Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 18 03:32:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c95_16502/07_2023/8c95_16502.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c95_16502/07_2023/8c95_16502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c95_16502/07_2023/8c95_16502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c95_16502/07_2023/8c95_16502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c95_16502/07_2023/8c95_16502.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c95_16502/07_2023/8c95_16502.pdb" } resolution = 4.92 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.069 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 1339 5.49 5 S 27 5.16 5 C 20007 2.51 5 N 7484 2.21 5 O 11315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 40172 Number of models: 1 Model: "" Number of chains: 16 Chain: "2" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 292 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "A" Number of atoms: 26210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1220, 26210 Classifications: {'RNA': 1220} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 59, 'rna3p_pur': 599, 'rna3p_pyr': 443} Link IDs: {'rna2p': 177, 'rna3p': 1042} Chain breaks: 7 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "E" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1519 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 1 Chain: "F" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1379 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 725 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain breaks: 1 Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 1 Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 513 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Time building chain proxies: 19.25, per 1000 atoms: 0.48 Number of scatterers: 40172 At special positions: 0 Unit cell: (182.5, 218.75, 172.5, 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 27 16.00 P 1339 15.00 O 11315 8.00 N 7484 7.00 C 20007 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 - 3.50 Amino acid : False - 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: 20.30 Conformation dependent library (CDL) restraints added in 2.2 seconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 18 sheets defined 38.4% alpha, 15.5% beta 436 base pairs and 648 stacking pairs defined. Time for finding SS restraints: 16.40 Creating SS restraints... Processing helix chain '2' and resid 10 through 17 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 38 Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.727A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG E 21 " --> pdb=" O THR E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.582A pdb=" N ALA E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.619A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.892A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 removed outlier: 4.255A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 20 removed outlier: 4.095A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 92 through 106 removed outlier: 4.100A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.625A pdb=" N VAL F 145 " --> pdb=" O TYR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 172 Processing helix chain 'J' and resid 24 through 37 removed outlier: 3.906A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 96 through 107 removed outlier: 3.932A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'L' and resid 2 through 6 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'O' and resid 3 through 19 removed outlier: 3.660A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'Q' and resid 5 through 19 removed outlier: 4.261A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 72 removed outlier: 4.128A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.796A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 25 No H-bonds generated for 'chain 'S' and resid 23 through 25' Processing helix chain 'S' and resid 28 through 38 removed outlier: 4.209A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 Processing helix chain 'V' and resid 13 through 23 removed outlier: 3.996A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 52 Processing helix chain 'V' and resid 53 through 58 removed outlier: 3.756A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 34 removed outlier: 4.673A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 43 removed outlier: 3.901A pdb=" N LEU Y 42 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU Y 43 " --> pdb=" O SER Y 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 39 through 43' Processing helix chain 'Y' and resid 45 through 56 removed outlier: 3.691A pdb=" N ASP Y 49 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'E' and resid 119 through 121 removed outlier: 6.115A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.140A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 