Starting phenix.real_space_refine on Fri Jul 3 07:07:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28pr_56722/07_2026/28pr_56722.cif Found real_map, /net/cci-nas-00/data/ceres_data/28pr_56722/07_2026/28pr_56722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28pr_56722/07_2026/28pr_56722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28pr_56722/07_2026/28pr_56722.map" model { file = "/net/cci-nas-00/data/ceres_data/28pr_56722/07_2026/28pr_56722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28pr_56722/07_2026/28pr_56722.cif" } resolution = 2.4 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= 0.010 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 Ca 2 9.91 5 Fe 6 7.16 5 S 44 5.16 5 C 7623 2.51 5 N 1899 2.21 5 O 2809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12383 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5608 Classifications: {'peptide': 711} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 676} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5606 Classifications: {'peptide': 710} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 674} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Ad-hoc single atom residues: {' CA': 1, ' FE': 1} Unusual residues: {'HEM': 2, 'HQE': 1, 'LMT': 1, 'UQ5': 1} Classifications: {'undetermined': 5} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UQ5:plan-2': 1, 'UQ5:plan-5': 1, 'UQ5:plan-6': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 160 Ad-hoc single atom residues: {' CA': 1, ' FE': 1} Unusual residues: {'HEM': 2, 'HQE': 1, 'LMT': 2} Classifications: {'undetermined': 5} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 421 Classifications: {'water': 421} Link IDs: {None: 420} Chain: "B" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 431 Classifications: {'water': 431} Link IDs: {None: 430} Time building chain proxies: 3.24, per 1000 atoms: 0.26 Number of scatterers: 12383 At special positions: 0 Unit cell: (114.7, 92.5, 110.26, 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) Fe 6 26.01 Ca 2 19.99 S 44 16.00 O 2809 8.00 N 1899 7.00 C 7623 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 520.4 milliseconds 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 6 sheets defined 79.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.766A pdb=" N GLY A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.547A pdb=" N ILE A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 82 through 104 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 112 through 129 removed outlier: 3.968A pdb=" N ALA A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 Processing helix chain 'A' and resid 142 through 161 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 182 through 202 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 226 through 253 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 307 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 323 through 355 Proline residue: A 352 - end of helix removed outlier: 3.919A pdb=" N ASN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 390 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 412 through 439 removed outlier: 3.719A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 512 through 537 removed outlier: 5.176A pdb=" N ILE A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) Proline residue: A 533 - end of helix Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.622A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 560 removed outlier: 3.869A pdb=" N GLU A 559 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 556 through 560' Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.569A pdb=" N MET A 583 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 585 " --> pdb=" O TRP A 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 585' Processing helix chain 'A' and resid 586 through 603 Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.523A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 4.006A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 4.769A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 682 removed outlier: 3.639A pdb=" N SER A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 710 through 720 Processing helix chain 'A' and resid 720 through 744 Processing helix chain 'A' and resid 746 through 750 removed outlier: 3.522A pdb=" N ALA A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 32 removed outlier: 3.987A pdb=" N GLY