Starting phenix.real_space_refine (version: dev) on Sat Feb 25 02:06:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/02_2023/7xct_33127_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/02_2023/7xct_33127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/02_2023/7xct_33127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/02_2023/7xct_33127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/02_2023/7xct_33127_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/02_2023/7xct_33127_updated.pdb" } resolution = 2.72 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= -0.000 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5945 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 278": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18633 Number of models: 1 Model: "" Number of chains: 16 Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "K" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2656 Classifications: {'peptide': 326} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 307} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "M" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2671 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 308} Chain: "N" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 residue: pdb=" N GLY L 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY L 76 " occ=0.25 residue: pdb=" N LEU N 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU N 73 " occ=0.45 residue: pdb=" N ARG N 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG N 74 " occ=0.45 residue: pdb=" N GLY N 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY N 75 " occ=0.25 residue: pdb=" N GLY N 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY N 76 " occ=0.25 Time building chain proxies: 10.25, per 1000 atoms: 0.55 Number of scatterers: 18633 At special positions: 0 Unit cell: (151.2, 123.12, 150.12, 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 40 16.00 P 290 15.00 O 4051 8.00 N 3399 7.00 C 10853 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: 8.42 Conformation dependent library (CDL) restraints added in 2.3 seconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2966 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 4 sheets defined 44.1% alpha, 5.3% beta 125 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 7.30 Creating SS restraints... Processing helix chain 'L' and resid 23 through 33 removed outlier: 4.357A pdb=" N GLN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 59 No H-bonds generated for 'chain 'L' and resid 57 through 59' Processing helix chain 'F' and resid 31 through 34 No H-bonds generated for 'chain 'F' and resid 31 through 34' Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 50 through 56 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 93 through 99 removed outlier: 5.675A pdb=" N ARG G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 48 removed outlier: 3.517A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 83 removed outlier: 3.553A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 105 through 123 Processing helix chain 'K' and resid 36 through 44 removed outlier: 3.689A pdb=" N ARG K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL K 44 " --> pdb=" O THR K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 54 No H-bonds generated for 'chain 'K' and resid 51 through 54' Processing helix chain 'K' and resid 69 through 72 No H-bonds generated for 'chain 'K' and resid 69 through 72' Processing helix chain 'K' and resid 76 through 79 No H-bonds generated for 'chain 'K' and resid 76 through 79' Processing helix chain 'K' and resid 83 through 89 removed outlier: 5.726A pdb=" N LEU K 88 " --> pdb=" O SER K 84 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP K 89 " --> pdb=" O ILE K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 118 removed outlier: 3.505A pdb=" N ASN K 116 " --> pdb=" O GLN K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'K' and resid 141 through 151 Processing helix chain 'K' and resid 168 through 174 Processing helix chain 'K' and resid 189 through 208 removed outlier: 3.540A pdb=" N GLU K 196 " --> pdb=" O ALA K 192 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG K 203 " --> pdb=" O ASP K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 233 removed outlier: 4.366A pdb=" N GLU K 230 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 255 removed outlier: 3.738A pdb=" N GLU K 255 " --> pdb=" O HIS K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 259 No H-bonds generated for 'chain 'K' and resid 257 through 259' Processing helix chain 'K' and resid 287 through 289 No H-bonds generated for 'chain 'K' and resid 287 through 289' Processing helix chain 'K' and resid 321 through 324 No H-bonds generated for 'chain 'K' and resid 321 through 324' Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.692A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 112 removed outlier: 3.578A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.525A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.605A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 removed outlier: 3.551A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.612A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 