) SS BOND : angle 0.95133 / 0.56 ( 14) hydrogen bonds : bond 0.29514 / 18.96 ( 283) hydrogen bonds : angle 9.43504 / 6.56 ( 797) metal coordination : bond 0.06436 / 3.38 ( 2) link_NAG-ASN : bond 0.00148 / 0.09 ( 5) link_NAG-ASN : angle 1.44606 / 0.88 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8115 (p) cc_final: 0.7690 (t) REVERT: A 79 LEU cc_start: 0.8070 (mt) cc_final: 0.7867 (mp) REVERT: A 98 GLN cc_start: 0.8329 (tt0) cc_final: 0.7717 (mm110) REVERT: A 217 TYR cc_start: 0.8174 (t80) cc_final: 0.7328 (t80) REVERT: A 259 ILE cc_start: 0.8398 (pt) cc_final: 0.8148 (mp) REVERT: A 270 MET cc_start: 0.2479 (tpp) cc_final: 0.2262 (tpp) REVERT: A 323 MET cc_start: 0.7078 (mmp) cc_final: 0.5950 (mmt) REVERT: A 411 SER cc_start: 0.8513 (m) cc_final: 0.8295 (p) REVERT: A 513 ILE cc_start: 0.6925 (tp) cc_final: 0.6477 (tt) REVERT: A 531 GLN cc_start: 0.7367 (tt0) cc_final: 0.7059 (tp40) REVERT: E 356 LYS cc_start: 0.8394 (tttp) cc_final: 0.8133 (ttmm) REVERT: E 422 ASN cc_start: 0.8531 (m-40) cc_final: 0.8188 (m110) REVERT: E 461 LEU cc_start: 0.8610 (mt) cc_final: 0.8378 (mt) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.0724 time to fit residues: 19.7867 Evaluate side-chains 128 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 101 GLN A 239 HIS A 305 GLN A 373 HIS A 380 GLN A 524 GLN A 598 GLN E 501 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.175378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.149376 restraints weight = 7908.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.148992 restraints weight = 10566.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.150069 restraints weight = 8719.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.150157 restraints weight = 6458.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.150567 restraints weight = 6233.174| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6682 Z= 0.175 Angle : 0.649 9.632 9093 Z= 0.340 Chirality : 0.047 0.329 961 Planarity : 0.005 0.035 1171 Dihedral : 4.674 17.345 862 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.87 % Allowed : 9.35 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: -1.06 (0.27), residues: 788 helix: -1.03 (0.23), residues: 400 sheet: -0.10 (0.60), residues: 59 loop : -0.11 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 169 TYR 0.024 0.002 TYR E 495 PHE 0.025 0.003 PHE E 497 TRP 0.024 0.002 TRP A 302 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 6668) covalent geometry : angle 0.64672 / 0.34 ( 9064) SS BOND : bond 0.00928 / 0.47 ( 7) SS BOND : angle 1.13011 / 0.60 ( 14) hydrogen bonds : bond 0.04654 / 3.01 ( 283) hydrogen bonds : angle 5.28701 / 3.71 ( 797) metal coordination : bond 0.00057 / 0.03 ( 2) link_NAG-ASN : bond 0.00227 / 0.12 ( 5) link_NAG-ASN : angle 1.32507 / 0.79 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7320 (m-30) cc_final: 0.6985 (t0) REVERT: A 194 ASN cc_start: 0.7129 (OUTLIER) cc_final: 0.6907 (t0) REVERT: A 207 TYR cc_start: 0.8376 (m-80) cc_final: 0.7560 (m-10) REVERT: A 217 TYR cc_start: 0.8072 (t80) cc_final: 0.6594 (t80) REVERT: A 219 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.7532 (mtm-85) REVERT: A 371 THR cc_start: 0.8495 (m) cc_final: 0.8222 (t) REVERT: A 483 GLU cc_start: 0.6320 (pt0) cc_final: 0.6072 (pt0) outliers start: 13 outliers final: 8 residues processed: 151 average time/residue: 0.0564 time to fit residues: 12.2626 Evaluate side-chains 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 8.9990 chunk 40 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 chunk 59 optimal weight: 0.0570 chunk 65 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 380 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.174683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.151842 restraints weight = 11862.