B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 removed outlier: 3.556A pdb=" N ILE B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 112 through 129 removed outlier: 3.939A pdb=" N ALA B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 136 Processing helix chain 'B' and resid 142 through 161 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 182 through 202 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 226 through 253 Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 307 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 323 through 355 Proline residue: B 352 - end of helix removed outlier: 3.887A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 390 removed outlier: 3.713A pdb=" N GLY B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 412 through 435 removed outlier: 3.697A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.781A pdb=" N THR B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 488 Processing helix chain 'B' and resid 494 through 508 Processing helix chain 'B' and resid 512 through 537 removed outlier: 5.239A pdb=" N ILE B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) Proline residue: B 533 - end of helix Processing helix chain 'B' and resid 545 through 555 removed outlier: 3.618A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 560 removed outlier: 3.679A pdb=" N GLU B 559 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 560 " --> pdb=" O ALA B 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 556 through 560' Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 571 through 576 removed outlier: 3.656A pdb=" N ARG B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.949A pdb=" N MET B 583 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN B 585 " --> pdb=" O TRP B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 585' Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 605 through 612 Processing helix chain 'B' and resid 613 through 621 removed outlier: 4.014A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 654 removed outlier: 4.780A pdb=" N PHE B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 682 removed outlier: 3.646A pdb=" N SER B 682 " --> pdb=" O MET B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 697 Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 704 through 709 Processing helix chain 'B' and resid 710 through 720 Processing helix chain 'B' and resid 720 through 744 Processing helix chain 'B' and resid 746 through 750 removed outlier: 3.527A pdb=" N ALA B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.181A pdb=" N ARG A 47 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N SER A 42 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU A 39 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU A 141 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA A 41 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.209A pdb=" N ARG B 47 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER B 42 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU B 39 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU B 141 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 41 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 313 771 hydrogen bonds defined for protein. 2241 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: 2.09 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 4655 1.38 - 1.55: 7166 1.55 - 1.73: 0 1.73 - 1.90: 84 1.90 - 2.07: 16 Bond restraints: 11921 Sorted by residual: bond pdb=" CB THR A 196 " pdb=" CG2 THR A 196 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 bond pdb=" CB THR B 196 " pdb=" CG2 THR B 196 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.72e+00 bond pdb=" CA GLU A 261 " pdb=" CB GLU A 261 " ideal model delta sigma weight residual 1.522 1.529 -0.007 7.00e-03 2.04e+04 1.01e+00 bond pdb=" CA ARG A 720 " pdb=" C ARG A 720 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.45e-02 4.76e+03 9.32e-01 bond pdb=" N ARG A 720 " pdb=" CA ARG A 720 " ideal model delta sigma weight residual 1.458 1.470 -0.012 1.29e-02 6.01e+03 9.25e-01 ... (remaining 11916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 16094 2.25 - 4.50: 181 4.50 - 6.76: 26 6.76 - 9.01: 7 9.01 - 11.26: 3 Bond angle restraints: 16311 Sorted by residual: angle pdb=" CB MET B 477 " pdb=" CG MET B 477 " pdb=" SD MET B 477 " ideal model delta sigma weight residual 112.70 122.07 -9.37 3.00e+00 1.11e-01 9.75e+00 angle pdb=" C GLU