93 through 99 removed outlier: 5.676A pdb=" N ARG C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.737A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.641A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 44 removed outlier: 3.690A pdb=" N ARG M 42 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TRP M 43 " --> pdb=" O GLU M 39 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL M 44 " --> pdb=" O THR M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 54 No H-bonds generated for 'chain 'M' and resid 51 through 54' Processing helix chain 'M' and resid 69 through 72 No H-bonds generated for 'chain 'M' and resid 69 through 72' Processing helix chain 'M' and resid 76 through 79 No H-bonds generated for 'chain 'M' and resid 76 through 79' Processing helix chain 'M' and resid 83 through 89 removed outlier: 5.726A pdb=" N LEU M 88 " --> pdb=" O SER M 84 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TRP M 89 " --> pdb=" O ILE M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 118 removed outlier: 3.505A pdb=" N ASN M 116 " --> pdb=" O GLN M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 126 Processing helix chain 'M' and resid 141 through 151 Processing helix chain 'M' and resid 168 through 174 Processing helix chain 'M' and resid 189 through 208 removed outlier: 3.540A pdb=" N GLU M 196 " --> pdb=" O ALA M 192 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR M 197 " --> pdb=" O LYS M 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG M 203 " --> pdb=" O ASP M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 233 removed outlier: 4.366A pdb=" N GLU M 230 " --> pdb=" O GLU M 226 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG M 231 " --> pdb=" O GLU M 227 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA M 233 " --> pdb=" O ARG M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 255 removed outlier: 3.737A pdb=" N GLU M 255 " --> pdb=" O HIS M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 259 No H-bonds generated for 'chain 'M' and resid 257 through 259' Processing helix chain 'M' and resid 287 through 289 No H-bonds generated for 'chain 'M' and resid 287 through 289' Processing helix chain 'M' and resid 321 through 324 No H-bonds generated for 'chain 'M' and resid 321 through 324' Processing helix chain 'N' and resid 23 through 33 removed outlier: 4.357A pdb=" N GLN N 31 " --> pdb=" O LYS N 27 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP N 32 " --> pdb=" O ALA N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing sheet with id= A, first strand: chain 'L' and resid 12 through 15 removed outlier: 3.566A pdb=" N VAL L 5 " --> pdb=" O ILE L 13 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS L 68 " --> pdb=" O ILE L 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 291 through 295 removed outlier: 4.007A pdb=" N PHE K 159 " --> pdb=" O HIS K 181 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU K 215 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N GLY K 184 " --> pdb=" O GLU K 215 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR K 217 " --> pdb=" O GLY K 184 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N GLU K 186 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU K 219 " --> pdb=" O GLU K 186 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 291 through 295 removed outlier: 4.008A pdb=" N PHE M 159 " --> pdb=" O HIS M 181 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU M 215 " --> pdb=" O HIS M 182 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLY M 184 " --> pdb=" O GLU M 215 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR M 217 " --> pdb=" O GLY M 184 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N GLU M 186 " --> pdb=" O THR M 217 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU M 219 " --> pdb=" O GLU M 186 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 12 through 15 removed outlier: 3.566A pdb=" N VAL N 5 " --> pdb=" O ILE N 13 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS N 68 " --> pdb=" O ILE N 44 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 305 hydrogen bonds 590 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 6.97 Time building geometry restraints manager: 8.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2539 1.31 - 1.44: 6617 1.44 - 1.56: 9780 1.56 - 1.69: 582 1.69 - 1.81: 74 Bond restraints: 19592 Sorted by residual: bond pdb=" C1' DC J 65 " pdb=" N1 DC J 65 " ideal model delta sigma weight residual 1.490 1.595 -0.105 3.00e-02 1.11e+03 1.22e+01 bond pdb=" CB THR H 96 " pdb=" CG2 THR H 96 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.09e+00 bond pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 1.523 1.563 -0.040 1.34e-02 5.57e+03 8.89e+00 bond pdb=" CB THR B 71 " pdb=" CG2 THR B 71 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.45e+00 bond pdb=" CB THR D 96 " pdb=" CG2 THR D 96 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.62e+00 ... (remaining 19587 not shown) Histogram of bond angle deviations from ideal: 97.99 - 106.69: 2380 106.69 - 115.39: 11697 115.39 - 124.08: 12233 124.08 - 132.78: 1395 132.78 - 141.48: 24 Bond angle restraints: 27729 Sorted by residual: angle pdb=" C ARG F 67 " pdb=" N ASP F 68 " pdb=" CA ASP F 68 " ideal model delta sigma weight residual 121.54 135.56 -14.02 1.91e+00 2.74e-01 5.39e+01 angle pdb=" C GLU M 47 " pdb=" N ILE M 48 " pdb=" CA ILE M 48 " ideal model delta sigma weight residual 123.00 141.48 -18.48 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C GLU K 47 " pdb=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 123.00 141.47 -18.47 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C TYR F 88 " pdb=" CA TYR F 88 " pdb=" CB TYR F 88 " ideal model delta sigma weight residual 109.83 103.87 5.96 9.90e-01 1.02e+00 3.62e+01 angle pdb=" CA GLU K 47 " pdb=" C GLU K 47 " pdb=" N ILE K 48 " ideal model delta sigma weight residual 119.01 126.49 -7.48 1.38e+00 5.25e-01 2.94e+01 ... (remaining 27724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 9471 35.58 - 71.16: 1300 71.16 - 106.74: 13 106.74 - 142.32: 1 142.32 - 177.90: 2 Dihedral angle restraints: 10787 sinusoidal: 6196 harmonic: 4591 Sorted by residual: dihedral pdb=" CA TRP K 22 " pdb=" C TRP K 22 " pdb=" N PRO K 23 " pdb=" CA PRO K 23 " ideal model delta harmonic sigma weight residual -180.00 -106.89 -73.11 0 5.00e+00 4.00e-02 2.14e+02 dihedral pdb=" CA TRP M 22 " pdb=" C TRP M 22 " pdb=" N PRO M 23 " pdb=" CA PRO M 23 " ideal model delta harmonic sigma weight residual -180.00 -106.90 -73.10 0 5.00e+00 4.00e-02 2.14e+02 dihedral pdb=" CA GLN F 27 " pdb=" C GLN F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta harmonic sigma weight residual 180.00 115.38 64.62 0 5.00e+00 4.00e-02 1.67e+02 ... (remaining 10784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2424 0.071 - 0.142: 588 0.142 - 0.213: 88 0.213 - 0.284: 13 0.284 - 0.354: 4 Chirality restraints: 3117 Sorted by residual: chirality pdb=" CB VAL F 43 " pdb=" CA VAL F 43 " pdb=" CG1 VAL F 43 " pdb=" CG2 VAL F 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB ILE M 48 " pdb=" CA ILE M 48 " pdb=" CG1 ILE M 48 " pdb=" CG2 ILE M 48 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE K 48 " pdb=" CA ILE K 48 " pdb=" CG1 ILE K 48 " pdb=" CG2 ILE K 48 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 3114 not shown) Planarity restraints: 2519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP K 22 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO K 23 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO K 23 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 23 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.025 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE G 25 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP M 22 " 0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO M 23 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO M 23 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO M 23 " 0.044 5.00e-02 4.00e+02 ... (remaining 2516 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2971 2.76 - 3.29: 15511 3.29 - 3.83: 33195 3.83 - 4.36: 42752 4.36 - 4.90: 63067 Nonbonded interactions: 157496 Sorted by model distance: nonbonded pdb=" OG1 THR F 82 " pdb=" O MET F 84 " model vdw 2.220 2.440 nonbonded pdb=" OP1 DG J 125 " pdb=" O LEU N 73 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.285 2.440 nonbonded pdb=" OE2 GLU K 186 " pdb=" O2' SAM K 500 " model vdw 2.302 2.440 nonbonded pdb=" OE2 GLU M 186 " pdb=" O2' SAM M 500 " model vdw 2.303 2.440 ... (remaining 157491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'M' and (resid 5 through 330 or resid 500)) } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 40 5.16 5 C 10853 2.51 5 N 3399 2.21 5 O 4051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 5.890 Check model and map are aligned: 0.280 Process input model: 54.290 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.190 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:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.012 0.111 19592 Z= 0.729 Angle : 1.111 18.479 27729 Z= 0.609 Chirality : 0.064 0.354 3117 Planarity : 0.008 0.081 2519 Dihedral : 22.719 177.902 7821 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.31 % Favored : 94.30 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.33 % 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: -5.11 (0.15), residues: 1545 helix: -4.25 (0.08), residues: 783 sheet: -1.05 (0.48), residues: 142 loop : -2.50 (0.20), residues: 620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 266 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 274 average time/residue: 2.0713 time to fit residues: 611.1945 Evaluate side-chains 180 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.2250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 0.0040 chunk 72 optimal weight: 0.7980 chunk 139 optimal weight: 40.0000 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 60 ASN F 18 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 24 GLN G 73 ASN G 82 HIS H 63 ASN H 84 ASN K 31 HIS K 79 ASN K 112 GLN K 113 GLN K 315 HIS E 68 GLN E 76 GLN A 68 GLN A 113 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS C 24 GLN C 82 HIS B 25 ASN M 31 HIS M 79 ASN M 117 HIS ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 315 HIS M 331 ASN N 60 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19592 Z= 0.187 Angle : 0.688 25.508 27729 Z= 