Starting phenix.real_space_refine on Sat Aug 23 00:35:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wiv_32537/08_2025/7wiv_32537.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wiv_32537/08_2025/7wiv_32537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wiv_32537/08_2025/7wiv_32537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wiv_32537/08_2025/7wiv_32537.map" model { file = "/net/cci-nas-00/data/ceres_data/7wiv_32537/08_2025/7wiv_32537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wiv_32537/08_2025/7wiv_32537.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 5511 2.51 5 N 1553 2.21 5 O 1565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8646 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4344 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 25, 'TRANS': 545} Chain: "B" Number of atoms: 4271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4271 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 25, 'TRANS': 550} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.29 Number of scatterers: 8646 At special positions: 0 Unit cell: (71.34, 95.94, 132.84, 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 14 16.00 P 3 15.00 O 1565 8.00 N 1553 7.00 C 5511 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: 1.01 Conformation dependent library (CDL) restraints added in 323.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 7 sheets defined 63.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 309 through 323 removed outlier: 3.559A pdb=" N VAL A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 375 removed outlier: 3.756A pdb=" N GLY A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 385 removed outlier: 4.136A pdb=" N PHE A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.627A pdb=" N LYS A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 407 removed outlier: 3.564A pdb=" N LEU A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 430 removed outlier: 3.720A pdb=" N VAL A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.837A pdb=" N VAL A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.512A pdb=" N TYR A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 479 removed outlier: 4.076A pdb=" N GLN A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 490 through 509 removed outlier: 3.665A pdb=" N ASP A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 513 removed outlier: 4.139A pdb=" N GLY A 513 " --> pdb=" O PRO A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 523 through 541 removed outlier: 3.510A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 548 Processing helix chain 'A' and resid 549 through 556 Processing helix chain 'A' and resid 558 through 571 removed outlier: 3.606A pdb=" N ARG A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 587 removed outlier: 4.104A pdb=" N ALA A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 586 " --> pdb=" O HIS A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.623A pdb=" N TYR A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.632A pdb=" N ILE A 704 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 734 through 737 removed outlier: 4.042A pdb=" N ASP A 737 " --> pdb=" O ASP A 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 734 through 737' Processing helix chain 'A' and resid 751 through 763 removed outlier: 3.672A pdb=" N THR A 755 " --> pdb=" O ARG A 751 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'A' and resid 778 through 781 removed outlier: 3.672A pdb=" N GLU A 781 " --> pdb=" O PRO A 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 778 through 781' Processing helix chain 'A' and resid 782 through 792 removed outlier: 3.710A pdb=" N ARG A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'B' and resid 17 through 25 removed outlier: 3.816A pdb=" N ALA B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.773A pdb=" N ARG B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 46 removed outlier: 3.821A pdb=" N LEU B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 54 through 97 removed outlier: 3.505A pdb=" N VAL B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 92 " --> pdb=" O HIS B 88 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 94 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.642A pdb=" N ALA