Starting phenix.real_space_refine on Mon Jun 16 13:52:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pq8_17821/06_2025/8pq8_17821.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pq8_17821/06_2025/8pq8_17821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pq8_17821/06_2025/8pq8_17821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pq8_17821/06_2025/8pq8_17821.map" model { file = "/net/cci-nas-00/data/ceres_data/8pq8_17821/06_2025/8pq8_17821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pq8_17821/06_2025/8pq8_17821.cif" } resolution = 3.21 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= 0.019 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 12114 2.51 5 N 3096 2.21 5 O 3708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18936 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "G" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "K" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "L" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "M" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "M" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "N" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "O" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "P" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "P" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "Q" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "Q" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "R" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 12.53, per 1000 atoms: 0.66 Number of scatterers: 18936 At special positions: 0 Unit cell: (169.342, 170.834, 58.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 3708 8.00 N 3096 7.00 C 12114 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: 4.76 Conformation dependent library (CDL) restraints added in 2.2 seconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4428 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 72 sheets defined 34.4% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'B' and resid 5 through 12 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 105 through 122 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'C' and resid 5 through 12 Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 105 through 122 Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'D' and resid 5 through 12 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 105 through 122 Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 105 through 122 Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'F' and resid 5 through 12 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 105 through 122 Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'G' and resid 5 through 12 Processing helix chain 'G' and resid 29 through 41 Processing helix chain 'G' and resid 105 through 122 Processing helix chain 'G' and resid 127 through 131 Processing helix chain 'H' and resid 5 through 12 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 105 through 122 Processing helix chain 'H' and resid 127 through 131 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 29 through 41 Processing helix chain 'I' and resid 105 through 122 Processing helix chain 'I' and resid 127 through 131 Processing helix chain 'J' and resid 5 through 12 Processing helix chain 'J' and resid 29 through 41 Processing helix chain 'J' and resid 105 through 122 Processing helix chain 'J' and resid 127 through 131 Processing helix chain 'K' and resid 5 through 12 Processing helix chain 'K' and resid 29 through 41 Processing helix chain 'K' and resid 105 through 122 Processing helix chain 'K' and resid 127 through 131 Processing helix chain 'L' and resid 5 through 12 Processing helix chain 'L' and resid 29 through 41 Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'L' and resid 127 through 131 Processing helix chain 'M' and resid 5 through 12 Processing helix chain 'M' and resid 29 through 41 Processing helix chain 'M' and resid 105 through 122 Processing helix chain 'M' and resid 127 through 131 Processing helix chain 'N' and resid 5 through 12 Processing helix chain 'N' and resid 29 through 41 Processing helix chain 'N' and resid 105 through 122 Processing helix chain 'N' and resid 127 through 131 