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.151367 restraints weight = 17716.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.152159 restraints weight = 7728.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.152842 restraints weight = 6384.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.153943 restraints weight = 4614.888| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6682 Z= 0.143 Angle : 0.580 7.838 9093 Z= 0.301 Chirality : 0.043 0.143 961 Planarity : 0.004 0.041 1171 Dihedral : 4.380 16.229 862 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.87 % Allowed : 12.66 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: -0.24 (0.28), residues: 788 helix: -0.22 (0.25), residues: 395 sheet: 0.07 (0.66), residues: 51 loop : 0.12 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 161 TYR 0.018 0.001 TYR E 495 PHE 0.017 0.002 PHE E 497 TRP 0.022 0.002 TRP A 594 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6668) covalent geometry : angle 0.57722 / 0.30 ( 9064) SS BOND : bond 0.00283 / 0.15 ( 7) SS BOND : angle 0.95721 / 0.51 ( 14) hydrogen bonds : bond 0.04226 / 2.74 ( 283) hydrogen bonds : angle 4.87970 / 3.42 ( 797) metal coordination : bond 0.00020 / 0.01 ( 2) link_NAG-ASN : bond 0.00120 / 0.06 ( 5) link_NAG-ASN : angle 1.31864 / 0.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7754 (tp30) cc_final: 0.7509 (tm-30) REVERT: A 67 ASP cc_start: 0.7258 (m-30) cc_final: 0.7044 (t0) REVERT: A 207 TYR cc_start: 0.8279 (m-80) cc_final: 0.7573 (m-10) REVERT: A 217 TYR cc_start: 0.8021 (t80) cc_final: 0.7686 (t80) REVERT: A 219 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.7812 (mtm-85) REVERT: A 366 MET cc_start: 0.8361 (tmm) cc_final: 0.7895 (tmm) REVERT: A 394 ASN cc_start: 0.7227 (t0) cc_final: 0.6217 (m110) REVERT: A 515 TYR cc_start: 0.7667 (m-80) cc_final: 0.7441 (m-10) REVERT: E 506 GLN cc_start: 0.8796 (mt0) cc_final: 0.8569 (mt0) outliers start: 13 outliers final: 9 residues processed: 120 average time/residue: 0.0600 time to fit residues: 10.2881 Evaluate side-chains 100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 168 TRP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 36 optimal weight: 0.0770 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN E 484 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.173277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.144688 restraints weight = 10134.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.146795 restraints weight = 12732.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.148607 restraints weight = 9252.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.149201 restraints weight = 6008.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.150446 restraints weight = 5373.206| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6682 Z= 0.134 Angle : 0.558 8.743 9093 Z= 0.286 Chirality : 0.043 0.142 961 Planarity : 0.004 0.043 1171 Dihedral : 4.208 15.972 862 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 13.81 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: 0.09 (0.29), residues: 788 helix: 0.18 (0.25), residues: 402 sheet: -0.00 (0.69), residues: 49 loop : 0.16 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.014 0.001 TYR E 495 PHE 0.014 0.002 PHE A 504 TRP 0.024 0.002 TRP A 594 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 