0.378 Chirality : 0.040 0.173 3117 Planarity : 0.006 0.076 2519 Dihedral : 28.054 172.942 4659 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.14 % Favored : 95.53 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.20 % 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: -2.59 (0.19), residues: 1545 helix: -1.66 (0.16), residues: 786 sheet: -0.66 (0.49), residues: 140 loop : -1.86 (0.22), residues: 619 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 204 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 13 residues processed: 227 average time/residue: 1.8780 time to fit residues: 462.6087 Evaluate side-chains 195 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 1.625 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.8557 time to fit residues: 7.1926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 134 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 174 optimal weight: 40.0000 chunk 144 optimal weight: 0.5980 chunk 160 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 19592 Z= 0.238 Angle : 0.668 24.948 27729 Z= 0.365 Chirality : 0.040 0.173 3117 Planarity : 0.005 0.081 2519 Dihedral : 28.112 171.803 4659 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.66 % Favored : 95.15 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -1.25 (0.21), residues: 1545 helix: -0.33 (0.19), residues: 799 sheet: -0.30 (0.50), residues: 140 loop : -1.52 (0.24), residues: 606 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 180 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 22 residues processed: 211 average time/residue: 1.7702 time to fit residues: 407.3941 Evaluate side-chains 192 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 14 residues processed: 8 average time/residue: 0.5492 time to fit residues: 7.5399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 46 optimal weight: 0.3980 chunk 143 optimal weight: 0.0980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN A 68 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 19592 Z= 0.267 Angle : 0.672 26.678 27729 Z= 0.366 Chirality : 0.041 0.232 3117 Planarity : 0.005 0.089 2519 Dihedral : 28.159 168.578 4659 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.85 % Favored : 94.95 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.20 % 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: -0.72 (0.22), residues: 1545 helix: 0.17 (0.19), residues: 790 sheet: -0.02 (0.51), residues: 140 loop : -1.35 (0.24), residues: 615 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 181 time to evaluate : 1.909 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 29 residues processed: 210 average time/residue: 1.7703 time to fit residues: 406.2043 Evaluate side-chains 207 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.763 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 17 residues processed: 12 average time/residue: 0.7558 time to fit residues: 13.4120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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-4877/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-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-dev-4877/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-dev-4877/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: 70.4155 > 50: distance: 18 - 23: 29.018 distance: 23 - 24: 56.438 distance: 24 - 25: 52.700 distance: 24 - 27: 51.340 distance: 25 - 26: 64.688 distance: 25 - 32: 48.418 distance: 27 - 28: 33.322 distance: 32 - 33: 25.835 distance: 32 - 38: 13.904 distance: 33 - 34: 57.153 distance: 33 - 36: 41.239 distance: 34 - 35: 23.598 distance: 34 - 39: 55.225 distance: 36 - 37: 12.853 distance: 37 - 38: 48.377 distance: 39 - 40: 39.889 distance: 40 - 41: 41.158 distance: 40 - 43: 23.931 distance: 41 - 47: 39.229 distance: 43 - 44: 12.324 distance: 44 - 45: 11.773 distance: 45 - 46: 69.992 distance: 47 - 48: 40.327 distance: 48 - 49: 42.868 distance: 48 - 51: 21.175 distance: 49 - 50: 32.510 distance: 49 - 56: 14.577 distance: 51 - 52: 18.905 distance: 52 - 53: 37.385 distance: 53 - 54: 21.982 distance: 54 - 55: 11.762 distance: 56 - 57: 19.760 distance: 57 - 58: 28.056 distance: 57 - 60: 17.295 distance: 58 - 59: 21.859 distance: 58 - 64: 44.104 distance: 60 - 61: 21.493 distance: 61 - 62: 42.577 distance: 61 - 63: 29.628 distance: 64 - 65: 33.910 distance: 65 - 66: 35.771 distance: 65 - 68: 9.482 distance: 66 - 67: 39.284 distance: 68 - 69: 6.206 distance: 69 - 71: 4.268 distance: 72 - 73: 56.069 distance: 73 - 74: 41.441 distance: 73 - 76: 51.586 distance: 74 - 75: 39.160 distance: 74 - 79: 52.280 distance: 76 - 77: 55.916 distance: 76 - 78: 34.565 distance: 79 - 80: 35.357 distance: 80 - 81: 56.981 distance: 81 - 82: 29.589 distance: 81 - 90: 28.238 distance: 83 - 84: 9.150 distance: 84 - 85: 33.133 distance: 85 - 86: 14.708 distance: 86 - 87: 18.607 distance: 87 - 88: 16.843 distance: 87 - 89: 12.097 distance: 90 - 91: 39.487 distance: 90 - 96: 39.876 distance: 91 - 92: 18.147 distance: 91 - 94: 37.136 distance: 92 - 93: 39.828 distance: 92 - 97: 62.760 distance: 94 - 95: 40.023 distance: 95 - 96: 3.295 distance: 97 - 98: 22.074 distance: 98 - 99: 46.092 distance: 98 - 101: 18.789 distance: 99 - 103: 34.664 distance: 101 - 102: 26.550