Processing helix chain 'O' and resid 5 through 12 Processing helix chain 'O' and resid 29 through 41 Processing helix chain 'O' and resid 105 through 122 Processing helix chain 'O' and resid 127 through 131 Processing helix chain 'P' and resid 5 through 12 Processing helix chain 'P' and resid 29 through 41 Processing helix chain 'P' and resid 105 through 122 Processing helix chain 'P' and resid 127 through 131 Processing helix chain 'Q' and resid 5 through 12 Processing helix chain 'Q' and resid 29 through 41 Processing helix chain 'Q' and resid 105 through 122 Processing helix chain 'Q' and resid 127 through 131 Processing helix chain 'R' and resid 5 through 12 Processing helix chain 'R' and resid 29 through 41 Processing helix chain 'R' and resid 105 through 122 Processing helix chain 'R' and resid 127 through 131 Processing sheet with id=1, first strand: chain 'A' and resid 19 through 22 Processing sheet with id=2, first strand: chain 'A' and resid 45 through 48 Processing sheet with id=3, first strand: chain 'A' and resid 45 through 48 Processing sheet with id=4, first strand: chain 'A' and resid 51 through 52 Processing sheet with id=5, first strand: chain 'B' and resid 19 through 22 Processing sheet with id=6, first strand: chain 'B' and resid 45 through 48 Processing sheet with id=7, first strand: chain 'B' and resid 45 through 48 Processing sheet with id=8, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=9, first strand: chain 'C' and resid 19 through 22 Processing sheet with id=10, first strand: chain 'C' and resid 45 through 48 Processing sheet with id=11, first strand: chain 'C' and resid 45 through 48 Processing sheet with id=12, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=13, first strand: chain 'D' and resid 19 through 22 Processing sheet with id=14, first strand: chain 'D' and resid 45 through 48 Processing sheet with id=15, first strand: chain 'D' and resid 45 through 48 Processing sheet with id=16, first strand: chain 'D' and resid 51 through 52 Processing sheet with id=17, first strand: chain 'E' and resid 19 through 22 Processing sheet with id=18, first strand: chain 'E' and resid 45 through 48 Processing sheet with id=19, first strand: chain 'E' and resid 45 through 48 Processing sheet with id=20, first strand: chain 'E' and resid 51 through 52 Processing sheet with id=21, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=22, first strand: chain 'F' and resid 45 through 48 Processing sheet with id=23, first strand: chain 'F' and resid 45 through 48 Processing sheet with id=24, first strand: chain 'F' and resid 51 through 52 Processing sheet with id=25, first strand: chain 'G' and resid 19 through 22 Processing sheet with id=26, first strand: chain 'G' and resid 45 through 48 Processing sheet with id=27, first strand: chain 'G' and resid 45 through 48 Processing sheet with id=28, first strand: chain 'G' and resid 51 through 52 Processing sheet with id=29, first strand: chain 'H' and resid 19 through 22 Processing sheet with id=30, first strand: chain 'H' and resid 45 through 48 Processing sheet with id=31, first strand: chain 'H' and resid 45 through 48 Processing sheet with id=32, first strand: chain 'H' and resid 51 through 52 Processing sheet with id=33, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=34, first strand: chain 'I' and resid 45 through 48 Processing sheet with id=35, first strand: chain 'I' and resid 45 through 48 Processing sheet with id=36, first strand: chain 'I' and resid 51 through 52 Processing sheet with id=37, first strand: chain 'J' and resid 19 through 22 Processing sheet with id=38, first strand: chain 'J' and resid 45 through 48 Processing sheet with id=39, first strand: chain 'J' and resid 45 through 48 Processing sheet with id=40, first strand: chain 'J' and resid 51 through 52 Processing sheet with id=41, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=42, first strand: chain 'K' and resid 45 through 48 Processing sheet with id=43, first strand: chain 'K' and resid 45 through 48 Processing sheet with id=44, first strand: chain 'K' and resid 51 through 52 Processing sheet with id=45, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=46, first strand: chain 'L' and resid 45 