6668) covalent geometry : angle 0.55602 / 0.29 ( 9064) SS BOND : bond 0.00255 / 0.13 ( 7) SS BOND : angle 0.77970 / 0.41 ( 14) hydrogen bonds : bond 0.03801 / 2.49 ( 283) hydrogen bonds : angle 4.69798 / 3.30 ( 797) metal coordination : bond 0.00060 / 0.03 ( 2) link_NAG-ASN : bond 0.00146 / 0.08 ( 5) link_NAG-ASN : angle 1.20024 / 0.72 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8276 (tp30) cc_final: 0.8051 (tp30) REVERT: A 57 GLU cc_start: 0.7821 (tp30) cc_final: 0.7612 (tm-30) REVERT: A 67 ASP cc_start: 0.7373 (m-30) cc_final: 0.7113 (t0) REVERT: A 207 TYR cc_start: 0.8232 (m-80) cc_final: 0.7491 (m-10) REVERT: A 217 TYR cc_start: 0.8045 (t80) cc_final: 0.7824 (t80) REVERT: A 219 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7677 (mtm-85) REVERT: A 259 ILE cc_start: 0.8459 (pt) cc_final: 0.8074 (mt) REVERT: A 394 ASN cc_start: 0.7346 (t0) cc_final: 0.6123 (m110) REVERT: E 506 GLN cc_start: 0.8938 (mt0) cc_final: 0.8619 (mt0) outliers start: 14 outliers final: 13 residues processed: 109 average time/residue: 0.0539 time to fit residues: 8.4611 Evaluate side-chains 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 168 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0535 > 50: distance: 44 - 134: 36.739 distance: 47 - 131: 32.660 distance: 59 - 119: 37.174 distance: 62 - 116: 31.751 distance: 89 - 126: 36.174 distance: 92 - 123: 32.459 distance: 111 - 116: 34.827 distance: 116 - 117: 56.953 distance: 117 - 118: 27.918 distance: 117 - 120: 40.563 distance: 118 - 119: 47.252 distance: 118 - 123: 48.217 distance: 120 - 121: 57.476 distance: 120 - 122: 56.981 distance: 123 - 124: 38.721 distance: 124 - 125: 35.700 distance: 124 - 127: 44.128 distance: 125 - 126: 36.235 distance: 125 - 131: 55.241 distance: 127 - 128: 10.726 distance: 128 - 129: 12.869 distance: 128 - 130: 27.151 distance: 131 - 132: 19.600 distance: 132 - 133: 55.483 distance: 132 - 135: 21.844 distance: 133 - 134: 17.452 distance: 133 - 137: 14.153 distance: 135 - 136: 40.335 distance: 137 - 138: 24.333 distance: 138 - 139: 51.264 distance: 138 - 141: 17.630 distance: 139 - 140: 26.105 distance: 139 - 148: 4.316 distance: 141 - 142: 33.640 distance: 142 - 143: 54.917 distance: 142 - 144: 5.542 distance: 143 - 145: 44.926 distance: 144 - 146: 16.860 distance: 145 - 147: 39.968 distance: 146 - 147: 39.853 distance: 148 - 149: 39.942 distance: 149 - 152: 7.923 distance: 150 - 151: 39.173 distance: 150 - 157: 34.361 distance: 152 - 153: 40.779 distance: 154 - 155: 45.970 distance: 157 - 158: 13.306 distance: 158 - 159: 17.538 distance: 159 - 160: 22.238 distance: 159 - 165: 25.620 distance: 161 - 162: 35.598 distance: 162 - 163: 39.807 distance: 162 - 164: 16.098 distance: 165 - 166: 37.175 distance: 166 - 167: 5.442 distance: 166 - 169: 12.286 distance: 167 - 168: 38.727 distance: 167 - 173: 29.117 distance: 169 - 170: 20.300 distance: 170 - 171: 54.275 distance: 170 - 172: 37.127 distance: 173 - 174: 42.342 distance: 174 - 175: 50.588 distance: 174 - 177: 40.489 distance: 175 - 176: 49.570 distance: 175 - 183: 10.303 distance: 177 - 178: 36.389 distance: 178 - 179: 52.642 distance: 178 - 180: 41.354 distance: 179 - 181: 59.556 distance: 180 - 182: 30.279 distance: 181 - 182: 41.169 distance: 183 - 184: 4.997 distance: 184 - 185: 26.112 distance: 184 - 187: 3.048 distance: 185 - 186: 47.559 distance: 185 - 188: 3.618 distance: 188 - 189: 43.643 distance: 188 - 194: 25.960 distance: 189 - 190: 26.885 distance: 190 - 191: 31.993 distance: 190 - 195: 22.807 distance: 192 - 193: 57.650 distance: 193 - 194: 46.215