B 407 " pdb=" N TYR B 408 " pdb=" CA TYR B 408 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.89e+00 angle pdb=" CA TRP A 338 " pdb=" CB TRP A 338 " pdb=" CG TRP A 338 " ideal model delta sigma weight residual 113.60 119.09 -5.49 1.90e+00 2.77e-01 8.36e+00 angle pdb=" CA TRP B 338 " pdb=" CB TRP B 338 " pdb=" CG TRP B 338 " ideal model delta sigma weight residual 113.60 119.08 -5.48 1.90e+00 2.77e-01 8.32e+00 angle pdb=" CB MET A 477 " pdb=" CG MET A 477 " pdb=" SD MET A 477 " ideal model delta sigma weight residual 112.70 120.95 -8.25 3.00e+00 1.11e-01 7.57e+00 ... (remaining 16306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 5988 17.62 - 35.24: 545 35.24 - 52.86: 153 52.86 - 70.48: 41 70.48 - 88.10: 24 Dihedral angle restraints: 6751 sinusoidal: 2710 harmonic: 4041 Sorted by residual: dihedral pdb=" CA VAL B 560 " pdb=" C VAL B 560 " pdb=" N VAL B 561 " pdb=" CA VAL B 561 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA GLY B 491 " pdb=" C GLY B 491 " pdb=" N PHE B 492 " pdb=" CA PHE B 492 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA GLU A 490 " pdb=" C GLU A 490 " pdb=" N GLY A 491 " pdb=" CA GLY A 491 " ideal model delta harmonic sigma weight residual -180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 6748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1020 0.028 - 0.056: 427 0.056 - 0.083: 176 0.083 - 0.111: 83 0.111 - 0.139: 22 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA VAL A 489 " pdb=" N VAL A 489 " pdb=" C VAL A 489 " pdb=" CB VAL A 489 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA PRO B 627 " pdb=" N PRO B 627 " pdb=" C PRO B 627 " pdb=" CB PRO B 627 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA THR B 546 " pdb=" N THR B 546 " pdb=" C THR B 546 " pdb=" CB THR B 546 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1725 not shown) Planarity restraints: 2017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 626 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO B 627 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 627 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 627 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 626 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 627 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 627 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 627 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 588 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO B 589 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.020 5.00e-02 4.00e+02 ... (remaining 2014 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 223 2.54 - 3.13: 9579 3.13 - 3.72: 21206 3.72 - 4.31: 30667 4.31 - 4.90: 48395 Nonbonded interactions: 110070 Sorted by model distance: nonbonded pdb="FE FE B 805 " pdb=" O HOH B1031 " model vdw 1.952 3.000 nonbonded pdb="FE FE A 804 " pdb=" O HOH A1021 " model vdw 1.960 3.000 nonbonded pdb=" NE2 HIS A 537 " pdb="FE FE A 804 " model vdw 2.126 3.080 nonbonded pdb=" NE2 HIS B 537 " pdb="FE FE B 805 " model vdw 2.145 3.080 nonbonded pdb=" OE1 GLU A 559 " pdb=" O HOH A 901 " model vdw 2.218 3.040 ... (remaining 110065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 439 or resid 465 through 750)) selection = (chain 'B' and (resid 18 through 439 or resid 465 through 750)) } 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: 0.010 Normalize map: mean=0, sd=1: 5.090 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.070 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 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 0.102 11925 Z= 0.145 Angle : 0.613 11.261 16311 Z= 0.303 Chirality : 0.040 0.139 1728 Planarity : 0.004 0.036 2017 Dihedral : 16.234 88.097 4179 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.04 % Favored : 96.74 % Rotamer: Outliers : 1.71 % Allowed : 15.36 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.23), residues: 1413 helix: 1.82 (0.17), residues: 994 sheet: 1.07 (1.17), residues: 20 loop : -0.78 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 31 TYR 0.019 0.002 TYR B 324 PHE 0.020 0.002 PHE B 635 TRP 0.023 0.002 TRP B 338 HIS 0.008 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (11921) covalent geometry : angle 0.61296 / 0.30 (16311) hydrogen bonds : bond 0.12931 / 8.61 ( 771) hydrogen bonds : angle 5.22706 / 3.81 ( 2241) Misc. bond : bond 0.06899 / 3.44 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.498 Fit side-chains REVERT: A 488 TRP