Starting phenix.real_space_refine on Thu Sep 18 05:57:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z8j_39848/09_2025/8z8j_39848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z8j_39848/09_2025/8z8j_39848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z8j_39848/09_2025/8z8j_39848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z8j_39848/09_2025/8z8j_39848.map" model { file = "/net/cci-nas-00/data/ceres_data/8z8j_39848/09_2025/8z8j_39848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z8j_39848/09_2025/8z8j_39848.cif" } resolution = 3.16 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 80 5.16 5 C 8698 2.51 5 N 2387 2.21 5 O 2587 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13766 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5021 Classifications: {'peptide': 621} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 589} Chain: "B" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5255 Classifications: {'peptide': 656} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 622} Chain breaks: 3 Chain: "C" Number of atoms: 3170 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 388, 3158 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 27, 'TRANS': 360} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 388, 3158 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 27, 'TRANS': 360} Chain breaks: 3 bond proxies already assigned to first conformer: 3228 Chain: "D" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER C 336 " occ=0.39 ... (10 atoms not shown) pdb=" OG BSER C 336 " occ=0.61 residue: pdb=" N ASER C 384 " occ=0.01 ... (10 atoms not shown) pdb=" OG BSER C 384 " occ=0.99 Time building chain proxies: 4.31, per 1000 atoms: 0.31 Number of scatterers: 13766 At special positions: 0 Unit cell: (89.8461, 101.526, 137.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 14 15.00 O 2587 8.00 N 2387 7.00 C 8698 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: 1.25 Conformation dependent library (CDL) restraints added in 855.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3182 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 16 sheets defined 47.5% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 4.547A pdb=" N THR A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 134 through 155 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.548A pdb=" N ASP A 236 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.631A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.734A pdb=" N ILE A 298 " --> pdb=" O HIS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.958A pdb=" N SER A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.165A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.494A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.531A pdb=" N SER A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 498 through 516 removed outlier: 4.014A pdb=" N ASN A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.509A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 3.758A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 33 through 47 removed outlier: 3.641A pdb=" N ARG B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 96 through 108 removed outlier: 3.792A pdb=" N LYS B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.615A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.494A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 278 through 287 removed outlier: 3.782A pdb=" N ALA B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.538A pdb=" N GLU B 307 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS B 308 " --> pdb=" O PHE B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 310 through 325 removed outlier: 3.937A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 Processing helix chain 'B' and resid 336 through 343 removed outlier: 3.554A pdb=" N PHE B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 406 removed outlier: 3.604A pdb=" N THR B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 432 through 449 removed outlier: 3.600A pdb=" N LYS B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 514 removed