Starting phenix.real_space_refine on Fri Jul 3 02:24:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wb1_32392/07_2026/7wb1_32392.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wb1_32392/07_2026/7wb1_32392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wb1_32392/07_2026/7wb1_32392.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wb1_32392/07_2026/7wb1_32392.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wb1_32392/07_2026/7wb1_32392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wb1_32392/07_2026/7wb1_32392.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wb1_32392/07_2026/7wb1_32392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wb1_32392/07_2026/7wb1_32392.map" } resolution = 3.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 178 5.49 5 S 28 5.16 5 C 6661 2.51 5 N 2059 2.21 5 O 2598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11524 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 614 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "C" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 547 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2577 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 59, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 106} Chain: "A" Number of atoms: 7786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7786 Classifications: {'peptide': 960} Link IDs: {'PTRANS': 37, 'TRANS': 922} Chain breaks: 2 Time building chain proxies: 2.83, per 1000 atoms: 0.25 Number of scatterers: 11524 At special positions: 0 Unit cell: (101.52, 141, 121.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 178 15.00 O 2598 8.00 N 2059 7.00 C 6661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 456.2 milliseconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 12 sheets defined 49.4% alpha, 13.1% beta 62 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 60 through 92 removed outlier: 3.735A pdb=" N ARG A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 195 through 201 removed outlier: 3.552A pdb=" N ILE A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 222 through 271 removed outlier: 3.577A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 309 Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.605A pdb=" N GLU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.748A pdb=" N GLY A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 removed outlier: 3.755A pdb=" N GLU A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.807A pdb=" N LYS A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 413 through 443 removed outlier: 4.041A pdb=" N VAL A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR A 418 " --> pdb=" O TRP A 414 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 466 removed outlier: 4.200A pdb=" N LYS A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 472 through 493 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 697 through 717 removed outlier: 3.602A pdb=" N LYS A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 715 " --> pdb=" O VAL A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 725 through 750 Processing helix chain 'A' and resid 770 through 774 Processing helix chain 'A' and resid 776 through 789 Processing helix chain 'A' and resid 793 through 798 removed outlier: 4.163A pdb=" N TYR A 797 " --> pdb=" O PRO A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 829 removed outlier: 3.504A pdb=" N LYS A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 874 Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 886 through 901 removed outlier: 3.754A pdb=" N GLU A 892 " --> pdb=" O GLY A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 937 removed outlier: 3.835A pdb=" N GLN A 924 " --> pdb=" O HIS A 920 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 937 " --> pdb=" O TRP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 949 Processing helix chain 'A' and resid 954 through 971 removed outlier: 3.805A pdb=" N PHE A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.505A pdb=" N SER A 502 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 614 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU A 611 