B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.571A pdb=" N VAL B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.543A pdb=" N LEU B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) Proline residue: B 142 - end of helix removed outlier: 3.889A pdb=" N LEU B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 162 through 193 removed outlier: 4.057A pdb=" N LEU B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'B' and resid 202 through 208 removed outlier: 3.610A pdb=" N LEU B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 3.647A pdb=" N ALA B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 265 removed outlier: 3.991A pdb=" N LEU B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 5.916A pdb=" N PHE B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N SER B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 253 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.525A pdb=" N THR B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 312 removed outlier: 3.748A pdb=" N ARG B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 422 through 428 Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.842A pdb=" N VAL B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 457 through 461 removed outlier: 3.648A pdb=" N ASN B 460 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 503 through 514 Processing helix chain 'B' and resid 554 through 558 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.867A pdb=" N PHE B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 610 through 613 removed outlier: 3.811A pdb=" N GLN A 672 " --> pdb=" O VAL A 669 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 615 through 617 removed outlier: 5.112A pdb=" N VAL A 615 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 687 through 689 removed outlier: 6.527A pdb=" N THR A 639 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU A 823 " --> pdb=" O VAL A 815 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 698 through 699 removed outlier: 3.689A pdb=" N GLY A 698 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 355 through 356 Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 339 removed outlier: 7.359A pdb=" N PHE B 339 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP B 350 " --> pdb=" O PHE B 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 412 removed outlier: 6.397A pdb=" N LEU B 491 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL B 524 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 493 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR B 362 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR B 361 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU B 538 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA B 363 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL B 540 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 365 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 547 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP B 541 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL B 545 " --> pdb=" O ASP B 541 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1405 1.27 - 1.41: 2094 1.41 - 1.54: 5206 1.54 - 1.67: 81 1.67 - 1.80: 25 Bond restraints: 8811 Sorted by residual: bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C LYS B 486 " pdb=" O LYS B 486 " ideal model delta sigma weight residual 1.235 1.141 0.093 1.26e-02 6.30e+03 5.48e+01 bond pdb=" C VAL B 270 " pdb=" O VAL B 270 " ideal model delta sigma weight residual 1.240 1.171 0.068 1.26e-02 6.30e+03 2.95e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C THR B 269 " pdb=" O THR B 269 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.32e-02 5.74e+03 2.71e+01 ... (remaining 8806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 11889 3.58 - 7.16: 139 7.16 - 10.75: 11 10.75 - 14.33: 3 14.33 - 17.91: 1 Bond angle restraints: 12043 Sorted by residual: angle pdb=" N GLY B 388 " pdb=" CA GLY B 388 " pdb=" C GLY B 388 " ideal model delta sigma weight residual 110.21 119.62 -9.41 9.10e-01 1.21e+00 1.07e+02 angle pdb=" C THR B 267 " pdb=" CA THR B 267 " pdb=" CB THR B 267 " ideal model delta sigma weight residual 110.96 123.88 -12.92 1.54e+00 4.22e-01 7.04e+01 angle pdb=" N ALA B 442 " pdb=" CA ALA B 442 " pdb=" C ALA B 442 " ideal