through 48 Processing sheet with id=47, first strand: chain 'L' and resid 45 through 48 Processing sheet with id=48, first strand: chain 'L' and resid 51 through 52 Processing sheet with id=49, first strand: chain 'M' and resid 19 through 22 Processing sheet with id=50, first strand: chain 'M' and resid 45 through 48 Processing sheet with id=51, first strand: chain 'M' and resid 45 through 48 Processing sheet with id=52, first strand: chain 'M' and resid 51 through 52 Processing sheet with id=53, first strand: chain 'N' and resid 19 through 22 Processing sheet with id=54, first strand: chain 'N' and resid 45 through 48 Processing sheet with id=55, first strand: chain 'N' and resid 45 through 48 Processing sheet with id=56, first strand: chain 'N' and resid 51 through 52 Processing sheet with id=57, first strand: chain 'O' and resid 19 through 22 Processing sheet with id=58, first strand: chain 'O' and resid 45 through 48 Processing sheet with id=59, first strand: chain 'O' and resid 45 through 48 Processing sheet with id=60, first strand: chain 'O' and resid 51 through 52 Processing sheet with id=61, first strand: chain 'P' and resid 19 through 22 Processing sheet with id=62, first strand: chain 'P' and resid 45 through 48 Processing sheet with id=63, first strand: chain 'P' and resid 45 through 48 Processing sheet with id=64, first strand: chain 'P' and resid 51 through 52 Processing sheet with id=65, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id=66, first strand: chain 'Q' and resid 45 through 48 Processing sheet with id=67, first strand: chain 'Q' and resid 45 through 48 Processing sheet with id=68, first strand: chain 'Q' and resid 51 through 52 Processing sheet with id=69, first strand: chain 'R' and resid 19 through 22 Processing sheet with id=70, first strand: chain 'R' and resid 45 through 48 Processing sheet with id=71, first strand: chain 'R' and resid 45 through 48 Processing sheet with id=72, first strand: chain 'R' and resid 51 through 52 990 hydrogen bonds defined for protein. 2484 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: 5.98 Time building geometry restraints manager: 5.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3168 1.32 - 1.44: 5472 1.44 - 1.56: 10638 1.56 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 19296 Sorted by residual: bond pdb=" N ILE M 56 " pdb=" CA ILE M 56 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ILE L 56 " pdb=" CA ILE L 56 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ILE G 56 " pdb=" CA ILE G 56 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.17e+01 bond pdb=" N ILE E 56 " pdb=" CA ILE E 56 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.17e+01 bond pdb=" N ILE R 56 " pdb=" CA ILE R 56 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.17e+01 ... (remaining 19291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 19767 1.65 - 3.29: 5588 3.29 - 4.94: 817 4.94 - 6.59: 36 6.59 - 8.23: 54 Bond angle restraints: 26262 Sorted by residual: angle pdb=" N HIS G 124 " pdb=" CA HIS G 124 " pdb=" C HIS G 124 " ideal model delta sigma weight residual 110.53 102.56 7.97 1.29e+00 6.01e-01 3.82e+01 angle pdb=" N HIS I 124 " pdb=" CA HIS I 124 " pdb=" C HIS I 124 " ideal model delta sigma weight residual 110.53 102.57 7.96 1.29e+00 6.01e-01 3.81e+01 angle pdb=" N HIS M 124 " pdb=" CA HIS M 124 " pdb=" C HIS M 124 " ideal model delta sigma weight residual 110.53 102.57 7.96 1.29e+00 6.01e-01 3.81e+01 angle pdb=" N HIS C 124 " pdb=" CA HIS C 124 " pdb=" C HIS C 124 " ideal model delta sigma weight residual 110.53 102.57 7.96 1.29e+00 6.01e-01 3.80e+01 angle pdb=" N HIS B 124 " pdb=" CA HIS B 124 " pdb=" C HIS B 124 " ideal model delta sigma weight residual 110.53 102.57 7.96 1.29e+00 6.01e-01 3.80e+01 ... (remaining 26257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.13: 10242 12.13 - 24.27: 540 24.27 - 36.40: 414 36.40 - 48.53: 36 48.53 - 60.67: 108 Dihedral angle restraints: 11340 sinusoidal: 4482 harmonic: 6858 Sorted by residual: dihedral pdb=" CB LYS F 111 " pdb=" CG LYS F 111 " pdb=" CD LYS F 111 " pdb=" CE LYS F 111 " ideal model delta sinusoidal sigma weight residual 60.00 9.67 50.33 3 1.50e+01 4.44e-03 8.89e+00 dihedral pdb=" CB LYS P 111 " pdb=" CG