Starting phenix.real_space_refine on Sun Jun 8 21:11:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlc_22239/06_2025/6xlc_22239.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlc_22239/06_2025/6xlc_22239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xlc_22239/06_2025/6xlc_22239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlc_22239/06_2025/6xlc_22239.map" model { file = "/net/cci-nas-00/data/ceres_data/6xlc_22239/06_2025/6xlc_22239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlc_22239/06_2025/6xlc_22239.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 18 5.16 5 C 6286 2.51 5 N 1620 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9858 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "B" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.24, per 1000 atoms: 0.63 Number of scatterers: 9858 At special positions: 0 Unit cell: (98.487, 92.133, 131.316, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 6 15.00 Mg 2 11.99 O 1926 8.00 N 1620 7.00 C 6286 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: 2.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2324 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 10 sheets defined 43.8% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 4.074A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 52 removed outlier: 4.311A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 123 through 129 removed outlier: 3.566A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.762A pdb=" N TYR A 184 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 197 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 384 through 405 removed outlier: 3.938A pdb=" N ILE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 415 removed outlier: 3.547A pdb=" N PHE A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.502A pdb=" N ILE A 421 " --> pdb=" O PHE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.834A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 removed outlier: 3.650A pdb=" N ARG A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.594A pdb=" N VAL A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 490 removed outlier: 3.833A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.521A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.892A pdb=" N GLU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 555 Processing helix chain 'A' and resid 582 through 592 removed outlier: 3.634A pdb=" N GLU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.712A pdb=" N LYS A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 627 " --> pdb=" O LYS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.816A pdb=" N LYS A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 638 " --> pdb=" O THR A 634 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 removed outlier: 3.827A pdb=" N PHE A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.447A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 52 removed outlier: 4.376A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.521A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 128 " --> pdb=" O TYR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.664A pdb=" N TYR B 184 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 198 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 383 through 405 removed outlier: 3.625A pdb=" N VAL B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 437 removed outlier: 3.790A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 459 removed outlier: 3.603A pdb=" N THR B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.536A pdb=" N VAL B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 490 removed outlier: 3.519A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.553A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 Processing helix chain 'B' and resid 543 through 555 Processing helix chain 'B' and resid 582 through 590 removed outlier: 3.823A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 627 removed outlier: 3.573A pdb=" N LYS B 623 " --> pdb=" O LYS B 619 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 651 removed outlier: 3.630A pdb=" N LYS B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 638 " --> pdb=" O THR B 634 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 removed outlier: 3.967A pdb=" N PHE B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.548A pdb=" N GLU A 4 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 133 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG B 174 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE B 64 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU B 208 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE B 66 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 6.475A pdb=" N GLN A 9 " --> pdb=" O ILE B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 265 removed outlier: 6.058A pdb=" N ILE A 64 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU A 208 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE A 66 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 67 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 76 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 133 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 4 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 307 removed outlier: 3.512A pdb=" N TYR A 301 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR A 347 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 341 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N PHE A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 442 through 443 removed outlier: 4.048A pdb=" N ASN A 442 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N LEU A 495 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR A 468 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU A 497 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 470 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE A 467 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 563 removed outlier: 3.524A pdb=" N ILE A 611 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 307 removed outlier: 3.515A pdb=" N VAL B 364 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU B 339 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 442 through 443 removed outlier: 3.885A pdb=" N ASN B 442 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N LEU B 495 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR B 468 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU B 497 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 470 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE B 467 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 561 through 563 removed outlier: 3.526A pdb=" N ILE B 611 " --> pdb=" O VAL B 562 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1170 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: 3.88 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3212 1.34 - 1.46: 1542 1.46 - 1.57: 5220 1.57 - 1.69: 10 1.69 - 1.80: 38 Bond restraints: 10022 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O5' ANP B 801 " pdb=" PA ANP B 801 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 10017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 13486 3.46 - 6.93: 30 6.93 - 10.39: 7 10.39 - 13.86: 1 13.86 - 17.32: 2 Bond angle restraints: 13526 Sorted by residual: angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.63 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.73 17.22 3.00e+00 1.11e-01 3.30e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.60 10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.69 10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" N ILE A 20 " pdb=" CA ILE A 20 " pdb=" C ILE A 20 " ideal model delta sigma weight residual 113.71 110.65 3.06 9.50e-01 1.11e+00 1.04e+01 ... (remaining 13521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 5759 17.80 - 35.60: 330 35.60 - 53.39: 67 53.39 - 71.19: 21 71.19 - 88.99: 15 Dihedral angle restraints: 6192 sinusoidal: 2628 harmonic: 3564 Sorted by residual: dihedral pdb=" CB GLU B 76 " pdb=" CG GLU B 76 " pdb=" CD GLU B 76 " pdb=" OE1 GLU B 76 " ideal model delta sinusoidal sigma weight residual 0.00 -88.99 88.99 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 513 " pdb=" CG GLU B 513 " pdb=" CD GLU B 513 " pdb=" OE1 GLU B 513 " ideal model delta sinusoidal sigma weight residual 0.00 88.90 -88.90 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" O1B ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PB ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sinusoidal sigma weight residual 35.15 -53.13 88.28 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1325 0.055 - 0.109: 188 0.109 - 0.164: 19 0.164 - 0.218: 0 0.218 - 0.273: 2 Chirality restraints: 1534 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1531 not shown) Planarity restraints: 1724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO A 355 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 20 " -0.005 2.00e-02 2.50e+03 9.43e-03 8.90e-01 pdb=" C ILE A 20 " 0.016 2.00e-02 2.50e+03 pdb=" O ILE A 20 " -0.006 2.00e-02 2.50e+03 pdb=" N ASN A 21 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 543 " 0.005 2.00e-02 2.50e+03 6.32e-03 8.00e-01 pdb=" CG TYR B 543 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 543 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 543 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 543 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 543 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 543 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 543 " -0.000 2.00e-02 2.50e+03 ... (remaining 1721 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 128 2.64 - 3.21: 8674 3.21 - 3.77: 15184 3.77 - 4.34: 21623 4.34 - 4.90: 34910 Nonbonded interactions: 80519 Sorted by model distance: nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.079 2.170 nonbonded pdb=" O1B ANP A 801 " pdb="MG MG A 802 " model vdw 2.089 2.170 