outlier: 3.598A pdb=" N ALA B 502 " --> pdb=" O MET B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 537 removed outlier: 3.547A pdb=" N TYR B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.707A pdb=" N GLU B 551 " --> pdb=" O ARG B 547 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 552 " --> pdb=" O PHE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 588 through 595 Processing helix chain 'B' and resid 646 through 666 removed outlier: 4.103A pdb=" N ASN B 650 " --> pdb=" O LYS B 646 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 679 through 694 Processing helix chain 'B' and resid 698 through 709 Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.660A pdb=" N ARG C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 115 through 123 removed outlier: 4.195A pdb=" N LEU C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 191 through 207 Proline residue: C 202 - end of helix removed outlier: 3.620A pdb=" N LYS C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 234 through 240 removed outlier: 3.575A pdb=" N GLU C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 415 removed outlier: 3.619A pdb=" N GLY C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 removed outlier: 3.957A pdb=" N GLY C 420 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 446 removed outlier: 3.607A pdb=" N PHE C 435 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER C 444 " --> pdb=" O PHE C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 455 removed outlier: 3.555A pdb=" N LEU C 451 " --> pdb=" O HIS C 447 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 3.524A pdb=" N LYS A 97 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 119 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 removed outlier: 3.681A pdb=" N GLY B 300 " --> pdb=" O PHE B 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242 removed outlier: 6.823A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 6.761A pdb=" N ILE A 414 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N MET A 428 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS A 412 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU A 430 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR A 410 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531 Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.537A pdb=" N SER B 126 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 131 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 245 removed outlier: 3.796A pdb=" N ASN B 227 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 226 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB3, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AB5, first strand: chain 'C' and resid 348 through 354 removed outlier: 3.510A pdb=" N LYS C 349 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 353 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 370 through 376 removed outlier: 4.319A pdb=" N GLU C 392 " --> pdb=" O ASER C 384 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR C 482 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 393 " --> pdb=" O THR C 482 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 456 through 457 removed outlier: 3.520A pdb=" N LYS C 477 " --> pdb=" O ASP C 457 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1612 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: 2.57 Time building geometry restraints manager: 1.70 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: 4411 1.34 - 1.46: 2420 1.46 - 1.58: 7123 1.58 - 1.70: 27 1.70 - 1.82: 129 Bond restraints: 14110 Sorted by residual: bond pdb=" CB PRO C 343 " pdb=" CG PRO C 343 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.23e+00 bond pdb=" CB LYS C 458 " pdb=" CG LYS C 458 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.95e-01 bond pdb=" C GLU C 418 " pdb=" N PRO C 419 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.90e-01 bond pdb=" CA ASN A 156 " pdb=" CB ASN A 156 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.77e-01 bond pdb=" CB ASN C 80 " pdb=" CG ASN C 80 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.48e-01 ... (remaining 14105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 18907 2.04 - 4.08: 228 4.08 - 6.13: 27 6.13 - 8.17: 6 8.17 - 10.21: 2 Bond angle restraints: 19170 Sorted by residual: angle pdb=" N VAL C 230 " pdb=" CA VAL C 230 " pdb=" C VAL C 230 " ideal model delta sigma weight residual 112.96 107.93 5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" C ASN A 155 " pdb=" N ASN A 156 " pdb=" CA ASN A 156 " ideal model delta sigma weight residual 121.54 127.88 -6.34 1.91e+00 2.74e-01 1.10e+01 angle pdb=" CA PRO C 343 " pdb=" N PRO C 343 " pdb=" CD PRO C 343 " ideal model delta sigma weight residual 112.00 107.49 4.51 1.40e+00 5.10e-01 1.04e+01 angle pdb=" N GLU B 653 " pdb=" CA GLU B 653 " pdb=" CB GLU B 653 " ideal model delta sigma weight residual 110.28 115.26 -4.98 1.55e+00 4.16e-01 1.03e+01 angle pdb=" CA LEU A 402 " pdb=" CB LEU A 402 " pdb=" CG LEU A 402 " ideal model delta sigma weight residual 116.30 126.51 -10.21 3.50e+00 8.16e-02 8.51e+00 ... (remaining 19165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7820 17.95 - 35.90: 641 35.90 - 53.85: 103 53.85 - 71.80: 30 71.80 - 89.75: 11 Dihedral angle restraints: 8605 sinusoidal: 3706 harmonic: 4899 Sorted by residual: dihedral pdb=" CA GLU C 418 " pdb=" C GLU C 418 " pdb=" N PRO C 419 " pdb=" CA PRO C 419 " ideal model delta harmonic sigma weight residual 180.00 -162.13 -17.87 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CB GLU B 372 " pdb=" CG GLU B 372 " pdb=" CD GLU B 372 " pdb=" OE1 GLU B 372 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 550 " pdb=" CG GLU B 550 " pdb=" CD GLU B 550 " pdb=" OE1 GLU B 550 " ideal model delta sinusoidal sigma weight residual 0.00 -88.89 88.89 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1387 0.032 - 0.064: 511 0.064 - 0.095: 165 0.095 - 0.127: 64 0.127 - 0.159: 8 Chirality restraints: 2135 Sorted by residual: chirality pdb=" CB ILE B 620 " pdb=" CA ILE B 620 " pdb=" CG1 ILE B 620 " pdb=" CG2 ILE B 620 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA ASN A 156 " pdb=" N ASN A 156 " pdb=" C ASN A 156 " pdb=" CB ASN A 156 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA GLU C 405 " pdb=" N GLU C 405 " pdb=" C GLU C 405 " pdb=" CB GLU C 405 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 2132 not shown) Planarity restraints: 2401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 342 " 0.046 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO C 343 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 343 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 343 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 234 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO C 235 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 235 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 235 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 96 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO B 97 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 97 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 97 " -0.032 5.00e-02 4.00e+02 ... (remaining 2398 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1765 2.75 - 3.29: 13745 3.29 - 3.83: 23114 3.83 - 4.36: 27698 4.36 - 4.90: 47543 Nonbonded interactions: 113865 Sorted by model distance: nonbonded pdb=" O SER A 482 " pdb=" O2' A D 3 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 295 " pdb=" O PRO B 464 " model vdw 2.256 3.040 nonbonded pdb=" ND2 ASN A 558 " pdb=" O PRO B 25 " model vdw 2.256 3.120 nonbonded pdb=" O ILE C 122 " pdb=" NE2 GLN C 207 " model vdw 2.258 3.120 nonbonded pdb=" OG1 THR B 245 " pdb=" NH2 ARG B 251 " model vdw 2.268 3.120 ... (remaining 113860 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=0.01 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.730 Find NCS groups from input model: 0.060 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.002 0.075 14110 Z= 0.105 Angle : 0.549 10.211 19170 Z= 0.279 Chirality : 0.040 0.159 2135 Planarity : 0.005 0.067 2401 Dihedral : 13.582 89.746 5423 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.26 (0.21), residues: 1653 helix: 1.02 (0.20), residues: 721 sheet: -0.55 (0.40), residues: 172 loop : -1.25 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 704 TYR 0.023 0.001 TYR B 176 PHE 0.029 0.001 PHE B 290 TRP 0.011 0.001 TRP B 220 HIS 0.007 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00238 (14110) covalent geometry : angle 0.54919 (19170) hydrogen bonds : bond 0.18599 ( 578) hydrogen bonds : angle 6.39146 ( 1612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8160 (t0) cc_final: 0.6862 (t0) REVERT: A 83 ASP cc_start: 0.7768 (m-30) cc_final: 0.7518 (m-30) REVERT: A 163 GLU cc_start: 0.8831 (tp30) cc_final: 0.8510 (tp30) REVERT: A 447 ILE cc_start: 0.9270 (mm) cc_final: 0.9052 (mm) REVERT: B 393 MET cc_start: 0.7460 (tpt) cc_final: 0.6911 (tpt) REVERT: B 422 ASP cc_start: 0.7992 (p0) cc_final: 0.7783 (p0) REVERT: B 653 GLU cc_start: 0.8184 (mp0) cc_final: 0.7647 (mp0) REVERT: C 378 GLN cc_start: 0.8881 (mm110) cc_final: 0.8522 (mm110) REVERT: C 405 GLU cc_start: 0.7240 (pp20) cc_final: 0.6954 (pp20) REVERT: C 410 ILE cc_start: 0.8818 (mt) cc_final: 0.8552 (mt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1324 time to fit residues: 42.4734 Evaluate side-chains 188 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS B 336 ASN B 453 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095953 restraints weight = 45689.758| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.61 r_work: 0.3015 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14110 Z= 0.123 Angle : 0.560 7.094 19170 Z= 0.285 Chirality : 0.041 0.163 2135 Planarity : 0.005 0.059 2401 Dihedral : 8.459 74.711 2033 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.67 % Allowed : 6.74 % Favored : 92.59 % 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 (0.21), residues: 1653 helix: 1.21 (0.20), residues: 729 sheet: -0.74 (0.38), residues: 190 loop : -1.19 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 704 TYR 0.022 0.001 TYR C 382 PHE 0.017 0.001 PHE C 41 TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00279 (14110) covalent geometry : angle 0.55961 (19170) hydrogen bonds : bond 0.04241 ( 578) hydrogen bonds : angle 4.94239 ( 1612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 0.556 Fit side-chains REVERT: A 47 ASN cc_start: 0.8549 (t0) cc_final: 0.8052 (t0) REVERT: A 163 GLU cc_start: 0.8901 (tp30) cc_final: 0.8491 (tp30) REVERT: A 621 TYR cc_start: 0.8419 (m-80) cc_final: 0.8028 (m-80) REVERT: B 140 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8213 (tm-30) REVERT: B 283 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8323 (tppt) REVERT: B 393 MET cc_start: 0.7962 (tpt) cc_final: 0.7341 (tpt) REVERT: B 409 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7705 (mm-30) REVERT: B 653 GLU cc_start: 0.8512 (mp0) cc_final: 0.7958 (mp0) REVERT: C 377 ASP cc_start: 0.8668 (t0) cc_final: 0.8201 (t0) REVERT: C 378 GLN cc_start: 0.8863 (mm110) cc_final: 0.8487 (mm110) REVERT: C 410 ILE cc_start: 0.8892 (mt) cc_final: 0.8653 (mt) REVERT: C 423 GLN cc_start: 0.7922 (tp40) cc_final: 0.7656 (tp-100) outliers start: 10 outliers final: 10 residues processed: 212 average time/residue: 0.1404 time to fit residues: 42.9295 Evaluate side-chains 189 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 129 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 156 optimal weight: 30.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.091388 restraints weight = 53833.243| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.97 r_work: 0.2931 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14110 Z= 0.158 Angle : 0.560 7.217 19170 Z= 0.283 Chirality : 0.041 0.166 2135 Planarity : 0.005 0.058 2401 Dihedral : 8.501 74.868 2033 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.20 % Allowed : 8.34 % Favored : 90.45 % 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 (0.21), residues: 1653 helix: 1.33 (0.20), residues: 728 sheet: -1.02 (0.37), residues: 170 loop : -1.13 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 82 TYR 0.034 0.002 TYR C 363 PHE 0.017 0.001 PHE C 374 TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00368 (14110) covalent