65 through 66 removed outlier: 7.216A pdb=" N THR F 156 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE F 33 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR F 154 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR F 127 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 17 through 19 removed outlier: 6.339A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AA7, first strand: chain 'O' and resid 47 through 52 removed outlier: 6.811A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA O 50 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA O 37 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER O 52 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE O 35 " --> pdb=" O SER O 52 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU O 26 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 11 through 14 Processing sheet with id=AA9, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.953A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 72 through 78 removed outlier: 3.955A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 5 through 10 removed outlier: 4.924A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER S 101 " --> pdb=" O ALA S 10 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 63 through 65 removed outlier: 7.298A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS U 23 " --> pdb=" O GLU U 36 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE U 72 " --> pdb=" O GLU U 9 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP U 80 " --> pdb=" O ILE U 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'U' and resid 40 through 44 removed outlier: 3.845A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 82 through 84 Processing sheet with id=AB6, first strand: chain 'V' and resid 3 through 5 removed outlier: 6.854A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG V 79 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU V 86 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'W' and resid 32 through 35 removed outlier: 6.314A pdb=" N ILE W 32 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA W 57 " --> pdb=" O ILE W 32 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL W 34 " --> pdb=" O LEU W 55 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY W 48 " --> pdb=" O PHE W 56 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 41 through 43 removed outlier: 6.233A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Z' and resid 35 through 38 454 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1107 hydrogen bonds 1772 hydrogen bond angles 0 basepair planarities 436 basepair parallelities 648 stacking parallelities Total time for adding SS restraints: 31.50 Time building geometry restraints manager: 21.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6248 1.33 - 1.45: 17950 1.45 - 1.57: 16840 1.57 - 1.69: 2669 1.69 - 1.81: 52 Bond restraints: 43759 Sorted by residual: bond pdb=" P A A 973 " pdb=" O5' A A 973 " ideal model delta sigma weight residual 1.593 1.642 -0.049 1.50e-02 4.44e+03 1.05e+01 bond pdb=" O5' G A 974 " pdb=" C5' G A 974 " ideal model delta sigma weight residual 1.424 1.470 -0.046 1.50e-02 4.44e+03 9.55e+00 bond pdb=" O5' A A 973 " pdb=" C5' A A 973 " ideal model delta sigma weight residual 1.420 1.462 -0.042 1.50e-02 4.44e+03 7.82e+00 bond pdb=" P G A 974 " pdb=" O5' G A 974 " ideal model delta sigma weight residual 1.593 1.625 -0.032 1.50e-02 4.44e+03 4.45e+00 bond pdb=" O5' U A2390 " pdb=" C5' U A2390 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.83e+00 ... (remaining 43754 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.16: 7615 106.16 - 113.12: 25514 113.12 - 120.07: 15646 120.07 - 127.03: 13679 127.03 - 133.98: 3247 Bond angle restraints: 65701 Sorted by residual: angle pdb=" C3' A A 972 " pdb=" O3' A A 972 " pdb=" P A A 973 " ideal model delta sigma weight residual 120.20 105.02 15.18 1.50e+00 4.44e-01 1.02e+02 angle pdb=" C3' U A2390 " pdb=" O3' U A2390 " pdb=" P G A2391 " ideal model delta sigma weight residual 120.20 109.84 10.36 1.50e+00 4.44e-01 4.77e+01 angle pdb=" C3' A A 973 " pdb=" O3' A A 973 " pdb=" P G A 974 " ideal model delta sigma weight residual 120.20 128.19 -7.99 1.50e+00 4.44e-01 2.84e+01 angle pdb=" N ILE L 23 " pdb=" CA ILE L 23 " pdb=" C ILE L 23 " ideal model delta sigma weight residual 112.96 108.10 4.86 1.00e+00 1.00e+00 2.36e+01 angle pdb=" C3' A A 973 " pdb=" C2' A A 973 " pdb=" C1' A A 973 " ideal model delta sigma weight residual 101.30 106.03 -4.73 1.00e+00 1.00e+00 2.24e+01 ... (remaining 65696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 22304 35.95 - 71.90: 770 71.90 - 107.85: 89 107.85 - 143.80: 11 143.80 - 179.75: 1 Dihedral angle restraints: 23175 sinusoidal: 19015 harmonic: 4160 Sorted by residual: dihedral pdb=" C4' A A 973 " pdb=" C3' A A 973 " pdb=" C2' A A 973 " pdb=" C1' A A 973 " ideal model delta sinusoidal sigma weight residual 36.00 -6.91 42.91 1 8.00e+00 1.56e-02 