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A 640 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN A 613 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 36 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 35 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 4.525A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 135 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 128 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 4.525A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 155 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 145 removed outlier: 3.629A pdb=" N GLN A 144 " --> pdb=" O HIS A 152 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 152 " --> pdb=" O GLN A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 542 through 545 removed outlier: 3.504A pdb=" N ARG A 542 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 573 " --> pdb=" O ARG A 542 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 572 " --> pdb=" O PHE A 556 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL A 559 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE A 517 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N ASN A 561 " --> pdb=" O CYS A 515 " (cutoff:3.500A) removed outlier: 12.651A pdb=" N CYS A 515 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 622 through 623 Processing sheet with id=AA8, first strand: chain 'A' and resid 691 through 694 removed outlier: 4.777A pdb=" N ALA A 756 " --> pdb=" O ILE A 658 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR A 801 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE A 755 " --> pdb=" O THR A 801 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 682 Processing sheet with id=AB1, first strand: chain 'A' and resid 830 through 831 removed outlier: 3.513A pdb=" N LYS A 830 " --> pdb=" O MET A 837 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 850 through 853 removed outlier: 4.192A pdb=" N TYR A 853 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL A 862 " --> pdb=" O TYR A 853 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 910 through 911 382 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 150 hydrogen bonds 276 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2385 1.33 - 1.45: 3515 1.45 - 1.57: 5830 1.57 - 1.69: 353 1.69 - 1.81: 41 Bond restraints: 12124 Sorted by residual: bond pdb=" C3' DT C 14 " pdb=" C2' DT C 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DG B 19 " pdb=" C2' DG B 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.65e+00 bond pdb=" C3' DC C 23 " pdb=" C2' DC C 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.67e+00 bond pdb=" C3' DC C 25 " pdb=" C2' DC C 25 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.52e+00 bond pdb=" C3' DG B 4 " pdb=" C2' DG B 4 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.93e+00 ... (remaining 12119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 16323 1.32 - 2.64: 713 2.64 - 3.96: 109 3.96 - 5.28: 15 5.28 - 6.60: 11 Bond angle restraints: 17171 Sorted by residual: angle pdb=" O4' DT B 8 " pdb=" C4' DT B 8 " pdb=" C3' DT B 8 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT B 14 " pdb=" C4 DT B 14 " pdb=" O4 DT B 14 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT B 11 " pdb=" C4 DT B 11 " pdb=" O4 DT B 11 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT B 8 " pdb=" C4 DT B 8 " pdb=" O4 DT B 8 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" O4' DT C 8 " pdb=" C4' DT C 8 " pdb=" C3' DT C 8 " ideal model delta sigma weight residual 106.00 103.47 2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 17166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 6521 35.91 - 71.82: 375 71.82 - 107.73: 27 107.73 - 143.64: 3 143.64 - 179.55: 6 Dihedral angle restraints: 6932 sinusoidal: 4130 harmonic: 2802 Sorted by residual: dihedral pdb=" O4' U D 11 " pdb=" C1' U D 11 " pdb=" N1 U D 11 " pdb=" C2 U D 11 " ideal model delta sinusoidal sigma weight residual -128.00 51.55 -179.55 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U D 17 " pdb=" C1' U D 17 " pdb=" N1 U D 17 " pdb=" C2 U D 17 " ideal model delta sinusoidal sigma weight residual -128.00 50.22 -178.22 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U D 9 " pdb=" C1' U D 9 " pdb=" N1 U D 9 " pdb=" C2 U D 9 " ideal model delta sinusoidal sigma weight residual -160.00 -100.01 -59.99 1 1.50e+01 4.44e-03 2.13e+01 ... (remaining 6929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1585 0.045 - 0.089: 299 0.089 - 0.134: 86 0.134 - 0.178: 7 0.178 - 0.223: 2 Chirality restraints: 1979 Sorted by residual: chirality pdb=" C1' G D 73 " pdb=" O4' G D 73 " pdb=" C2' G D 73 " pdb=" N9 G D 73 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C3' DG B 18 " pdb=" C4' DG B 18 " pdb=" O3' DG B 18 " pdb=" C2' DG B 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" C3' C D 41 " pdb=" C4' C D 41 " pdb=" O3' C D 41 " pdb=" C2' C D 41 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 1976 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C D 104 " 0.009 2.00e-02 2.50e+03 2.56e-02 1.47e+01 pdb=" N1 C D 104 " -0.006 2.00e-02 2.50e+03 pdb=" C2 C D 104 " -0.063 2.00e-02 2.50e+03 pdb=" O2 C D 104 " 0.039 2.00e-02 2.50e+03 pdb=" N3 C D 104 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C D 104 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C D 104 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C D 104 " 0.010 2.00e-02 2.50e+03 pdb=" C6 C D 104 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C D 118 " 0.022 2.00e-02 2.50e+03 1.66e-02 6.17e+00 pdb=" N1 C D 118 " -0.033 2.00e-02 2.50e+03 pdb=" C2 C D 118 " 0.007 2.00e-02 2.50e+03 pdb=" O2 C D 118 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C D 118 " -0.000 2.00e-02 2.50e+03 pdb=" C4 C D 118 " 0.025 2.00e-02 2.50e+03 pdb=" N4 C D 118 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C D 118 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C D 118 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 56 " -0.006 2.00e-02 2.50e+03 1.42e-02 5.57e+00 pdb=" N9 A D 56 " -0.000 2.00e-02 2.50e+03 pdb=" C8 A D 56 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 56 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A D 56 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A D 56 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A D 56 " 0.000 2.00e-02 2.50e+03 pdb=" N1 A D 56 " -0.033 2.00e-02 2.50e+03 pdb=" C2 A D 56 " 0.031 2.00e-02 2.50e+03 pdb=" N3 A D 56 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A D 56 " -0.002 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 183 2.62 - 3.19: 9664 3.19 - 3.76: 19864 3.76 - 4.33: 25399 4.33 - 4.90: 38127 Nonbonded interactions: 93237 Sorted by model distance: nonbonded pdb=" N2 G D 59 " pdb=" O2 C D 94 " model vdw 2.046 2.496 nonbonded pdb=" OP2 G D 101 " pdb=" NH2 ARG A 591 " model vdw 2.182 3.120 nonbonded pdb=" NZ LYS A 521 " pdb=" OE2 GLU A 605 " model vdw 2.227 3.120 nonbonded pdb=" O6 DG B 22 " pdb=" NZ LYS A 227 " model vdw 2.236 3.120 nonbonded pdb=" OG1 THR A 202 " pdb=" OE1 GLU A 204 " model vdw 2.263 3.040 ... (remaining 93232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.820 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.270 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 : 0.004 0.043 12124 Z= 0.267 Angle : 0.633 6.604 17171 Z= 0.428 Chirality : 0.039 0.223 1979 Planarity : 0.004 0.044 1546 Dihedral : 19.609 179.554 5122 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.28), residues: 954 helix: 1.86 (0.26), residues: 412 sheet: -0.69 (0.45), residues: 140 loop : -0.80 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 764 TYR 0.017 0.001 TYR A 857 PHE 0.016 0.001 PHE A 332 TRP 0.009 0.001 TRP A 962 HIS 0.015 0.002 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.27 (12124) covalent geometry : angle 0.63285 / 0.43 (17171) hydrogen bonds : bond 0.17607 / 19.78 ( 531) hydrogen bonds : angle 5.88496 / 7.54 ( 1371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.349 Fit side-chains REVERT: A 29 MET cc_start: 0.6905 (ppp) cc_final: 0.5886 (ppp) REVERT: A 375 GLN cc_start: 0.7736 (mm110) cc_final: 0.7534 (tp40) REVERT: A 570 MET cc_start: 0.7668 (tpt) cc_final: 0.7458 (mmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1044 time to fit residues: 13.0058 Evaluate side-chains 58 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 HIS A 251 HIS A 729 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.093398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.067595 restraints weight = 44178.