geometry : angle 0.55959 (19170) hydrogen bonds : bond 0.03927 ( 578) hydrogen bonds : angle 4.63019 ( 1612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8923 (tp30) cc_final: 0.8504 (tp30) REVERT: A 267 LYS cc_start: 0.8954 (mppt) cc_final: 0.8666 (tmtt) REVERT: A 365 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: A 451 MET cc_start: 0.9246 (mtt) cc_final: 0.8945 (mtt) REVERT: B 140 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8270 (tm-30) REVERT: B 393 MET cc_start: 0.8038 (tpt) cc_final: 0.7486 (tpt) REVERT: B 422 ASP cc_start: 0.8490 (p0) cc_final: 0.8177 (p0) REVERT: B 503 MET cc_start: 0.9051 (mpp) cc_final: 0.8750 (mpp) REVERT: B 704 ARG cc_start: 0.8983 (ttp-110) cc_final: 0.8775 (ttp-110) REVERT: C 410 ILE cc_start: 0.8903 (mt) cc_final: 0.8689 (mt) REVERT: C 423 GLN cc_start: 0.8068 (tp40) cc_final: 0.7851 (tp40) outliers start: 18 outliers final: 11 residues processed: 206 average time/residue: 0.1479 time to fit residues: 43.3508 Evaluate side-chains 200 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 629 CYS Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 ASN B 433 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.089243 restraints weight = 45306.544| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.55 r_work: 0.2923 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14110 Z= 0.170 Angle : 0.562 7.261 19170 Z= 0.284 Chirality : 0.042 0.162 2135 Planarity : 0.005 0.057 2401 Dihedral : 8.532 75.019 2033 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.40 % Allowed : 10.15 % Favored : 88.45 % 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: -0.05 (0.21), residues: 1653 helix: 1.29 (0.20), residues: 735 sheet: -1.15 (0.36), residues: 174 loop : -1.10 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 82 TYR 0.024 0.001 TYR C 382 PHE 0.019 0.002 PHE C 374 TRP 0.012 0.001 TRP A 336 HIS 0.003 0.001 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00399 (14110) covalent geometry : angle 0.56171 (19170) hydrogen bonds : bond 0.03718 ( 578) hydrogen bonds : angle 4.49453 ( 1612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8558 (t0) cc_final: 0.8198 (t0) REVERT: A 48 MET cc_start: 0.7922 (ppp) cc_final: 0.7679 (ppp) REVERT: A 163 GLU cc_start: 0.8936 (tp30) cc_final: 0.8509 (tp30) REVERT: A 365 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8398 (m-30) REVERT: A 451 MET cc_start: 0.9243 (mtt) cc_final: 0.8993 (mtt) REVERT: B 140 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8266 (tm-30) REVERT: B 283 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8394 (tppt) REVERT: B 422 ASP cc_start: 0.8554 (p0) cc_final: 0.8290 (p0) REVERT: B 503 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8573 (mpp) REVERT: B 704 ARG cc_start: 0.8944 (ttp-110) cc_final: 0.8667 (ttp-110) REVERT: C 410 ILE cc_start: 0.8905 (mt) cc_final: 0.8696 (mt) REVERT: C 423 GLN cc_start: 0.8101 (tp40) cc_final: 0.7819 (tp40) outliers start: 21 outliers final: 13 residues processed: 201 average time/residue: 0.1458 time to fit residues: 41.6316 Evaluate side-chains 195 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 102 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 33 optimal weight: 0.0040 chunk 82 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 ASN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.090131 restraints weight = 45631.357| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.60 r_work: 0.2934 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14110 Z= 0.131 Angle : 0.540 7.254 19170 Z= 0.271 Chirality : 0.041 0.161 2135 Planarity : 0.004 0.057 2401 Dihedral : 8.460 75.293 2033 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.54 % Allowed : 10.35 % Favored : 88.12 % 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: 0.02 (0.21), residues: 1653 helix: 1.37 (0.20), residues: 735 sheet: -1.12 (0.36), residues: 174 loop : -1.07 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 82 TYR 0.021 0.001 TYR C 363 PHE 0.018 0.001 PHE C 41 TRP 0.012 0.001 TRP A 336 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00309 (14110) covalent