4.01e+01 dihedral pdb=" O4' A A 973 " pdb=" C4' A A 973 " pdb=" C3' A A 973 " pdb=" C2' A A 973 " ideal model delta sinusoidal sigma weight residual -35.00 7.54 -42.54 1 8.00e+00 1.56e-02 3.95e+01 dihedral pdb=" C5' A A 973 " pdb=" C4' A A 973 " pdb=" C3' A A 973 " pdb=" O3' A A 973 " ideal model delta sinusoidal sigma weight residual 82.00 122.84 -40.84 1 8.00e+00 1.56e-02 3.65e+01 ... (remaining 23172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 8431 0.128 - 0.257: 11 0.257 - 0.385: 1 0.385 - 0.513: 2 0.513 - 0.642: 1 Chirality restraints: 8446 Sorted by residual: chirality pdb=" P G A 974 " pdb=" OP1 G A 974 " pdb=" OP2 G A 974 " pdb=" O5' G A 974 " both_signs ideal model delta sigma weight residual True 2.41 -3.05 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P A A 973 " pdb=" OP1 A A 973 " pdb=" OP2 A A 973 " pdb=" O5' A A 973 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" P U A2390 " pdb=" OP1 U A2390 " pdb=" OP2 U A2390 " pdb=" O5' U A2390 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 8443 not shown) Planarity restraints: 3325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 259 " 0.015 2.00e-02 2.50e+03 1.66e-02 8.27e+00 pdb=" N9 G A 259 " -0.009 2.00e-02 2.50e+03 pdb=" C8 G A 259 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 259 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G A 259 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 259 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G A 259 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G A 259 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 259 " -0.042 2.00e-02 2.50e+03 pdb=" N2 G A 259 " 0.032 2.00e-02 2.50e+03 pdb=" N3 G A 259 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 259 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 418 " 0.023 2.00e-02 2.50e+03 1.81e-02 7.37e+00 pdb=" N1 C A 418 " -0.023 2.00e-02 2.50e+03 pdb=" C2 C A 418 " 0.031 2.00e-02 2.50e+03 pdb=" O2 C A 418 " -0.024 2.00e-02 2.50e+03 pdb=" N3 C A 418 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C A 418 " 0.012 2.00e-02 2.50e+03 pdb=" N4 C A 418 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C A 418 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 418 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 398 " -0.007 2.00e-02 2.50e+03 1.56e-02 5.51e+00 pdb=" N1 C A 398 " 0.006 2.00e-02 2.50e+03 pdb=" C2 C A 398 " 0.039 2.00e-02 2.50e+03 pdb=" O2 C A 398 " -0.023 2.00e-02 2.50e+03 pdb=" N3 C A 398 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C A 398 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C A 398 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C A 398 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 398 " -0.001 2.00e-02 2.50e+03 ... (remaining 3322 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 382 2.49 - 3.09: 27863 3.09 - 3.69: 76709 3.69 - 4.30: 106695 4.30 - 4.90: 147329 Nonbonded interactions: 358978 Sorted by model distance: nonbonded pdb=" OP1 U B 5 " pdb=" O2' G B 61 " model vdw 1.886 2.440 nonbonded pdb=" O2' A A 299 " pdb=" O4' A A 300 " model vdw 1.900 2.440 nonbonded pdb=" O2' A A 191 " pdb=" O2 C A 678 " model vdw 1.911 2.440 nonbonded pdb=" O2' U A2312 " pdb=" OD1 ASN F 36 " model vdw 1.929 2.440 nonbonded pdb=" O6 G A1206 " pdb=" O2 U A1240 " model vdw 1.959 2.432 ... (remaining 358973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.770 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: 9.360 Check model and map are aligned: 0.540 Set scattering table: 0.340 Process input model: 123.690 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.002 0.049 43759 Z= 0.100 Angle : 0.418 15.179 65701 Z= 0.221 Chirality : 0.029 0.642 8446 Planarity : 0.003 0.033 3325 Dihedral : 14.452 179.750 20485 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.09 % 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: 0.20 (0.23), residues: 1423 helix: 1.66 (0.24), residues: 502 sheet: -0.49 (0.33), residues: 254 loop : -0.76 (0.25), residues: 667 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 2.339 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 outliers start: 1 outliers final: 1 residues processed: 195 average time/residue: 0.5640 time to fit residues: 173.8328 Evaluate side-chains 104 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 2.233 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4196 time to fit residues: 2.9303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 chunk 70 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 159 optimal weight: 20.0000 chunk 247 optimal weight: 40.0000 overall best weight: 12.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 16 HIS ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS J 58 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS U 52 ASN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.136 43759 Z= 0.434 Angle : 0.905 12.841 65701 Z= 0.444 Chirality : 0.042 0.312 8446 Planarity : 0.007 0.086 3325 Dihedral : 16.367 179.847 17644 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 41.