LYS P 111 " pdb=" CD LYS P 111 " pdb=" CE LYS P 111 " ideal model delta sinusoidal sigma weight residual 60.00 9.67 50.33 3 1.50e+01 4.44e-03 8.89e+00 dihedral pdb=" CB LYS B 111 " pdb=" CG LYS B 111 " pdb=" CD LYS B 111 " pdb=" CE LYS B 111 " ideal model delta sinusoidal sigma weight residual 60.00 9.71 50.29 3 1.50e+01 4.44e-03 8.88e+00 ... (remaining 11337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1219 0.047 - 0.094: 653 0.094 - 0.141: 664 0.141 - 0.188: 264 0.188 - 0.235: 80 Chirality restraints: 2880 Sorted by residual: chirality pdb=" CA TRP D 88 " pdb=" N TRP D 88 " pdb=" C TRP D 88 " pdb=" CB TRP D 88 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA TRP Q 88 " pdb=" N TRP Q 88 " pdb=" C TRP Q 88 " pdb=" CB TRP Q 88 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA TRP K 88 " pdb=" N TRP K 88 " pdb=" C TRP K 88 " pdb=" CB TRP K 88 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2877 not shown) Planarity restraints: 3348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 88 " 0.027 2.00e-02 2.50e+03 2.24e-02 1.25e+01 pdb=" CG TRP P 88 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP P 88 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP P 88 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP P 88 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP P 88 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP P 88 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 88 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 88 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP P 88 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 88 " 0.027 2.00e-02 2.50e+03 2.23e-02 1.25e+01 pdb=" CG TRP K 88 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP K 88 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP K 88 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP K 88 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 88 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP K 88 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 88 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 88 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP K 88 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 88 " 0.027 2.00e-02 2.50e+03 2.23e-02 1.25e+01 pdb=" CG TRP E 88 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP E 88 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP E 88 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 88 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 88 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 88 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 88 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 88 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 88 " 0.001 2.00e-02 2.50e+03 ... (remaining 3345 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 7241 2.90 - 3.40: 16951 3.40 - 3.90: 30426 3.90 - 4.40: 32410 4.40 - 4.90: 58225 Nonbonded interactions: 145253 Sorted by model distance: nonbonded pdb=" OD1 ASN Q 110 " pdb=" O HOH Q 201 " model vdw 2.394 3.040 nonbonded pdb=" OD1 ASN L 110 " pdb=" O HOH L 201 " model vdw 2.395 3.040 nonbonded pdb=" OD1 ASN N 110 " pdb=" O HOH N 201 " model vdw 2.395 3.040 nonbonded pdb=" OD1 ASN B 110 " pdb=" O HOH B 201 " model vdw 2.395 3.040 nonbonded pdb=" OD1 ASN K 110 " pdb=" O HOH K 201 " model vdw 2.395 3.040 ... (remaining 145248 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'R' } 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: 7.210 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 44.900 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.120 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.011 0.042 19296 Z= 0.856 Angle : 1.486 8.232 26262 Z= 1.132 Chirality : 0.090 0.235 2880 Planarity : 0.005 0.022 3348 Dihedral : 12.409 60.666 6912 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % 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: -0.24 (0.16), residues: 2268 helix: 0.75 (0.21), residues: 648 sheet: -0.03 (0.23), residues: 378 loop : -0.66 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.008 TRP P 88 HIS 0.004 0.002 HIS G 53 PHE 0.009 0.001 PHE F 7 TYR 0.023 0.003 TYR M 32 ARG 0.001 0.000 ARG H 95 Details of bonding type rmsd hydrogen