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.069663 restraints weight = 23723.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.070967 restraints weight = 16700.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.071718 restraints weight = 13670.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.072103 restraints weight = 12228.215| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12124 Z= 0.189 Angle : 0.649 7.906 17171 Z= 0.352 Chirality : 0.041 0.245 1979 Planarity : 0.005 0.050 1546 Dihedral : 21.694 179.036 3112 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.31 % Allowed : 7.03 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.28), residues: 954 helix: 1.66 (0.25), residues: 425 sheet: -1.03 (0.43), residues: 144 loop : -0.81 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 624 TYR 0.015 0.002 TYR A 857 PHE 0.019 0.002 PHE A 399 TRP 0.020 0.002 TRP A 366 HIS 0.009 0.002 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (12124) covalent geometry : angle 0.64903 / 0.35 (17171) hydrogen bonds : bond 0.07694 / 8.68 ( 531) hydrogen bonds : angle 4.83931 / 6.09 ( 1371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.366 Fit side-chains REVERT: A 486 TRP cc_start: 0.6976 (m-10) cc_final: 0.6761 (m-10) REVERT: A 570 MET cc_start: 0.8065 (tpt) cc_final: 0.7678 (mmm) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.0816 time to fit residues: 8.2430 Evaluate side-chains 64 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 934 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.4947 > 50: distance: 28 - 34: 21.353 distance: 34 - 35: 19.120 distance: 35 - 36: 25.693 distance: 35 - 38: 24.364 distance: 36 - 37: 9.300 distance: 36 - 42: 16.379 distance: 38 - 39: 23.795 distance: 39 - 40: 12.230 distance: 39 - 41: 8.314 distance: 42 - 43: 29.270 distance: 42 - 231: 22.437 distance: 43 - 44: 17.149 distance: 43 - 46: 21.253 distance: 44 - 45: 11.590 distance: 44 - 49: 29.716 distance: 45 - 228: 7.859 distance: 46 - 47: 38.657 distance: 46 - 48: 45.816 distance: 49 - 50: 34.631 distance: 50 - 51: 27.206 distance: 50 - 53: 25.031 distance: 51 - 52: 29.142 distance: 51 - 60: 37.606 distance: 52 - 199: 19.318 distance: 53 - 54: 6.891 distance: 54 - 55: 24.313 distance: 55 - 56: 13.430 distance: 56 - 57: 5.984 distance: 57 - 58: 14.911 distance: 57 - 59: 13.635 distance: 60 - 61: 17.074 distance: 61 - 62: 12.165 distance: 61 - 64: 19.235 distance: 62 - 63: 16.636 distance: 62 - 67: 20.528 distance: 64 - 65: 38.680 distance: 64 - 66: 23.054 distance: 67 - 68: 10.502 distance: 68 - 69: 16.302 distance: 68 - 71: 17.237 distance: 69 - 70: 43.970 distance: 69 - 75: 34.251 distance: 71 - 72: 15.390 distance: 72 - 73: 15.677 distance: 73 - 74: 13.323 distance: 75 - 76: 42.312 distance: 76 - 77: 12.756 distance: 76 - 79: 21.745 distance: 77 - 78: 4.745 distance: 77 - 82: 32.958 distance: 78 - 105: 28.565 distance: 79 - 80: 21.464 distance: 79 - 81: 36.466 distance: 82 - 83: 22.635 distance: 82 - 88: 18.809 distance: 83 - 84: 28.268 distance: 83 - 86: 24.691 distance: 84 - 85: 26.743 distance: 84 - 89: 9.887 distance: 85 - 116: 13.769 distance: 86 - 87: 25.234 distance: 87 - 88: 18.232 distance: 89 - 90: 28.827 distance: 90 - 91: 18.943 distance: 90 - 93: 12.693 distance: 91 - 92: 9.762 distance: 91 - 97: 38.706 distance: 92 - 125: 22.423 distance: 93 - 94: 15.609 distance: 94 - 95: 13.278 distance: 94 - 96: 11.100 distance: 97 - 98: 27.394 distance: 98 - 99: 17.646 distance: 98 - 101: 19.438 distance: 99 - 100: 17.286 distance: 99 - 105: 6.856 distance: 100 - 136: 19.351 distance: 101 - 102: 13.200 distance: 102 - 103: 19.470 distance: 102 - 104: 11.749 distance: 105 - 106: 23.145 distance: 106 - 107: 28.344 distance: 106 - 109: 16.023 distance: 107 - 108: 27.014 distance: 107 - 116: 16.546 distance: 108 - 143: 35.654 distance: 109 - 110: 23.519 distance: 110 - 111: 7.043 distance: 111 - 112: 10.286 distance: 113 - 114: 3.141 distance: 113 - 115: 3.333