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.85 % Favored : 91.08 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1423 helix: -0.01 (0.22), residues: 506 sheet: -0.92 (0.33), residues: 244 loop : -1.33 (0.23), residues: 673 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 2.130 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 outliers start: 6 outliers final: 2 residues processed: 128 average time/residue: 0.5390 time to fit residues: 114.2573 Evaluate side-chains 86 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 2.215 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4092 time to fit residues: 3.7185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 248 optimal weight: 1.9990 chunk 268 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 199 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN Y 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 43759 Z= 0.200 Angle : 0.574 12.280 65701 Z= 0.289 Chirality : 0.031 0.182 8446 Planarity : 0.004 0.039 3325 Dihedral : 16.243 178.601 17644 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 26.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.22), residues: 1423 helix: 0.28 (0.22), residues: 506 sheet: -1.22 (0.33), residues: 244 loop : -1.12 (0.24), residues: 673 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 2.203 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 outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.5497 time to fit residues: 116.3822 Evaluate side-chains 87 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 2.199 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4396 time to fit residues: 2.9731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 7.9990 chunk 186 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 249 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 236 optimal weight: 40.0000 chunk 71 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS L 99 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 43759 Z= 0.205 Angle : 0.574 12.768 65701 Z= 0.288 Chirality : 0.031 0.220 8446 Planarity : 0.004 0.044 3325 Dihedral : 16.314 177.049 17644 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 28.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer Outliers : 0.17 % 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: -0.96 (0.22), residues: 1423 helix: 0.35 (0.23), residues: 504 sheet: -1.21 (0.33), residues: 234 loop : -1.12 (0.24), residues: 685 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.5480 time to fit residues: 114.9640 Evaluate side-chains 89 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 2.240 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 40.0000 chunk 149 optimal weight: 6.9990 chunk 3 optimal weight: 30.0000 chunk 196 optimal weight: 0.4980 chunk 108 optimal weight: 30.0000 chunk 225 optimal weight: 30.0000 chunk 182 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 236 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 overall best weight: 10.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 ASN L 99 ASN Q 55 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 43759 Z= 0.366 Angle : 0.818 13.595 65701 Z= 0.405 Chirality : 0.040 0.266 8446 Planarity : 0.006 0.066 3325 Dihedral : 17.539 178.988 17644 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 51.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.77 % Favored : 90.09 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.21), residues: 1423 helix: -0.51 (0.22), residues: 490 sheet: -1.62 (0.31), residues: 226 loop : -1.53 (0.24), residues: 707 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 2.401 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 outliers start: 2 outliers final: 2 residues processed: 118 average time/residue: 0.5439 time to fit residues: 106.2033 Evaluate side-chains 79 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 2.295 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4065 time to fit residues: 3.8166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 20.0000 chunk 237 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 154 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 264 optimal weight: 0.3980 chunk 219 optimal weight: 0.9990 chunk 122 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 overall best weight: 4.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 43759 Z= 0.184 Angle : 0.611 13.787 65701 Z= 0.307 Chirality : 0.033 0.242 8446 Planarity : 0.004 0.039 3325 Dihedral : 17.134 175.074 17644 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 32.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.22), residues: 1423 helix: -0.14 (0.22), residues: 502 sheet: -1.49 (0.33), residues: 215 loop : -1.28 (0.23), residues: 706 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.5815 time to fit residues: 117.5536 Evaluate side-chains 88 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.300 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 150 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 222 optimal weight: 0.0670 chunk 147 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 121 optimal weight: 40.0000 overall best weight: 6.