cc_start: 0.6909 (m-10) cc_final: 0.6154 (m-90) REVERT: B 147 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: B 583 MET cc_start: 0.7320 (ppp) cc_final: 0.6941 (ppp) outliers start: 19 outliers final: 6 residues processed: 128 average time/residue: 0.6840 time to fit residues: 94.7200 Evaluate side-chains 94 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 568 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.068217 restraints weight = 19255.205| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.42 r_work: 0.2609 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 11925 Z= 0.142 Angle : 0.619 12.752 16311 Z= 0.290 Chirality : 0.040 0.146 1728 Planarity : 0.004 0.035 2017 Dihedral : 8.552 87.966 1775 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.26 % Favored : 96.53 % Rotamer: Outliers : 2.16 % Allowed : 16.71 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.23), residues: 1413 helix: 2.13 (0.17), residues: 1008 sheet: 0.77 (1.11), residues: 20 loop : -0.76 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 703 TYR 0.012 0.001 TYR B 324 PHE 0.013 0.001 PHE B 635 TRP 0.021 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (11921) covalent geometry : angle 0.61892 / 0.29 (16311) hydrogen bonds : bond 0.04890 / 3.24 ( 771) hydrogen bonds : angle 4.26079 / 3.11 ( 2241) Misc. bond : bond 0.10129 / 5.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 477 MET cc_start: 0.8374 (tmm) cc_final: 0.7999 (tmm) REVERT: A 488 TRP cc_start: 0.6949 (m-10) cc_final: 0.5958 (m-90) REVERT: A 494 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7279 (tm-30) REVERT: A 508 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8648 (mp) REVERT: B 147 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: B 477 MET cc_start: 0.8479 (tmm) cc_final: 0.8195 (tmm) REVERT: B 494 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7274 (tm-30) REVERT: B 583 MET cc_start: 0.7438 (ppp) cc_final: 0.6839 (ppp) outliers start: 24 outliers final: 7 residues processed: 113 average time/residue: 0.6937 time to fit residues: 84.5366 Evaluate side-chains 96 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 610 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 107 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 HIS B 213 ASN B 217 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.066336 restraints weight = 19751.199| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.42 r_work: 0.2574 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 11925 Z= 0.153 Angle : 0.599 11.880 16311 Z= 0.280 Chirality : 0.040 0.141 1728 Planarity : 0.004 0.046 2017 Dihedral : 8.330 89.209 1771 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.40 % Favored : 96.39 % Rotamer: Outliers : 1.98 % Allowed : 17.07 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.23), residues: 1413 helix: 2.21 (0.17), residues: 1010 sheet: 0.53 (1.11), residues: 20 loop : -0.69 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 267 TYR 0.012 0.001 TYR B 324 PHE 0.015 0.001 PHE B 635 TRP 0.020 0.001 TRP A 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (11921) covalent geometry : angle 0.59900 / 0.28 (16311) hydrogen bonds : bond 0.05135 / 3.40 ( 771) hydrogen bonds : angle 4.14500 / 3.02 ( 2241) Misc. bond : bond 0.12761 / 6.33 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.470 Fit side-chains REVERT: A 488 TRP cc_start: 0.7001 (m-10) cc_final: 0.5969 (m-90) REVERT: A 494 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7348 (tm-30) REVERT: A 508 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8610 (mp) REVERT: A 559 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: A 583 MET cc_start: 0.8650 (tpp) cc_final: 0.8213 (mpp) REVERT: A 610 MET cc_start: 0.8978 (mmp) cc_final: 0.7896 (ttp) REVERT: B 147 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: B 168 ARG cc_start: 0.8461 (tpt90) cc_final: 0.8251 (tpt170) REVERT: B 488 TRP cc_start: 0.6526 (m-10) cc_final: 0.5893 (m-90) REVERT: B 494 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7413 (tm-30) REVERT: B 583 MET cc_start: 0.7585 (ppp) cc_final: 0.6946 (ppp) outliers start: 22 outliers final: 14 residues processed: 109 average time/residue: 0.6203 time to fit residues: 73.8729 Evaluate side-chains 103 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 610 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 3 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.065609 restraints weight = 19688.978| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.43 r_work: 0.2565 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 11925 Z= 0.164 Angle : 0.617 12.883 16311 Z= 0.284 Chirality : 0.040 0.139 1728 Planarity : 0.004 0.036 2017 Dihedral : 8.268 89.093 1771 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.61 % Favored : 96.18 % Rotamer: Outliers : 2.34 % Allowed : 16.98 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.23), residues: 1413 helix: 2.29 (0.17), residues: 996 sheet: 0.15 (1.13), residues: 20 loop : -0.81 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 267 TYR 0.012 0.001 TYR B 324 PHE 0.016 0.001 PHE B 635 TRP 0.020 0.001 TRP B 338 HIS 0.008 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.16 (11921) covalent geometry : angle 0.61665 / 0.28 (16311) hydrogen bonds : bond 0.05138 / 3.40 ( 771) hydrogen bonds : angle 4.09831 / 2.99 ( 2241) Misc. bond : bond 0.12993 / 6.42 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.478 Fit side-chains REVERT: A 101 ARG cc_start: 0.8324 (tpt170) cc_final: 0.7934 (mpt180) REVERT: A 477 MET cc_start: 0.8396 (tmm) cc_final: 0.8036 (tmm) REVERT: A 488 TRP cc_start: 0.7055 (m-10) cc_final: 0.5988 (m-90) REVERT: A 494 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 508 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8548 (mp) REVERT: A 559 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: A 583 MET cc_start: 0.8656 (tpp) cc_final: 0.8178 (mpp) REVERT: A 610 MET cc_start: 0.9010 (mmp) cc_final: 0.7918 (ttp) REVERT: B 126 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: B 488 TRP cc_start: 0.6562 (m-10) cc_final: 0.5899 (m-90) REVERT: B 494 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7498 (tm-30) REVERT: B 583 MET cc_start: 0.7801 (ppp) cc_final: 0.7200 (ppp) outliers start: 26 outliers final: 15 residues processed: 108 average time/residue: 0.6949 time to fit residues: 81.2498 Evaluate side-chains 104 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 610 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 122 optimal weight: 0.0030 chunk 117 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.099640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.067841 restraints weight = 19762.677| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.46 r_work: 0.2620 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 11925 Z= 0.115 Angle : 0.573 12.677 16311 Z= 0.265 Chirality : 0.038 0.134 1728 Planarity : 0.004 0.042 2017 Dihedral : 7.834 89.985 1768 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.97 % Favored : 96.82 % Rotamer: Outliers : 1.89 % Allowed : 17.97 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.23), residues: 1413 helix: 2.42 (0.17), residues: 997 sheet: 0.01 (1.14), residues: 20 loop : -0.82 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 267 TYR 0.010 0.001 TYR A 156 PHE 0.011 0.001 PHE B 635 TRP 0.020 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (11921) covalent geometry : angle 0.57252 / 0.26 (16311) hydrogen bonds : bond 0.04269 / 2.81 ( 771) hydrogen bonds : angle 3.95355 / 2.88 ( 2241) Misc. bond : bond 0.06133 / 3.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.450 Fit side-chains REVERT: A 51 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8023 (ttm-80) REVERT: A 101 ARG cc_start: 0.8337 (tpt170) cc_final: 0.7903 (mpt180) REVERT: A 477 MET cc_start: 0.8378 (tmm) cc_final: 0.8017 (tmm) REVERT: A 488 TRP cc_start: 0.7031 (m-10) cc_final: 0.5978 (m-90) REVERT: A 494 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 559 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: A 583 MET cc_start: 0.8636 (tpp) cc_final: 0.8127 (mpp) REVERT: A 610 MET cc_start: 0.9032 (mmp) cc_final: 0.7936 (ttp) REVERT: B 51 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7454 (ttm-80) REVERT: B 126 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: B 477 MET cc_start: 0.8457 (tmm) cc_final: 0.8168 (tmm) REVERT: B 488 TRP cc_start: 0.6549 (m-10) cc_final: 0.5940 (m-90) REVERT: B 494 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7507 (tm-30) REVERT: B 583 MET cc_start: 0.7806 (ppp) cc_final: 0.7160 (ppp) outliers start: 21 outliers final: 6 residues processed: 110 average time/residue: 0.7107 time to fit residues: 84.7062 Evaluate side-chains 98 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 568 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 73 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.064962 