geometry : angle 0.53980 (19170) hydrogen bonds : bond 0.03452 ( 578) hydrogen bonds : angle 4.37349 ( 1612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8517 (t0) cc_final: 0.7966 (t0) REVERT: A 48 MET cc_start: 0.7916 (ppp) cc_final: 0.7646 (ppp) REVERT: A 163 GLU cc_start: 0.8933 (tp30) cc_final: 0.8487 (tp30) REVERT: A 365 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8383 (m-30) REVERT: B 140 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 393 MET cc_start: 0.7871 (tpt) cc_final: 0.7529 (tpt) REVERT: B 503 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8523 (mpp) REVERT: B 704 ARG cc_start: 0.8921 (ttp-110) cc_final: 0.8643 (ttp-110) REVERT: C 410 ILE cc_start: 0.8903 (mt) cc_final: 0.8684 (mt) REVERT: C 423 GLN cc_start: 0.8123 (tp40) cc_final: 0.7834 (tp40) outliers start: 23 outliers final: 17 residues processed: 198 average time/residue: 0.1348 time to fit residues: 38.7318 Evaluate side-chains 196 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 567 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.090350 restraints weight = 50216.386| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.76 r_work: 0.2937 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14110 Z= 0.118 Angle : 0.527 7.228 19170 Z= 0.267 Chirality : 0.040 0.161 2135 Planarity : 0.004 0.057 2401 Dihedral : 8.386 75.474 2033 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.54 % Allowed : 11.01 % Favored : 87.45 % 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: 0.12 (0.21), residues: 1653 helix: 1.46 (0.20), residues: 735 sheet: -1.03 (0.36), residues: 173 loop : -1.04 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 82 TYR 0.019 0.001 TYR C 412 PHE 0.018 0.001 PHE C 41 TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00274 (14110) covalent geometry : angle 0.52744 (19170) hydrogen bonds : bond 0.03286 ( 578) hydrogen bonds : angle 4.28521 ( 1612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8570 (t0) cc_final: 0.7919 (t0) REVERT: A 163 GLU cc_start: 0.8954 (tp30) cc_final: 0.8498 (tp30) REVERT: A 365 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8371 (m-30) REVERT: A 451 MET cc_start: 0.9135 (mtt) cc_final: 0.8891 (mtt) REVERT: B 140 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8314 (tm-30) REVERT: B 283 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8371 (tppt) REVERT: B 393 MET cc_start: 0.7843 (tpt) cc_final: 0.7524 (tpt) REVERT: B 503 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8558 (mpp) REVERT: B 704 ARG cc_start: 0.8914 (ttp-110) cc_final: 0.8628 (ttp-110) REVERT: C 371 LYS cc_start: 0.9058 (ttmm) cc_final: 0.8547 (tppt) REVERT: C 410 ILE cc_start: 0.8895 (mt) cc_final: 0.8678 (mt) REVERT: C 423 GLN cc_start: 0.8109 (tp40) cc_final: 0.7810 (tp40) outliers start: 23 outliers final: 15 residues processed: 200 average time/residue: 0.1265 time to fit residues: 36.9092 Evaluate side-chains 199 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 125 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 138 optimal weight: 0.0770 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN B 132 ASN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.088253 restraints weight = 39673.997| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.31 r_work: 0.2909 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14110 Z= 0.197 Angle : 0.583 12.308 19170 Z= 0.292 Chirality : 0.042 0.169 2135 Planarity : 0.004 0.056 2401 Dihedral : 8.525 75.051 2033 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.40 % Allowed : 11.68 % Favored : 86.92 % 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 (0.21), residues: 1653 helix: 1.39 (0.20), residues: 736 sheet: -1.12 (0.36), residues: 173 loop : -1.04 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 687 TYR 0.038 0.002 TYR C 179 PHE 0.018 0.002 PHE C 440 TRP 0.012 0.001 TRP A 336 HIS 0.007 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00470 (14110) covalent geometry : angle 0.58261 (19170) hydrogen bonds : bond 0.03703 ( 578) hydrogen bonds : angle 4.40822 ( 1612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8930 (tp30) cc_final: 0.8504 (tp30) REVERT: A 365 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8399 (m-30) REVERT: A 451 MET cc_start: 0.9166 (mtt) cc_final: 0.8953 (mtt) REVERT: B 140 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8278 (tm-30) REVERT: B 499 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 503 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8366 (mpp) REVERT: B 704 ARG cc_start: 0.8881 (ttp-110) cc_final: 0.8591 (ttp-110) REVERT: C 410 ILE cc_start: 0.8895 (mt) cc_final: 0.8687 (mt) outliers start: 21 outliers final: 13 residues processed: 194 average time/residue: 0.1328 time to fit residues: 37.4689 Evaluate side-chains 189 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.092461 restraints weight = 51283.952| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.57 r_work: 0.2931 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14110 Z= 0.127 Angle : 0.563 10.230 19170 Z= 0.281 Chirality : 0.041 0.162 2135 Planarity : 0.004 0.057 2401 Dihedral : 8.442 75.570 2033 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.47 % Allowed : 12.28 % Favored : 86.25 % 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: 0.12 (0.21), residues: 1653 helix: 1.43 (0.20), residues: 736 sheet: -1.02 (0.36), residues: 182 loop : -1.02 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 687 TYR 0.032 0.001 TYR C 179 PHE 0.019 0.001 PHE C 41 TRP 0.012 0.001 TRP A 336 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00296 (14110) covalent geometry : angle 0.56295 (19170) hydrogen bonds : bond 0.03403 ( 578) hydrogen bonds : angle 4.30708 ( 1612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8908 (tp30) cc_final: 0.8488 (tp30) REVERT: A 451 MET cc_start: 0.9133 (mtt) cc_final: 0.8882 (mtt) REVERT: B 140 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 499 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8085 (p) REVERT: B 503 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8611 (mpp) REVERT: B 551 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8645 (pm20) REVERT: B 704 ARG cc_start: 0.8860 (ttp-110) cc_final: 0.8585 (ttp-110) REVERT: C 410 ILE cc_start: 0.8931 (mt) cc_final: 0.8715 (mt) outliers start: 22 outliers final: 15 residues processed: 197 average time/residue: 0.1318 time to fit residues: 37.8555 Evaluate side-chains 192 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 101 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.091931 restraints weight = 37319.447| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.07 r_work: 0.2950 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14110 Z= 0.155 Angle : 0.584 14.552 19170 Z= 0.291 Chirality : 0.042 0.195 2135 Planarity : 0.004 0.057 2401 Dihedral : 8.455 75.402 2033 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.13 % Allowed : 12.55 % Favored : 86.32 % 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: 0.09 (0.21), residues: 1653 helix: 1.42 (0.20), residues: 736 sheet: -1.09 (0.35), residues: 173 loop : -1.02 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 687 TYR 0.018 0.001 TYR C 363 PHE 0.019 0.001 PHE B 290 TRP 0.012 0.001 TRP A 336 HIS 0.006 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00366 (14110) covalent geometry : angle 0.58398 (19170) hydrogen bonds : bond 0.03468 ( 578) hydrogen bonds : angle 4.30828 ( 1612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8483 (t0) cc_final: 0.8173 (t0) REVERT: A 163 GLU cc_start: 0.8894 (tp30) cc_final: 0.8497 (tp30) REVERT: A 451 MET cc_start: 0.9133 (mtt) cc_final: 0.8888 (mtt) REVERT: B 140 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8236 (tm-30) REVERT: B 499 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7731 (m) REVERT: B 503 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8239 (mpp) REVERT: B 551 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8642 (pm20) REVERT: C 410 ILE cc_start: 0.8935 (mt) cc_final: 0.8729 (mt) REVERT: C 472 GLU cc_start: 0.8428 (pp20) cc_final: 0.8158 (pp20) outliers start: 17 outliers final: 13 residues processed: 189 average time/residue: 0.1360 time to fit residues: 37.4125 Evaluate