nonbonded pdb=" O1A ANP B 801 " pdb="MG MG B 802 " model vdw 2.249 2.170 nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.250 2.170 nonbonded pdb=" OH TYR B 456 " pdb=" O GLU B 493 " model vdw 2.255 3.040 ... (remaining 80514 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.510 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 10022 Z= 0.176 Angle : 0.523 17.324 13526 Z= 0.249 Chirality : 0.039 0.273 1534 Planarity : 0.002 0.029 1724 Dihedral : 12.917 88.987 3868 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.20), residues: 1196 helix: -1.88 (0.19), residues: 492 sheet: -0.99 (0.34), residues: 218 loop : -1.87 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 273 HIS 0.001 0.000 HIS A 197 PHE 0.006 0.001 PHE A 652 TYR 0.016 0.001 TYR B 543 ARG 0.001 0.000 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.22192 ( 417) hydrogen bonds : angle 7.79497 ( 1170) covalent geometry : bond 0.00349 (10022) covalent geometry : angle 0.52260 (13526) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6542 (mm-30) REVERT: A 610 GLU cc_start: 0.7411 (mp0) cc_final: 0.7104 (mp0) REVERT: A 614 LYS cc_start: 0.6948 (pttm) cc_final: 0.6537 (ptmm) REVERT: B 379 LEU cc_start: 0.5857 (pt) cc_final: 0.5552 (pp) REVERT: B 386 LYS cc_start: 0.6026 (mmtm) cc_final: 0.5820 (tptp) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.3277 time to fit residues: 115.8873 Evaluate side-chains 146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN A 466 ASN A 673 ASN B 304 HIS B 380 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.131379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.115859 restraints weight = 20755.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.119028 restraints weight = 12347.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.121169 restraints weight = 8480.666| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 10022 Z= 0.238 Angle : 0.726 9.040 13526 Z= 0.375 Chirality : 0.048 0.187 1534 Planarity : 0.005 0.049 1724 Dihedral : 6.760 81.223 1358 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.86 % Allowed : 12.64 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.22), residues: 1196 helix: -0.71 (0.22), residues: 490 sheet: -0.79 (0.35), residues: 208 loop : -1.51 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 357 HIS 0.005 0.001 HIS A 426 PHE 0.021 0.003 PHE B 652 TYR 0.025 0.002 TYR B 125 ARG 0.010 0.001 ARG A 174 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 417) hydrogen bonds : angle 5.35992 ( 1170) covalent geometry : bond 0.00563 (10022) covalent geometry : angle 0.72622 (13526) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 205 ILE cc_start: 0.7588 (mm) cc_final: 0.7279 (mt) REVERT: A 314 ARG cc_start: 0.7711 (mpt-90) cc_final: 0.7412 (mmt-90) REVERT: A 589 MET cc_start: 0.7632 (mmt) cc_final: 0.7428 (mmt) REVERT: B 205 ILE cc_start: 0.7489 (mm) cc_final: 0.7116 (mt) REVERT: B 386 LYS cc_start: 0.7302 (mmtm) cc_final: 0.6886 (tptp) REVERT: B 589 MET cc_start: 0.7355 (mmt) cc_final: 0.7065 (mmt) outliers start: 31 outliers final: 17 residues processed: 158 average time/residue: 0.2401 time to fit residues: 52.6357 Evaluate side-chains 114 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 611 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 105 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 35 optimal weight: 0.0770 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 466 ASN B 426 HIS B 431 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.133256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.118495 restraints weight = 20723.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.121579 restraints weight = 12484.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123643 restraints weight = 8556.309| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10022 Z= 0.104 Angle : 0.515 8.041 13526 Z= 0.263 Chirality : 0.041 0.169 1534 Planarity : 0.003 0.039 1724 Dihedral : 6.225 79.331 1358 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.29 % Allowed : 16.42 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.24), residues: 1196 helix: 0.15 (0.24), residues: 490 sheet: -0.85 (0.34), residues: 216 loop : -1.16 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.003 0.000 HIS B 426 PHE 0.023 0.001 PHE A 579 TYR 0.009 0.001 TYR A 125 ARG 0.005 0.000 ARG A 174 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 417) hydrogen bonds : angle 4.78422 ( 1170) covalent geometry : bond 0.00241 (10022) covalent geometry : angle 0.51487 (13526) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7125 (mm-30) REVERT: A 205 ILE cc_start: 0.7483 (mm) cc_final: 0.7115 (mt) REVERT: A 610 GLU cc_start: 0.7975 (mp0) cc_final: 0.7737 (mt-10) REVERT: B 105 MET cc_start: 0.7964 (mmm) cc_final: 0.7731 (mmm) REVERT: B 116 MET cc_start: 0.7288 (mpp) cc_final: 0.6816 (mtt) REVERT: B 205 ILE cc_start: 0.7370 (mm) cc_final: 0.6866 (mt) REVERT: B 386 LYS cc_start: 0.7278 (mmtm) cc_final: 0.6806 (tptp) REVERT: B 589 MET cc_start: 0.7197 (mmt) cc_final: 0.6965 (mmt) REVERT: B 614 LYS cc_start: 0.7817 (mmtm) cc_final: 0.7022 (tmtt) outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 0.2128 time to fit residues: 37.3339 Evaluate side-chains 96 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 642 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 21 optimal weight: 0.0770 chunk 68 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 43 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.131521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.116365 restraints weight = 20447.