restraints weight = 19674.632| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.42 r_work: 0.2556 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.207 11925 Z= 0.185 Angle : 0.630 12.605 16311 Z= 0.291 Chirality : 0.041 0.139 1728 Planarity : 0.004 0.036 2017 Dihedral : 7.958 89.353 1767 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.54 % Favored : 96.25 % Rotamer: Outliers : 2.16 % Allowed : 17.79 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.23), residues: 1413 helix: 2.33 (0.17), residues: 997 sheet: -0.14 (1.17), residues: 20 loop : -0.79 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 267 TYR 0.014 0.001 TYR B 324 PHE 0.018 0.001 PHE B 635 TRP 0.018 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.18 (11921) covalent geometry : angle 0.63028 / 0.29 (16311) hydrogen bonds : bond 0.05271 / 3.49 ( 771) hydrogen bonds : angle 4.07659 / 2.97 ( 2241) Misc. bond : bond 0.15844 / 7.79 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.419 Fit side-chains REVERT: A 51 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8076 (ttm-80) REVERT: A 101 ARG cc_start: 0.8364 (tpt170) cc_final: 0.7967 (tpt170) REVERT: A 488 TRP cc_start: 0.7050 (m-10) cc_final: 0.5968 (m-90) REVERT: A 494 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7340 (tm-30) REVERT: A 508 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8510 (mp) REVERT: A 559 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: A 583 MET cc_start: 0.8703 (tpp) cc_final: 0.8296 (mpp) REVERT: A 610 MET cc_start: 0.9034 (mmp) cc_final: 0.7961 (ttp) REVERT: B 51 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8186 (ttm-80) REVERT: B 126 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8617 (tt0) REVERT: B 488 TRP cc_start: 0.6573 (m-10) cc_final: 0.5901 (m-90) REVERT: B 494 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7471 (tm-30) REVERT: B 583 MET cc_start: 0.7885 (ppp) cc_final: 0.7224 (ppp) outliers start: 24 outliers final: 14 residues processed: 99 average time/residue: 0.6645 time to fit residues: 71.5362 Evaluate side-chains 100 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 610 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 141 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.099166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.069311 restraints weight = 20331.528| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.37 r_work: 0.2704 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 11925 Z= 0.139 Angle : 0.600 13.070 16311 Z= 0.277 Chirality : 0.039 0.178 1728 Planarity : 0.004 0.038 2017 Dihedral : 7.906 89.140 1767 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.04 % Favored : 96.74 % Rotamer: Outliers : 1.80 % Allowed : 18.15 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.23), residues: 1413 helix: 2.37 (0.17), residues: 998 sheet: -0.31 (1.19), residues: 20 loop : -0.82 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 267 TYR 0.011 0.001 TYR B 324 PHE 0.014 0.001 PHE B 635 TRP 0.020 0.001 TRP B 338 HIS 0.007 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (11921) covalent geometry : angle 0.59995 / 0.28 (16311) hydrogen bonds : bond 0.04717 / 3.11 ( 771) hydrogen bonds : angle 3.99484 / 2.91 ( 2241) Misc. bond : bond 0.10483 / 5.23 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.514 Fit side-chains REVERT: A 51 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8091 (ttm-80) REVERT: A 101 ARG cc_start: 0.8369 (tpt170) cc_final: 0.7951 (tpt170) REVERT: A 477 MET cc_start: 0.8408 (tmm) cc_final: 0.8052 (tmm) REVERT: A 488 TRP cc_start: 0.7076 (m-10) cc_final: 0.5997 (m-90) REVERT: A 494 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7353 (tm-30) REVERT: A 559 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: A 583 MET cc_start: 0.8751 (tpp) cc_final: 0.8192 (mpp) REVERT: A 610 MET cc_start: 0.9037 (mmp) cc_final: 0.7995 (ttp) REVERT: B 51 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7386 (ttm-80) REVERT: B 126 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: B 477 MET cc_start: 0.8467 (tmm) cc_final: 0.8174 (tmm) REVERT: B 494 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7422 (tm-30) REVERT: B 583 MET cc_start: 0.7865 (ppp) cc_final: 0.7240 (ppp) outliers start: 20 outliers final: 13 residues processed: 100 average time/residue: 0.7057 time to fit residues: 76.4995 Evaluate side-chains 99 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 