bonds : bond 0.25955 ( 918) hydrogen bonds : angle 7.19379 ( 2484) covalent geometry : bond 0.01129 (19296) covalent geometry : angle 1.48625 (26262) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 SER cc_start: 0.8768 (m) cc_final: 0.8339 (t) REVERT: B 103 SER cc_start: 0.8827 (m) cc_final: 0.8392 (t) REVERT: C 103 SER cc_start: 0.8741 (m) cc_final: 0.8311 (t) REVERT: D 103 SER cc_start: 0.8811 (m) cc_final: 0.8386 (t) REVERT: E 103 SER cc_start: 0.8860 (m) cc_final: 0.8403 (t) REVERT: F 103 SER cc_start: 0.8781 (m) cc_final: 0.8370 (t) REVERT: G 103 SER cc_start: 0.8760 (m) cc_final: 0.8308 (t) REVERT: G 108 ASP cc_start: 0.8002 (m-30) cc_final: 0.7672 (m-30) REVERT: H 103 SER cc_start: 0.8786 (m) cc_final: 0.8385 (t) REVERT: I 103 SER cc_start: 0.8755 (m) cc_final: 0.8357 (t) REVERT: J 103 SER cc_start: 0.8769 (m) cc_final: 0.8340 (t) REVERT: K 103 SER cc_start: 0.8799 (m) cc_final: 0.8377 (t) REVERT: L 103 SER cc_start: 0.8725 (m) cc_final: 0.8312 (t) REVERT: M 103 SER cc_start: 0.8818 (m) cc_final: 0.8400 (t) REVERT: N 103 SER cc_start: 0.8839 (m) cc_final: 0.8383 (t) REVERT: O 103 SER cc_start: 0.8809 (m) cc_final: 0.8382 (t) REVERT: P 103 SER cc_start: 0.8766 (m) cc_final: 0.8323 (t) REVERT: P 108 ASP cc_start: 0.8009 (m-30) cc_final: 0.7700 (m-30) REVERT: Q 103 SER cc_start: 0.8814 (m) cc_final: 0.8393 (t) REVERT: R 103 SER cc_start: 0.8752 (m) cc_final: 0.8357 (t) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.3696 time to fit residues: 228.7455 Evaluate side-chains 322 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 2.136 ------------------------------------------------------------------------------- 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-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7933 > 50: distance: 7 - 29: 17.587 distance: 11 - 34: 26.106 distance: 16 - 44: 27.534 distance: 19 - 29: 19.781 distance: 20 - 53: 6.609 distance: 29 - 30: 23.783 distance: 30 - 31: 56.656 distance: 30 - 33: 29.798 distance: 31 - 32: 55.810 distance: 31 - 34: 12.095 distance: 32 - 62: 28.125 distance: 34 - 35: 27.217 distance: 35 - 36: 55.321 distance: 35 - 38: 70.793 distance: 36 - 37: 69.555 distance: 36 - 44: 59.840 distance: 37 - 70: 37.136 distance: 38 - 39: 68.766 distance: 39 - 40: 57.891 distance: 39 - 41: 57.897 distance: 40 - 42: 56.061 distance: 41 - 43: 58.535 distance: 42 - 43: 62.213 distance: 44 - 45: 32.616 distance: 45 - 46: 27.664 distance: 45 - 48: 41.204 distance: 46 - 47: 15.741 distance: 46 - 53: 8.353 distance: 47 - 79: 33.785 distance: 48 - 49: 49.980 distance: 49 - 50: 60.880 distance: 50 - 51: 26.292 distance: 50 - 52: 36.147 distance: 53 - 54: 11.844 distance: 54 - 55: 18.901 distance: 54 - 57: 16.359 distance: 55 - 56: 27.018 distance: 55 - 62: 18.758 distance: 56 - 88: 56.106 distance: 57 - 58: 22.881 distance: 58 - 59: 12.885 distance: 59 - 60: 8.362 distance: 59 - 61: 5.600 distance: 62 - 63: 18.194 distance: 63 - 64: 10.334 distance: 63 - 66: 12.811 distance: 64 - 65: 18.259 distance: 64 - 70: 27.684 distance: 65 - 96: 43.385 distance: 66 - 67: 21.347 distance: 67 - 68: 27.059 distance: 67 - 69: 34.761 distance: 70 - 71: 38.470 distance: 71 - 72: 27.674 distance: 71 - 74: 18.187 distance: 72 - 73: 26.588 distance: 72 - 79: 6.138 distance: 74 - 75: 28.396 distance: 75 - 76: 4.909 distance: 76 - 77: 56.734 distance: 77 - 78: 29.996 distance: 79 - 80: 44.402 distance: 80 - 81: 50.895 distance: 80 - 83: 42.384 distance: 81 - 82: 61.906 distance: 81 - 88: 22.073 distance: 83 - 84: 69.590 distance: 84 - 85: 16.209 distance: 85 - 86: 20.092 distance: 86 - 87: 6.998 distance: 88 - 89: 54.557 distance: 89 - 90: 57.405 distance: 89 - 92: 50.225 distance: 90 - 91: 40.077 distance: 90 - 96: 58.295 distance: 92 - 93: 60.929 distance: 92 - 94: 38.938 distance: 93 - 95: 24.501 distance: 96 - 97: 36.374 distance: 97 - 98: 41.665 distance: 97 - 100: 51.504 distance: 98 - 99: 51.093 distance: 98 - 104: 25.129 distance: 100 - 101: 22.219 distance: 101 - 102: 14.160 distance: 101 - 103: 21.620 distance: 104 - 105: 17.257 distance: 104 - 110: 43.638 distance: 105 - 106: 7.669 distance: 105 - 108: 20.386 distance: 106 - 107: 17.012 distance: 106 - 111: 14.821 distance: 108 - 109: 42.797 distance: 109 - 110: 33.356