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 43759 Z= 0.235 Angle : 0.634 12.893 65701 Z= 0.320 Chirality : 0.034 0.266 8446 Planarity : 0.005 0.040 3325 Dihedral : 17.180 176.173 17644 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 37.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1423 helix: -0.04 (0.23), residues: 495 sheet: -1.75 (0.31), residues: 224 loop : -1.26 (0.24), residues: 704 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.199 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 outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.5582 time to fit residues: 109.8931 Evaluate side-chains 90 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.344 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 1.9990 chunk 105 optimal weight: 30.0000 chunk 157 optimal weight: 0.6980 chunk 79 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 179 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 206 optimal weight: 30.0000 overall best weight: 8.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 43759 Z= 0.288 Angle : 0.712 13.347 65701 Z= 0.358 Chirality : 0.037 0.273 8446 Planarity : 0.005 0.056 3325 Dihedral : 17.667 175.547 17644 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 44.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.22), residues: 1423 helix: -0.28 (0.22), residues: 495 sheet: -1.84 (0.30), residues: 229 loop : -1.44 (0.24), residues: 699 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.5624 time to fit residues: 109.9286 Evaluate side-chains 88 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.282 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 4.9990 chunk 252 optimal weight: 0.0970 chunk 229 optimal weight: 8.9990 chunk 245 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 106 optimal weight: 50.0000 chunk 192 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 221 optimal weight: 7.9990 chunk 231 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 43759 Z= 0.198 Angle : 0.613 13.666 65701 Z= 0.310 Chirality : 0.033 0.268 8446 Planarity : 0.004 0.037 3325 Dihedral : 17.402 173.471 17644 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 34.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1423 helix: -0.05 (0.23), residues: 497 sheet: -1.86 (0.30), residues: 233 loop : -1.33 (0.24), residues: 693 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.5462 time to fit residues: 110.7638 Evaluate side-chains 90 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.558 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.7145 > 50: distance: 61 - 81: 31.954 distance: 76 - 81: 28.238 distance: 81 - 82: 27.233 distance: 82 - 83: 4.108 distance: 82 - 85: 49.367 distance: 83 - 84: 58.671 distance: 83 - 87: 17.652 distance: 85 - 86: 37.084 distance: 87 - 88: 31.417 distance: 88 - 89: 33.119 distance: 89 - 90: 17.223 distance: 89 - 91: 27.769 distance: 91 - 92: 39.115 distance: 92 - 93: 55.386 distance: 92 - 95: 5.915 distance: 93 - 94: 47.017 distance: 93 - 100: 9.996 distance: 95 - 96: 48.208 distance: 96 - 97: 5.255 distance: 97 - 98: 42.513 distance: 97 - 99: 41.244 distance: 101 - 102: 20.219 distance: 101 - 104: 63.300 distance: 102 - 103: 43.877 distance: 102 - 109: 18.894 distance: 104 - 105: 57.917 distance: 105 - 106: 41.989 distance: 106 - 107: 11.845 distance: 107 - 108: 26.900 distance: 109 - 110: 38.894 distance: 109 - 115: 36.440 distance: 110 - 111: 55.390 distance: 110 - 113: 40.470 distance: 111 - 112: 53.388 distance: 111 - 116: 23.688 distance: 113 - 114: 47.910 distance: 114 - 115: 43.589 distance: 116 - 117: 17.590 distance: 116 - 194: 28.456 distance: 117 - 118: 42.625 distance: 117 - 120: 26.805 distance: 118 - 119: 30.902 distance: 118 - 124: 35.334 distance: 119 - 191: 28.399 distance: 120 - 121: 36.429 distance: 121 - 122: 38.731 distance: 121 - 123: 40.142 distance: 124 - 125: 37.870 distance: 125 - 126: 43.928 distance: 125 - 128: 23.866 distance: 126 - 127: 15.075 distance: 126 - 132: 9.492 distance: 128 - 129: 34.177 distance: 128 - 130: 27.882 distance: 129 - 131: 40.846 distance: 132 - 133: 47.290 distance: 133 - 134: 52.392 distance: 133 - 136: 32.928 distance: 134 - 135: 10.199 distance: 134 - 139: 3.226 distance: 136 - 137: 51.872 distance: 136 - 138: 7.935 distance: 139 - 140: 14.108 distance: 140 - 141: 3.723 distance: 140 - 143: 57.168 distance: 141 - 142: 40.725 distance: 141 - 148: 25.095 distance: 143 - 144: 54.729 distance: 144 - 145: 48.256 distance: 145 - 146: 39.946 distance: 146 - 147: 27.127 distance: 148 - 149: 46.836 distance: 149 - 150: 50.452 distance: 149 - 152: 37.445 distance: 150 - 151: 54.582 distance: 150 - 153: 31.754