model delta sigma weight residual 114.64 102.34 12.30 1.52e+00 4.33e-01 6.55e+01 angle pdb=" N ILE B 531 " pdb=" CA ILE B 531 " pdb=" C ILE B 531 " ideal model delta sigma weight residual 113.71 106.97 6.74 9.50e-01 1.11e+00 5.03e+01 angle pdb=" N GLN A 454 " pdb=" CA GLN A 454 " pdb=" C GLN A 454 " ideal model delta sigma weight residual 114.16 104.32 9.84 1.48e+00 4.57e-01 4.42e+01 ... (remaining 12038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4716 17.31 - 34.62: 414 34.62 - 51.93: 71 51.93 - 69.25: 19 69.25 - 86.56: 13 Dihedral angle restraints: 5233 sinusoidal: 1972 harmonic: 3261 Sorted by residual: dihedral pdb=" C THR B 267 " pdb=" N THR B 267 " pdb=" CA THR B 267 " pdb=" CB THR B 267 " ideal model delta harmonic sigma weight residual -122.00 -139.89 17.89 0 2.50e+00 1.60e-01 5.12e+01 dihedral pdb=" CA ARG B 389 " pdb=" C ARG B 389 " pdb=" N VAL B 390 " pdb=" CA VAL B 390 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA SER B 368 " pdb=" C SER B 368 " pdb=" N GLY B 369 " pdb=" CA GLY B 369 " ideal model delta harmonic sigma weight residual 180.00 152.37 27.63 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 5230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 1422 0.115 - 0.229: 37 0.229 - 0.344: 5 0.344 - 0.459: 1 0.459 - 0.573: 1 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CA THR B 267 " pdb=" N THR B 267 " pdb=" C THR B 267 " pdb=" CB THR B 267 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" CA LEU B 268 " pdb=" N LEU B 268 " pdb=" C LEU B 268 " pdb=" CB LEU B 268 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA LYS B 486 " pdb=" N LYS B 486 " pdb=" C LYS B 486 " pdb=" CB LYS B 486 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1463 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 836 " -0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ARG A 836 " 0.075 2.00e-02 2.50e+03 pdb=" O ARG A 836 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR A 837 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 342 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C ASP B 342 " -0.066 2.00e-02 2.50e+03 pdb=" O ASP B 342 " 0.025 2.00e-02 2.50e+03 pdb=" N GLY B 343 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 545 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO A 546 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 546 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 546 " 0.039 5.00e-02 4.00e+02 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1210 2.75 - 3.29: 8558 3.29 - 3.82: 13573 3.82 - 4.36: 17386 4.36 - 4.90: 29541 Nonbonded interactions: 70268 Sorted by model distance: nonbonded pdb=" NH2 ARG A 364 " pdb=" OG1 THR B 228 " model vdw 2.209 3.120 nonbonded pdb=" OG SER B 27 " pdb=" OD1 ASP B 71 " model vdw 2.220 3.040 nonbonded pdb=" N3B ANP A 901 " pdb=" O2A ANP A 901 " model vdw 2.251 3.120 nonbonded pdb=" OD1 ASN B 221 " pdb=" N ALA B 222 " model vdw 2.273 3.120 nonbonded pdb=" O LEU B 70 " pdb=" OG1 THR B 74 " model vdw 2.285 3.040 ... (remaining 70263 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.550 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: 0.010 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.008 0.150 8811 Z= 0.403 Angle : 1.023 17.912 12043 Z= 0.626 Chirality : 0.056 0.573 1466 Planarity : 0.005 0.072 1537 Dihedral : 14.501 86.558 3131 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.36 % Favored : 90.20 % Rotamer: Outliers : 0.68 % Allowed : 5.34 % Favored : 93.98 % Cbeta Deviations : 0.38 % 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: -5.21 (0.19), residues: 1143 helix: -3.11 (0.15), residues: 698 sheet: -3.96 (0.47), residues: 60 loop : -3.68 (0.26), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 824 TYR 0.013 0.002 TYR A 837 PHE 0.016 0.002 PHE B 244 TRP 0.015 0.002 TRP B 154 HIS 0.008 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00828 ( 8811) covalent geometry : angle 1.02348 (12043) hydrogen bonds : bond 0.25094 ( 452) hydrogen bonds : angle 8.60265 ( 1305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.318 Fit side-chains REVERT: A 359 ASP cc_start: 0.8596 (t70) cc_final: 0.8379 (OUTLIER) REVERT: A 392 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8476 (tmmt) REVERT: A 436 VAL cc_start: 0.9043 (t) cc_final: 0.8782 (m) REVERT: A 515 LYS cc_start: 0.8946 (mttt) cc_final: 0.8728 (mttp) REVERT: B 71 ASP cc_start: 0.7719 (m-30) cc_final: 0.7507 (m-30) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.7762 time to fit residues: 62.1107 Evaluate side-chains 45 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 329 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS A 463 GLN A 597 HIS A 743 ASN A 752 GLN A 802 HIS B 11 ASN B 109 ASN B 237 GLN B 241 GLN B 426 ASN B 533 HIS B 568 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.108224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.088724 restraints weight = 13815.608| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.17 r_work: 0.3017 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8811 Z= 0.139 Angle : 0.705 9.652 12043 Z= 0.363 Chirality : 0.043 0.136 1466 Planarity : 0.005 0.059 1537 Dihedral : 8.052 56.045 1281 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.14 % Favored : 91.69 % Rotamer: Outliers : 1.70 % Allowed : 9.89 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.25 (0.22), residues: 1143 helix: -1.48 (0.18), residues: 715 sheet: -3.20 (0.47), residues: 75 loop : -3.04 (0.28), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 403 TYR 0.016 0.001 TYR A 568 PHE 0.009 0.001 PHE B 244 TRP 0.015 0.001 TRP A 529 HIS 0.004 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8811) covalent geometry : angle 0.70531 (12043) hydrogen bonds : bond 0.04440 ( 452) hydrogen bonds : angle 4.79222 ( 1305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.336 Fit side-chains REVERT: A 392 LYS cc_start: 0.8840 (ttpp) cc_final: 0.8585 (tmtt) REVERT: A 515 LYS cc_start: 0.9114 (mttt) cc_final: 0.8869 (mttp) REVERT: A 517 LEU cc_start: 0.8913 (tp) cc_final: 0.8659 (mp) REVERT: B 48 GLU cc_start: 0.7913 (pm20) cc_final: 0.7695 (pm20) REVERT: B 71 ASP cc_start: 0.8681 (m-30) cc_final: 0.8405 (m-30) REVERT: B 161 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8717 (mt) REVERT: B 270 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8050 (t) REVERT: B 435 SER cc_start: 0.7226 (p) cc_final: 0.6904 (t) REVERT: B 447 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7662 (mpt-90) outliers start: 15 outliers final: 3 residues processed: 76 average time/residue: 0.5937 time to fit residues: 48.4248 Evaluate side-chains 58 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 447 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7426 > 50: distance: 32 - 193: 35.030 distance: 35 - 190: 32.914 distance: 120 - 124: 35.767 distance: 124 - 125: 40.235 distance: 125 - 126: 54.280 distance: 126 - 127: 53.432 distance: 126 - 134: 16.861 distance: 130 - 132: 36.652 distance: 131 - 133: 10.840 distance: 132 - 133: 25.051 distance: 134 - 135: 33.169 distance: 135 - 136: 13.453 distance: 135 - 138: 25.880 distance: 136 - 137: 42.481 distance: 136 - 143: 57.410 distance: 139 - 140: 56.615 distance: 140 - 142: 11.923 distance: 143 - 144: 54.656 distance: 143 - 149: 36.032 distance: 144 - 145: 39.299 distance: 144 - 147: 24.192 distance: 148 - 149: 39.653 distance: 151 - 152: 56.075 distance: 151 - 154: 56.656 distance: 154 - 155: 3.145 distance: 158 - 159: 39.995 distance: 158 - 161: 40.662 distance: 159 - 160: 19.737 distance: 159 - 168: 38.385 distance: 161 - 162: 47.368 distance: 162 - 163: 28.801 distance: 163 - 164: 16.296 distance: 165 - 166: 13.351 distance: 165 - 167: 27.951 distance: 169 - 170: 43.705 distance: 170 - 171: 44.469 distance: 170 - 172: 62.399 distance: 172 - 173: 40.326 distance: 173 - 174: 40.567 distance: 174 - 183: 41.128 distance: 177 - 178: 11.983 distance: 178 - 179: 6.662 distance: 179 - 180: 6.391 distance: 180 - 181: 41.270 distance: 180 - 182: 28.335 distance: 183 - 184: 6.089 distance: 184 - 187: 3.830 distance: 185 - 186: 33.853 distance: 187 - 188: 19.487 distance: 190 - 191: 39.776 distance: 191 - 192: 6.726 distance: 191 - 194: 55.515 distance: 192 - 193: 34.557 distance: 192 - 198: 35.829 distance: 194 - 195: 35.889 distance: 195 - 196: 40.482 distance: 195 - 197: 33.880 distance: 198 - 199: 9.965 distance: 198 - 219: 36.086 distance: 199 - 200: 7.812 distance: 199 - 202: 43.762 distance: 200 - 201: 20.131 distance: 200 - 206: 31.643 distance: 201 - 216: 27.002 distance: 202 - 204: 8.061 distance: 203 - 205: 12.151