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.119429 restraints weight = 12168.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.121510 restraints weight = 8318.533| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10022 Z= 0.105 Angle : 0.500 7.898 13526 Z= 0.254 Chirality : 0.041 0.168 1534 Planarity : 0.003 0.039 1724 Dihedral : 6.139 79.088 1358 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.29 % Allowed : 16.79 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1196 helix: 0.53 (0.25), residues: 486 sheet: -0.75 (0.35), residues: 216 loop : -0.99 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 148 HIS 0.001 0.000 HIS A 426 PHE 0.016 0.001 PHE A 579 TYR 0.010 0.001 TYR B 289 ARG 0.004 0.000 ARG A 174 Details of bonding type rmsd hydrogen bonds : bond 0.02881 ( 417) hydrogen bonds : angle 4.61589 ( 1170) covalent geometry : bond 0.00250 (10022) covalent geometry : angle 0.49989 (13526) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 16 MET cc_start: 0.8599 (tpt) cc_final: 0.8364 (tpt) REVERT: A 144 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7285 (mm-30) REVERT: A 205 ILE cc_start: 0.7484 (mm) cc_final: 0.7143 (mt) REVERT: A 589 MET cc_start: 0.7722 (mmt) cc_final: 0.7471 (mmt) REVERT: B 105 MET cc_start: 0.8133 (mmm) cc_final: 0.7877 (mmm) REVERT: B 116 MET cc_start: 0.7091 (mpp) cc_final: 0.6786 (mtt) REVERT: B 205 ILE cc_start: 0.7511 (mm) cc_final: 0.7247 (mt) REVERT: B 386 LYS cc_start: 0.7344 (mmtm) cc_final: 0.6868 (tptp) REVERT: B 547 THR cc_start: 0.7091 (p) cc_final: 0.6779 (p) REVERT: B 614 LYS cc_start: 0.7792 (mmtm) cc_final: 0.7105 (tmtt) outliers start: 14 outliers final: 8 residues processed: 119 average time/residue: 0.2222 time to fit residues: 38.7464 Evaluate side-chains 97 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 474 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.5732 > 50: distance: 19 - 205: 14.912 distance: 150 - 153: 35.549 distance: 153 - 154: 23.376 distance: 154 - 155: 38.148 distance: 154 - 157: 42.026 distance: 155 - 156: 29.736 distance: 155 - 162: 39.870 distance: 157 - 158: 56.425 distance: 158 - 159: 29.949 distance: 159 - 160: 13.594 distance: 160 - 161: 13.605 distance: 162 - 163: 22.577 distance: 163 - 164: 40.445 distance: 163 - 166: 24.886 distance: 164 - 165: 46.196 distance: 164 - 170: 20.681 distance: 166 - 167: 43.085 distance: 167 - 168: 42.008 distance: 167 - 169: 40.979 distance: 170 - 171: 39.524 distance: 171 - 172: 9.849 distance: 171 - 174: 17.202 distance: 172 - 173: 24.026 distance: 172 - 181: 45.710 distance: 174 - 175: 38.135 distance: 175 - 176: 11.561 distance: 175 - 177: 21.530 distance: 176 - 178: 27.512 distance: 177 - 179: 33.046 distance: 178 - 180: 8.852 distance: 179 - 180: 13.504 distance: 181 - 182: 25.865 distance: 182 - 183: 32.765 distance: 182 - 185: 41.967 distance: 183 - 184: 32.488 distance: 183 - 190: 43.229 distance: 185 - 186: 56.980 distance: 186 - 187: 42.133 distance: 187 - 188: 40.080 distance: 187 - 189: 30.812 distance: 190 - 191: 43.647 distance: 191 - 192: 18.384 distance: 191 - 194: 31.789 distance: 192 - 193: 45.370 distance: 192 - 197: 47.162 distance: 194 - 195: 19.550 distance: 194 - 196: 3.684 distance: 197 - 198: 15.459 distance: 198 - 199: 40.476 distance: 198 - 201: 20.178 distance: 199 - 200: 29.534 distance: 199 - 205: 42.378 distance: 201 - 202: 19.517 distance: 202 - 203: 17.922 distance: 202 - 204: 16.113 distance: 205 - 206: 13.993 distance: 206 - 207: 19.351 distance: 206 - 209: 31.489 distance: 207 - 208: 21.255 distance: 207 - 216: 44.206 distance: 209 - 210: 29.552 distance: 210 - 211: 10.403 distance: 210 - 212: 15.885 distance: 211 - 213: 28.362 distance: 212 - 214: 29.136 distance: 213 - 215: 6.526 distance: 214 - 215: 6.663 distance: 216 - 217: 7.275 distance: 217 - 218: 9.430 distance: 217 - 220: 45.163 distance: 218 - 224: 61.255 distance: 220 - 221: 43.255 distance: 221 - 222: 36.848 distance: 221 - 223: 35.405 distance: 224 - 225: 22.384 distance: 225 - 226: 25.893 distance: 225 - 228: 45.768 distance: 226 - 227: 53.220 distance: 226 - 231: 18.238 distance: 228 - 229: 34.483 distance: 228 - 230: 30.590 distance: 231 - 232: 41.654 distance: 232 - 233: 51.253 distance: 232 - 235: 50.954 distance: 233 - 234: 40.723 distance: 233 - 239: 34.222 distance: 235 - 236: 48.588 distance: 236 - 237: 53.259 distance: 236 - 238: 57.196