610 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.099345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.069510 restraints weight = 20365.849| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.37 r_work: 0.2727 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 11925 Z= 0.135 Angle : 0.605 12.389 16311 Z= 0.279 Chirality : 0.039 0.213 1728 Planarity : 0.004 0.037 2017 Dihedral : 7.856 89.274 1767 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.18 % Favored : 96.60 % Rotamer: Outliers : 2.16 % Allowed : 17.79 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.23), residues: 1413 helix: 2.40 (0.17), residues: 998 sheet: -0.39 (1.19), residues: 20 loop : -0.80 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 267 TYR 0.011 0.001 TYR B 324 PHE 0.014 0.001 PHE B 635 TRP 0.019 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 (11921) covalent geometry : angle 0.60463 / 0.28 (16311) hydrogen bonds : bond 0.04619 / 3.05 ( 771) hydrogen bonds : angle 3.96917 / 2.89 ( 2241) Misc. bond : bond 0.10196 / 5.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.377 Fit side-chains REVERT: A 51 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8119 (ttm-80) REVERT: A 101 ARG cc_start: 0.8392 (tpt170) cc_final: 0.7964 (tpt170) REVERT: A 477 MET cc_start: 0.8430 (tmm) cc_final: 0.8091 (tmm) REVERT: A 488 TRP cc_start: 0.7056 (m-10) cc_final: 0.5992 (m-90) REVERT: A 494 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7325 (tm-30) REVERT: A 559 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: A 583 MET cc_start: 0.8709 (tpp) cc_final: 0.8258 (mpp) REVERT: A 610 MET cc_start: 0.9059 (mmp) cc_final: 0.8027 (ttp) REVERT: B 51 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7455 (ttm-80) REVERT: B 126 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: B 477 MET cc_start: 0.8482 (tmm) cc_final: 0.8195 (tmm) REVERT: B 488 TRP cc_start: 0.6848 (m-10) cc_final: 0.5891 (m-90) REVERT: B 494 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7446 (tm-30) REVERT: B 583 MET cc_start: 0.7901 (ppp) cc_final: 0.7268 (ppp) outliers start: 24 outliers final: 14 residues processed: 102 average time/residue: 0.6521 time to fit residues: 72.0317 Evaluate side-chains 101 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 610 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 101 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.070082 restraints weight = 20378.874| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.38 r_work: 0.2717 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 11925 Z= 0.129 Angle : 0.593 12.180 16311 Z= 0.273 Chirality : 0.039 0.184 1728 Planarity : 0.004 0.040 2017 Dihedral : 7.740 89.187 1767 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.97 % Favored : 96.82 % Rotamer: Outliers : 1.80 % Allowed : 18.33 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.23), residues: 1413 helix: 2.41 (0.17), residues: 998 sheet: -0.49 (1.20), residues: 20 loop : -0.79 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 267 TYR 0.011 0.001 TYR B 324 PHE 0.015 0.001 PHE A 492 TRP 0.019 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (11921) covalent geometry : angle 0.59293 / 0.27 (16311) hydrogen bonds : bond 0.04488 / 2.96 ( 771) hydrogen bonds : angle 3.94370 / 2.88 ( 2241) Misc. bond : bond 0.09183 / 4.57 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.492 Fit side-chains REVERT: A 101 ARG cc_start: 0.8382 (tpt170) cc_final: 0.7944 (tpt170) REVERT: A 477 MET cc_start: 0.8425 (tmm) cc_final: 0.8104 (tmm) REVERT: A 488 TRP cc_start: 0.7046 (m-10) cc_final: 0.5958 (m-90) REVERT: A 494 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7320 (tm-30) REVERT: A 559 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: A 583 MET cc_start: 0.8780 (tpp) cc_final: 0.8207 (mpp) REVERT: A 610 MET cc_start: 0.9047 (mmp) cc_final: 0.8012 (ttp) REVERT: B 126 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: B 477 MET cc_start: 0.8453 (tmm) cc_final: 0.8154 (tmm) REVERT: B 494 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7373 (tm-30) REVERT: B 583 MET cc_start: 0.7894 (ppp) cc_final: 0.7259 (ppp) outliers start: 20 outliers final: 11 residues processed: 100 average time/residue: 0.7068 time to fit residues: 76.5676 Evaluate side-chains 95 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 563 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 107 