side-chains 188 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.087451 restraints weight = 62075.758| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.35 r_work: 0.2845 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14110 Z= 0.205 Angle : 0.612 12.308 19170 Z= 0.308 Chirality : 0.043 0.174 2135 Planarity : 0.005 0.057 2401 Dihedral : 8.579 75.216 2033 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.07 % Allowed : 12.68 % Favored : 86.25 % 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 (0.21), residues: 1653 helix: 1.33 (0.20), residues: 736 sheet: -1.14 (0.35), residues: 173 loop : -1.07 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 704 TYR 0.021 0.001 TYR C 412 PHE 0.020 0.002 PHE C 440 TRP 0.013 0.001 TRP A 336 HIS 0.014 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00488 (14110) covalent geometry : angle 0.61202 (19170) hydrogen bonds : bond 0.03759 ( 578) hydrogen bonds : angle 4.42524 ( 1612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 163 GLU cc_start: 0.9025 (tp30) cc_final: 0.8638 (tp30) REVERT: A 341 MET cc_start: 0.9131 (mmm) cc_final: 0.8814 (mmm) REVERT: A 451 MET cc_start: 0.9177 (mtt) cc_final: 0.8973 (mtt) REVERT: B 140 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8363 (tm-30) REVERT: B 499 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8086 (p) REVERT: B 503 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8468 (mpp) REVERT: B 551 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8618 (pm20) REVERT: C 410 ILE cc_start: 0.8861 (mt) cc_final: 0.8660 (mt) REVERT: C 472 GLU cc_start: 0.8527 (pp20) cc_final: 0.8248 (pp20) outliers start: 16 outliers final: 12 residues processed: 182 average time/residue: 0.1385 time to fit residues: 36.4146 Evaluate side-chains 182 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.7006 > 50: distance: 19 - 131: 12.714 distance: 22 - 128: 27.158 distance: 48 - 70: 33.478 distance: 66 - 70: 33.124 distance: 71 - 72: 45.903 distance: 72 - 73: 18.080 distance: 72 - 79: 23.313 distance: 76 - 77: 32.217 distance: 76 - 78: 40.167 distance: 79 - 80: 9.307 distance: 80 - 81: 8.271 distance: 80 - 83: 9.562 distance: 81 - 82: 45.022 distance: 81 - 90: 21.099 distance: 85 - 86: 33.781 distance: 86 - 87: 30.092 distance: 87 - 88: 31.249 distance: 87 - 89: 7.410 distance: 90 - 91: 41.036 distance: 91 - 92: 39.523 distance: 92 - 93: 48.611 distance: 92 - 101: 26.358 distance: 94 - 95: 40.757 distance: 95 - 96: 38.671 distance: 96 - 97: 56.751 distance: 98 - 99: 22.254 distance: 98 - 100: 44.227 distance: 101 - 102: 34.352 distance: 102 - 103: 35.680 distance: 102 - 105: 18.696 distance: 103 - 104: 54.129 distance: 103 - 110: 5.039 distance: 105 - 106: 33.901 distance: 106 - 107: 27.408 distance: 107 - 108: 28.533 distance: 107 - 109: 40.708 distance: 110 - 111: 22.769 distance: 111 - 112: 23.105 distance: 111 - 114: 24.647 distance: 112 - 113: 46.440 distance: 112 - 117: 17.440 distance: 114 - 115: 41.027 distance: 117 - 118: 38.939 distance: 117 - 217: 34.425 distance: 118 - 119: 17.265 distance: 118 - 121: 40.495 distance: 119 - 120: 34.076 distance: 119 - 128: 26.095 distance: 120 - 214: 36.302 distance: 122 - 123: 40.328 distance: 122 - 124: 29.047 distance: 124 - 126: 56.510 distance: 125 - 127: 40.698 distance: 126 - 127: 19.699 distance: 129 - 130: 59.069 distance: 129 - 132: 24.657 distance: 130 - 131: 40.907 distance: 130 - 136: 22.602 distance: 132 - 133: 41.221 distance: 133 - 135: 56.427 distance: 136 - 137: 45.898 distance: 136 - 142: 10.059 distance: 137 - 138: 34.321 distance: 138 - 139: 32.995 distance: 138 - 143: 45.770 distance: 140 - 141: 39.041 distance: 141 - 142: 65.274 distance: 143 - 144: 41.131 distance: 144 - 145: 24.692 distance: 144 - 147: 20.740 distance: 145 - 146: 12.807 distance: 145 - 154: 23.849 distance: 147 - 148: 4.256 distance: 148 - 149: 50.059 distance: 148 - 150: 29.109 distance: 149 - 151: 25.945 distance: 150 - 152: 40.452 distance: 151 - 153: 41.915 distance: 152 - 153: 50.374 distance: 154 - 155: 37.361 distance: 155 - 156: 23.022 distance: 156 - 157: 15.544 distance: 156 - 158: 28.653