Starting phenix.real_space_refine on Mon Nov 18 06:01:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cx6_45979/11_2024/9cx6_45979.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cx6_45979/11_2024/9cx6_45979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cx6_45979/11_2024/9cx6_45979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cx6_45979/11_2024/9cx6_45979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cx6_45979/11_2024/9cx6_45979.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cx6_45979/11_2024/9cx6_45979.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 30400 2.51 5 N 8600 2.21 5 O 10250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 200 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 49250 Number of models: 1 Model: "" Number of chains: 102 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "3" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "5" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "7" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "9" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "l" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "n" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "r" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "t" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "v" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "x" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AB" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AD" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AF" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AH" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AJ" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AL" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AN" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AP" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AR" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AS" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AT" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AV" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AX" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AY" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AZ" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A3" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A5" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A7" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A9" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "BA" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 538 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "BB" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 442 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "BA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BB" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Restraints were copied for chains: 0, 4, 8, A, E, AI, C, G, M, K, O, S, W, AQ, c, g, k, o, s, w, U, AY, 2, 6, A0, A2, A4, A6, A8, AA, AC, AE, AG, I, AK, AM, AO, Q, AS, AU, AW, Y, a, e, i, m, q, u, y, A1, D, H, L, P, T, X, d, h, l, p, t, x, A9, 3, 7, A5, B, F, J, N, R, V, Z, b, f, j, n, r, v, z, 1, A3, 5, A7, 9, AB, AD, AF, AH, AJ, AL, AN, AP, AR, AT, AV, AX, AZ Time building chain proxies: 10.16, per 1000 atoms: 0.21 Number of scatterers: 49250 At special positions: 0 Unit cell: (92.71, 110.96, 85.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 10250 8.00 N 8600 7.00 C 30400 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: 98.28 Conformation dependent library (CDL) restraints added in 6.9 seconds 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.62 Creating SS restraints... No hydrogen bonds 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: 0.02 Time building geometry restraints manager: 98.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 8800 1.28 - 1.34: 7585 1.34 - 1.41: 1415 1.41 - 1.48: 9150 1.48 - 1.54: 22200 Bond restraints: 49150 Sorted by residual: bond pdb=" CG HISA5 50 " pdb=" CD2 HISA5 50 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.48e+01 bond pdb=" CG HIS f 50 " pdb=" CD2 HIS f 50 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.48e+01 bond pdb=" CG HISAR 50 " pdb=" CD2 HISAR 50 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.47e+01 bond pdb=" CG HISA3 50 " pdb=" CD2 HISA3 50 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.47e+01 bond pdb=" CG HIS x 50 " pdb=" CD2 HIS x 50 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.47e+01 ... (remaining 49145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 