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 141 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.098864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.067393 restraints weight = 20001.940| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.46 r_work: 0.2581 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 11925 Z= 0.114 Angle : 0.582 11.697 16311 Z= 0.269 Chirality : 0.038 0.163 1728 Planarity : 0.004 0.043 2017 Dihedral : 7.433 89.442 1765 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.97 % Favored : 96.82 % Rotamer: Outliers : 1.17 % Allowed : 19.23 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.24), residues: 1413 helix: 2.44 (0.17), residues: 1000 sheet: -0.45 (1.20), residues: 20 loop : -0.76 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 267 TYR 0.010 0.001 TYR A 156 PHE 0.012 0.001 PHE B 635 TRP 0.021 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (11921) covalent geometry : angle 0.58197 / 0.27 (16311) hydrogen bonds : bond 0.04131 / 2.72 ( 771) hydrogen bonds : angle 3.89064 / 2.84 ( 2241) Misc. bond : bond 0.06531 / 3.26 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.503 Fit side-chains REVERT: A 51 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7503 (ttm-80) REVERT: A 101 ARG cc_start: 0.8278 (tpt170) cc_final: 0.7787 (tpt170) REVERT: A 126 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: A 477 MET cc_start: 0.8290 (tmm) cc_final: 0.7999 (tmm) REVERT: A 488 TRP cc_start: 0.6906 (m-10) cc_final: 0.5862 (m-90) REVERT: A 494 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7151 (tm-30) REVERT: A 559 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: A 583 MET cc_start: 0.8640 (tpp) cc_final: 0.8189 (mpp) REVERT: A 610 MET cc_start: 0.8934 (mmp) cc_final: 0.7930 (ttp) REVERT: B 126 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: B 477 MET cc_start: 0.8361 (tmm) cc_final: 0.8081 (tmm) REVERT: B 494 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7324 (tm-30) REVERT: B 583 MET cc_start: 0.7853 (ppp) cc_final: 0.7227 (ppp) outliers start: 13 outliers final: 6 residues processed: 99 average time/residue: 0.6785 time to fit residues: 73.1786 Evaluate side-chains 96 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.0542 > 50: distance: 48 - 55: 18.593 distance: 55 - 56: 9.030 distance: 56 - 57: 15.400 distance: 56 - 59: 11.028 distance: 57 - 58: 29.263 distance: 57 - 64: 6.995 distance: 58 - 88: 66.331 distance: 59 - 60: 9.300 distance: 60 - 61: 8.193 distance: 61 - 62: 15.245 distance: 61 - 63: 9.508 distance: 64 - 65: 18.499 distance: 65 - 66: 17.463 distance: 65 - 68: 32.646 distance: 66 - 67: 28.680 distance: 66 - 72: 34.621 distance: 67 - 97: 34.180 distance: 68 - 69: 25.310 distance: 69 - 70: 18.234 distance: 69 - 71: 31.616 distance: 72 - 73: 41.662 distance: 73 - 74: 40.744 distance: 73 - 76: 34.867 distance: 74 - 75: 40.529 distance: 74 - 80: 49.441 distance: 75 - 104: 52.840 distance: 76 - 77: 31.885 distance: 76 - 78: 28.839 distance: 77 - 79: 24.913 distance: 80 - 81: 49.306 distance: 81 - 82: 42.136 distance: 81 - 84: 5.649 distance: 82 - 83: 30.696 distance: 82 - 88: 37.355 distance: 83 - 112: 21.280 distance: 84 - 85: 8.077 distance: 85 - 86: 36.067 distance: 85 - 87: 53.884 distance: 88 - 89: 3.743 distance: 89 - 90: 13.947 distance: 89 - 92: 12.253 distance: 90 - 91: 13.215 distance: 90 - 97: 4.536 distance: 91 - 123: 14.416 distance: 92 - 93: 8.594 distance: 93 - 94: 20.714 distance: 94 - 95: 25.259 distance: 95 - 96: 15.051 distance: 97 - 98: 22.812 distance: 98 - 99: 53.984 distance: 98 - 101: 41.272 distance: 99 - 100: 52.114 distance: 99 - 104: 43.073 distance: 100 - 128: 23.110 distance: 101 - 102: 26.807 distance: 101 - 103: 24.929 distance: 104 - 105: 22.089 distance: 105 - 106: 16.176 distance: 105 - 108: 39.117 distance: 106 - 107: 14.350 distance: 106 - 112: 9.228 distance: 107 - 132: 21.853 distance: 108 - 109: 13.035 distance: 109 - 110: 27.185 distance: 109 - 111: 3.257 distance: 112 - 113: 13.078 distance: 113 - 114: 14.117 distance: 113 - 116: 10.678 distance: 114 - 115: 18.065 distance: 114 - 123: 6.324 distance: 116 - 117: 9.439 distance: 117 - 118: 7.744 distance: 118 - 119: 5.878 distance: 120 - 122: 9.219 distance: 123 - 124: 8.913 distance: 124 - 125: 8.842 distance: 124 - 127: 9.087 distance: 125 - 126: 28.004 distance: 125 - 128: 14.795 distance: 128 - 129: 10.655 distance: 129 - 130: 11.369 distance: 130 - 131: 20.603 distance: 130 - 132: 10.722