42348 1.17 - 2.34: 16585 2.34 - 3.52: 5712 3.52 - 4.69: 1311 4.69 - 5.86: 444 Bond angle restraints: 66400 Sorted by residual: angle pdb=" CA PHE B 94 " pdb=" CB PHE B 94 " pdb=" CG PHE B 94 " ideal model delta sigma weight residual 113.80 117.67 -3.87 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA PHEAB 94 " pdb=" CB PHEAB 94 " pdb=" CG PHEAB 94 " ideal model delta sigma weight residual 113.80 117.66 -3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA PHE f 94 " pdb=" CB PHE f 94 " pdb=" CG PHE f 94 " ideal model delta sigma weight residual 113.80 117.66 -3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA PHEAN 94 " pdb=" CB PHEAN 94 " pdb=" CG PHEAN 94 " ideal model delta sigma weight residual 113.80 117.66 -3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA PHE x 94 " pdb=" CB PHE x 94 " pdb=" CG PHE x 94 " ideal model delta sigma weight residual 113.80 117.66 -3.86 1.00e+00 1.00e+00 1.49e+01 ... (remaining 66395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 27850 14.74 - 29.47: 450 29.47 - 44.21: 50 44.21 - 58.94: 200 58.94 - 73.68: 300 Dihedral angle restraints: 28850 sinusoidal: 9550 harmonic: 19300 Sorted by residual: dihedral pdb=" CB LYS 8 80 " pdb=" CG LYS 8 80 " pdb=" CD LYS 8 80 " pdb=" CE LYS 8 80 " ideal model delta sinusoidal sigma weight residual 60.00 117.60 -57.60 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CB LYS A 80 " pdb=" CG LYS A 80 " pdb=" CD LYS A 80 " pdb=" CE LYS A 80 " ideal model delta sinusoidal sigma weight residual 60.00 117.57 -57.57 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CB LYSA2 80 " pdb=" CG LYSA2 80 " pdb=" CD LYSA2 80 " pdb=" CE LYSA2 80 " ideal model delta sinusoidal sigma weight residual 60.00 117.56 -57.56 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 28847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3073 0.038 - 0.076: 2627 0.076 - 0.114: 2198 0.114 - 0.152: 702 0.152 - 0.190: 50 Chirality restraints: 8650 Sorted by residual: chirality pdb=" CA HIS 4 50 " pdb=" N HIS 4 50 " pdb=" C HIS 4 50 " pdb=" CB HIS 4 50 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA HIS E 50 " pdb=" N HIS E 50 " pdb=" C HIS E 50 " pdb=" CB HIS E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA HIS 8 50 " pdb=" N HIS 8 50 " pdb=" C HIS 8 50 " pdb=" CB HIS 8 50 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 8647 not shown) Planarity restraints: 8350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 94 " -0.024 2.00e-02 2.50e+03 1.55e-02 4.23e+00 pdb=" CG PHE L 94 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE L 94 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE L 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE L 94 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE L 94 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE L 94 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 3 94 " -0.024 2.00e-02 2.50e+03 1.55e-02 4.20e+00 pdb=" CG PHE 3 94 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE 3 94 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE 3 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE 3 94 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE 3 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE 3 94 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 94 " -0.024 2.00e-02 2.50e+03 1.55e-02 4.19e+00 pdb=" CG PHE F 94 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE F 94 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE F 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE F 94 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE F 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 94 " -0.009 2.00e-02 2.50e+03 ... (remaining 8347 not shown) Histogram of nonbonded interaction distances: 0.18 - 1.13: 88559 1.13 - 2.07: 157950 2.07 - 3.01: 312255 3.01 - 3.96: 508171 3.96 - 4.90: 1081604 Warning: very small nonbonded interaction distances. Nonbonded interactions: 2148539 Sorted by model distance: nonbonded pdb=" O GLNAH 99 " pdb=" O GLNAP 99 " model vdw 0.182 3.040 nonbonded pdb=" C LYS V 97 " pdb=" C LYS 9 97 " model vdw 0.182 3.500 nonbonded pdb=" CA ASP 3 98 " pdb=" CA ASP b 98 " model vdw 0.182 3.900 nonbonded pdb=" CB GLN 3 99 " pdb=" CB GLN b 99 " model vdw 0.182 3.840 nonbonded pdb=" CD GLN p 99 " pdb=" CD GLNAD 99 " model vdw 0.183 3.500 ... (remaining 2148534 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 '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'A' selection = chain 'A0' selection = chain 'A2' selection = chain 'A4' selection = chain 'A6' selection = chain 'A8' selection = chain 'AA' selection = chain 'AC' selection = chain 'AE' selection = chain 'AG' selection = chain 'AI' selection = chain 'AK' selection = chain 'AM' selection = chain 'AO' selection = chain 'AQ' selection = chain 'AS' selection = chain 'AU' selection = chain 'AW' selection = chain 'AY' selection = chain 'BA' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 's' selection = chain 'u' selection = chain 'w' selection = chain 'y' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'A1' selection = chain 'A3' selection = chain 'A5' selection = chain 'A7' selection = chain 'A9' selection = chain 'AB' selection = chain 'AD' selection = chain 'AF' selection = chain 'AH' selection = chain 'AJ' selection = chain 'AL' selection = chain 'AN' selection = chain 'AP' selection = chain 'AR' selection = chain 'AT' selection = chain 'AV' selection = chain 'AX' selection = chain 'AZ' selection = chain 'B' selection = chain 'BB' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'r' selection = chain 't' selection = chain 'v' selection = chain 'x' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.040 Extract box with map and model: 2.010 Check model and map are aligned: 0.370 Set scattering table: 0.430 Process input model: 169.140 Find NCS groups from input model: 2.190 Set up NCS constraints: 1.170 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 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 : 0.009 0.042 49150 Z= 0.628 Angle : 1.458 5.862 66400 Z= 0.922 Chirality : 0.070 0.190 8650 Planarity : 0.006 0.017 8350 Dihedral : 12.628 73.678 16750 Min Nonbonded Distance : 0.182 Molprobity Statistics. All-atom Clashscore : 28.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.06), residues: 7000 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.04), residues: 7000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS L 50 PHE 0.028 0.012 PHE L 94 TYR 0.023 0.008 TYRAU 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 5.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8172 (mttt) cc_final: 0.7903 (mtpt) REVERT: A 79 GLN cc_start: 0.8575 (tt0) cc_final: 0.8368 (tt0) outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 1.1669 time to fit residues: 1209.2531 Evaluate side-chains 655 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 5.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.4905 > 50: distance: 535 - 539: 14.216 distance: 539 - 540: 14.785 distance: 540 - 541: 19.929 distance: 540 - 543: 9.280 distance: 541 - 542: 7.314 distance: 541 - 548: 27.331 distance: 543 - 544: 33.077 distance: 544 - 545: 4.930 distance: 545 - 546: 3.270 distance: 546 - 547: 22.908 distance: 548 - 549: 52.817 distance: 549 - 550: 19.723 distance: 549 - 552: 37.787 distance: 550 - 551: 23.963 distance: 550 - 555: 13.097 distance: 552 - 553: 33.715 distance: 552 - 554: 19.236 distance: 555 - 556: 13.549 distance: 556 - 557: 12.091 distance: 556 - 559: 16.978 distance: 557 - 558: 14.466 distance: 557 - 564: 16.852 distance: 559 - 560: 38.785 distance: 560 - 561: 12.625 distance: 561 - 562: 25.870 distance: 562 - 563: 23.795 distance: 565 - 566: 9.918 distance: 565 - 568: 8.495 distance: 566 - 567: 16.886 distance: 566 - 573: 19.256 distance: 568 - 569: 26.837 distance: 569 - 570: 15.807 distance: 570 - 571: 27.624 distance: 570 - 572: 7.887 distance: 573 - 574: 41.195 distance: 574 - 575: 39.517 distance: 575 - 577: 26.950 distance: 577 - 578: 39.081 distance: 578 - 579: 16.170 distance: 578 - 581: 34.963 distance: 579 - 580: 42.117 distance: 579 - 584: 14.527 distance: 581 - 582: 21.239 distance: 581 - 583: 20.146 distance: 584 - 585: 25.785 distance: 585 - 586: 12.835 distance: 585 - 588: 14.956 distance: 586 - 587: 24.384 distance: 586 - 591: 30.722 distance: 588 - 589: 36.980 distance: 588 - 590: 20.840 distance: 591 - 592: 19.315 distance: 592 - 593: 19.451 distance: 592 - 595: 24.675 distance: 593 - 594: 9.831 distance: 593 - 601: 34.345 distance: 595 - 596: 8.018 distance: 596 - 597: 15.437 distance: 596 - 598: 10.668 distance: 597 - 599: 9.509 distance: 598 - 600: 7.600 distance: 599 - 600: 5.252 distance: 601 - 602: 9.593 distance: 602 - 603: 42.484 distance: 603 - 604: 48.297 distance: 603 - 605: 4.365 distance: 605 - 606: 34.322 distance: 606 - 607: 20.571 distance: 606 - 609: 20.675 distance: 607 - 608: 11.683 distance: 607 - 612: 11.075 distance: 609 - 610: 9.231 distance: 609 - 611: 24.951