Starting phenix.real_space_refine on Mon Mar 11 02:43:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/03_2024/5lmu_4080_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/03_2024/5lmu_4080.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/03_2024/5lmu_4080_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/03_2024/5lmu_4080_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/03_2024/5lmu_4080_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/03_2024/5lmu_4080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/03_2024/5lmu_4080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/03_2024/5lmu_4080_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/03_2024/5lmu_4080_neut_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1610 5.49 5 Mg 80 5.21 5 S 59 5.16 5 C 28314 2.51 5 N 10386 2.21 5 O 14744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 9": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 52": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G ARG 79": "NH1" <-> "NH2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I GLU 2": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I ARG 128": "NH1" <-> "NH2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M GLU 69": "OE1" <-> "OE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "O GLU 7": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q GLU 49": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 78": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "T GLU 50": "OE1" <-> "OE2" Residue "T GLU 51": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "X GLU 73": "OE1" <-> "OE2" Residue "X ARG 123": "NH1" <-> "NH2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X GLU 126": "OE1" <-> "OE2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "X ARG 159": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 55195 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 32548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1515, 32548 Inner-chain residues flagged as termini: ['pdbres=" G A 567 "'] Classifications: {'RNA': 1515} Modifications used: {'5*END': 2, 'rna2p_pur': 109, 'rna2p_pyr': 76, 'rna3p_pur': 746, 'rna3p_pyr': 584} Link IDs: {'rna2p': 185, 'rna3p': 1329} Chain breaks: 5 Chain: "B" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1900 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 11, 'TRANS': 222} Chain: "C" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "E" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1146 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "F" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "G" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "H" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "J" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 792 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 885 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 970 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "M" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "N" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "O" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "P" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 700 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "Q" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 823 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "R" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 598 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "S" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 655 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "V" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 208 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "X" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1336 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 Chain: "Y" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 439 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain breaks: 1 Chain: "Z" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p': 5, 'rna3p_pur': 33, 'rna3p_pyr': 28} Link IDs: {'rna2p': 11, 'rna3p': 65} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Unusual residues: {' MG': 78} Classifications: {'undetermined': 78} Link IDs: {None: 77} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36119 SG CYS D 9 86.858 103.754 146.258 1.00 50.00 S ATOM 36262 SG CYS D 26 84.045 105.190 146.650 1.00 50.00 S ATOM 36302 SG CYS D 31 86.251 107.042 145.608 1.00 50.00 S ATOM 46910 SG CYS N 24 149.570 113.831 136.169 1.00 50.00 S ATOM 46934 SG CYS N 27 147.718 111.364 134.822 1.00 50.00 S ATOM 47041 SG CYS N 40 148.804 113.416 131.937 1.00 50.00 S ATOM 47066 SG CYS N 43 146.298 114.571 134.247 1.00 50.00 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="MG MG A1678 " occ=0.63 residue: pdb="ZN ZN N 101 " occ=0.92 Time building chain proxies: 21.23, per 1000 atoms: 0.38 Number of scatterers: 55195 At special positions: 0 Unit cell: (226.46, 180.9, 207.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 59 16.00 P 1610 15.00 Mg 80 11.99 O 14744 8.00 N 10386 7.00 C 28314 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: 26.51 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 300 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 31 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " Number of angles added : 6 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 21 sheets defined 34.4% alpha, 15.0% beta 520 base pairs and 881 stacking pairs defined. Time for finding SS restraints: 24.54 Creating SS restraints... Processing helix chain 'B' and resid 44 through 65 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 108 through 121 removed outlier: 3.652A pdb=" N ALA B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 145 removed outlier: 6.454A pdb=" N ARG B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 209 through 226 Processing helix chain 'C' and resid 8 through 10 No H-bonds generated for 'chain 'C' and resid 8 through 10' Processing helix chain 'C' and resid 29 through 47 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 144 Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 72 through 84 Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.595A pdb=" N PHE D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 114 through 122 Processing helix chain 'D' and resid 150 through 153 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'E' and resid 51 through 64 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.596A pdb=" N ALA E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 141 Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'F' and resid 16 through 33 Processing helix chain 'F' and resid 52 through 54 No H-bonds generated for 'chain 'F' and resid 52 through 54' Processing helix chain 'F' and resid 69 through 81 removed outlier: 4.363A pdb=" N ASN F 73 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP F 74 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 52 removed outlier: 4.312A pdb=" N ARG G 41 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'G' and resid 93 through 110 Processing helix chain 'G' and resid 116 through 129 removed outlier: 3.551A pdb=" N ILE G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 147 Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'H' and resid 5 through 19 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 103 through 106 Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'I' and resid 33 through 36 No H-bonds generated for 'chain 'I' and resid 33 through 36' Processing helix chain 'I' and resid 41 through 45 removed outlier: 3.823A pdb=" N VAL I 44 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 53 No H-bonds generated for 'chain 'I' and resid 50 through 53' Processing helix chain 'I' and resid 70 through 88 Processing helix chain 'I' and resid 92 through 95 Processing helix chain 'J' and resid 13 through 27 Processing helix chain 'J' and resid 81 through 87 removed outlier: 4.386A pdb=" N MET J 86 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing helix chain 'K' and resid 58 through 75 removed outlier: 3.727A pdb=" N TYR K 75 " --> pdb=" O LYS K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 101 Processing helix chain 'L' and resid 7 through 12 Processing helix chain 'L' and resid 117 through 120 Processing helix chain 'M' and resid 15 through 21 removed outlier: 3.612A pdb=" N TYR M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 37 removed outlier: 3.743A pdb=" N LYS M 31 " --> pdb=" O LYS M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 63 removed outlier: 3.595A pdb=" N LEU M 56 " --> pdb=" O GLU M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 83 Processing helix chain 'M' and resid 87 through 94 Processing helix chain 'M' and resid 108 through 111 No H-bonds generated for 'chain 'M' and resid 108 through 111' Processing helix chain 'N' and resid 43 through 50 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 Processing helix chain 'O' and resid 51 through 73 Processing helix chain 'O' and resid 75 through 85 Processing helix chain 'P' and resid 53 through 62 Processing helix chain 'P' and resid 68 through 77 Processing helix chain 'Q' and resid 82 through 98 removed outlier: 3.753A pdb=" N TYR Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU Q 96 " --> pdb=" O ARG Q 92 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER Q 97 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU Q 98 " --> pdb=" O ASN Q 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 40 No H-bonds generated for 'chain 'R' and resid 37 through 40' Processing helix chain 'R' and resid 53 through 56 No H-bonds generated for 'chain 'R' and resid 53 through 56' Processing helix chain 'R' and resid 60 through 76 Processing helix chain 'S' and resid 71 through 73 No H-bonds generated for 'chain 'S' and resid 71 through 73' Processing helix chain 'T' and resid 13 through 46 removed outlier: 3.877A pdb=" N GLU T 46 " --> pdb=" O GLN T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 68 Processing helix chain 'T' and resid 76 through 93 Processing helix chain 'V' and resid 10 through 15 Processing helix chain 'X' and resid 31 through 41 Processing helix chain 'X' and resid 62 through 77 Processing helix chain 'X' and resid 96 through 112 Processing helix chain 'X' and resid 129 through 143 Processing sheet with id= A, first strand: chain 'B' and resid 69 through 71 Processing sheet with id= B, first strand: chain 'C' and resid 55 through 59 removed outlier: 6.896A pdb=" N ASN C 102 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL C 70 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLN C 104 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 164 through 171 Processing sheet with id= D, first strand: chain 'D' and resid 126 through 128 Processing sheet with id= E, first strand: chain 'E' and resid 66 through 68 removed outlier: 3.940A pdb=" N GLN E 20 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 80 through 82 Processing sheet with id= G, first strand: chain 'F' and resid 44 through 47 removed outlier: 4.168A pdb=" N GLY F 44 " --> pdb=" O PHE F 60 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 73 through 80 Processing sheet with id= I, first strand: chain 'H' and resid 23 through 27 Processing sheet with id= J, first strand: chain 'H' and resid 82 through 85 Processing sheet with id= K, first strand: chain 'I' and resid 3 through 10 Processing sheet with id= L, first strand: chain 'J' and resid 94 through 96 removed outlier: 3.798A pdb=" N GLY J 10 " --> pdb=" O HIS J 68 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'J' and resid 43 through 50 Processing sheet with id= N, first strand: chain 'K' and resid 39 through 43 removed outlier: 6.585A pdb=" N ILE K 32 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP K 42 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL K 30 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N SER K 79 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA K 19 " --> pdb=" O SER K 79 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP K 81 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE K 21 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE K 83 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA K 23 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG K 85 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'L' and resid 82 through 85 removed outlier: 6.709A pdb=" N LYS L 57 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL L 40 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL L 55 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR L 42 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ARG L 53 " --> pdb=" O THR L 42 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'P' and resid 2 through 8 removed outlier: 6.490A pdb=" N VAL P 21 " --> pdb=" O LYS P 35 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LYS P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'Q' and resid 71 through 73 removed outlier: 15.382A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.625A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Q' and resid 55 through 58 removed outlier: 5.845A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU Q 76 " --> pdb=" O GLU Q 58 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S' and resid 31 through 33 Processing sheet with id= T, first strand: chain 'X' and resid 28 through 30 removed outlier: 3.603A pdb=" N MET X 29 " --> pdb=" O VAL X 16 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL X 19 " --> pdb=" O PRO X 55 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA X 57 " --> pdb=" O VAL X 19 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY X 49 " --> pdb=" O VAL X 56 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG X 58 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU X 47 " --> pdb=" O ARG X 58 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 85 through 91 removed outlier: 6.079A pdb=" N LYS X 115 " --> pdb=" O LYS X 86 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE X 88 " --> pdb=" O LYS X 115 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS X 117 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE X 90 " --> pdb=" O LYS X 117 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR X 119 " --> pdb=" O PHE X 90 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET X 152 " --> pdb=" O LEU X 164 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA X 166 " --> pdb=" O VAL X 150 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL X 150 " --> pdb=" O ALA X 166 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1395 hydrogen bonds 2398 hydrogen bond angles 0 basepair planarities 520 basepair parallelities 881 stacking parallelities Total time for adding SS restraints: 38.46 Time building geometry restraints manager: 28.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6384 1.32 - 1.45: 25137 1.45 - 1.57: 24722 1.57 - 1.70: 3215 1.70 - 1.82: 103 Bond restraints: 59561 Sorted by residual: bond pdb=" C4 5MU Z 54 " pdb=" C5 5MU Z 54 " ideal model delta sigma weight residual 1.802 1.490 0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" N1 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.635 1.360 0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" C5 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.155 1.404 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" N3 5MU Z 54 " pdb=" C4 5MU Z 54 " ideal model delta sigma weight residual 1.182 1.341 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C2 4SU Z 8 " pdb=" N3 4SU Z 8 " ideal model delta sigma weight residual 1.498 1.350 0.148 2.00e-02 2.50e+03 5.44e+01 ... (remaining 59556 not shown) Histogram of bond angle deviations from ideal: 83.86 - 94.55: 1 94.55 - 105.24: 7498 105.24 - 115.94: 42789 115.94 - 126.63: 33438 126.63 - 137.32: 4647 Bond angle restraints: 88373 Sorted by residual: angle pdb=" N GLU X 4 " pdb=" CA GLU X 4 " pdb=" CB GLU X 4 " ideal model delta sigma weight residual 110.95 83.86 27.09 1.73e+00 3.34e-01 2.45e+02 angle pdb=" O3' G A 266 " pdb=" C3' G A 266 " pdb=" C2' G A 266 " ideal model delta sigma weight residual 109.50 126.87 -17.37 1.50e+00 4.44e-01 1.34e+02 angle pdb=" O3' C A1145 " pdb=" C3' C A1145 " pdb=" C2' C A1145 " ideal model delta sigma weight residual 109.50 125.58 -16.08 1.50e+00 4.44e-01 1.15e+02 angle pdb=" O3' U A1498 " pdb=" C3' U A1498 " pdb=" C2' U A1498 " ideal model delta sigma weight residual 109.50 124.96 -15.46 1.50e+00 4.44e-01 1.06e+02 angle pdb=" C GLU X 4 " pdb=" CA GLU X 4 " pdb=" CB GLU X 4 " ideal model delta sigma weight residual 111.23 96.78 14.45 1.42e+00 4.96e-01 1.04e+02 ... (remaining 88368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 32520 35.83 - 71.66: 5299 71.66 - 107.48: 635 107.48 - 143.31: 22 143.31 - 179.14: 52 Dihedral angle restraints: 38528 sinusoidal: 31210 harmonic: 7318 Sorted by residual: dihedral pdb=" N GLU X 4 " pdb=" C GLU X 4 " pdb=" CA GLU X 4 " pdb=" CB GLU X 4 " ideal model delta harmonic sigma weight residual 122.80 87.21 35.59 0 2.50e+00 1.60e-01 2.03e+02 dihedral pdb=" C GLU X 4 " pdb=" N GLU X 4 " pdb=" CA GLU X 4 " pdb=" CB GLU X 4 " ideal model delta harmonic sigma weight residual -122.60 -94.01 -28.59 0 2.50e+00 1.60e-01 1.31e+02 dihedral pdb=" C5' U A 560 " pdb=" C4' U A 560 " pdb=" C3' U A 560 " pdb=" O3' U A 560 " ideal model delta sinusoidal sigma weight residual 147.00 66.87 80.13 1 8.00e+00 1.56e-02 1.24e+02 ... (remaining 38525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 10144 0.214 - 0.427: 887 0.427 - 0.641: 30 0.641 - 0.854: 19 0.854 - 1.068: 3 Chirality restraints: 11083 Sorted by residual: chirality pdb=" C3' G A 181 " pdb=" C4' G A 181 " pdb=" O3' G A 181 " pdb=" C2' G A 181 " both_signs ideal model delta sigma weight residual False -2.74 -1.68 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" C3' A A 792 " pdb=" C4' A A 792 " pdb=" O3' A A 792 " pdb=" C2' A A 792 " both_signs ideal model delta sigma weight residual False -2.74 -1.81 -0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" C3' U A1498 " pdb=" C4' U A1498 " pdb=" O3' U A1498 " pdb=" C2' U A1498 " both_signs ideal model delta sigma weight residual False -2.74 -1.83 -0.91 2.00e-01 2.50e+01 2.07e+01 ... (remaining 11080 not shown) Planarity restraints: 5227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' G7M Z 46 " -0.112 2.00e-02 2.50e+03 4.46e-01 4.47e+03 pdb=" C4' G7M Z 46 " -0.382 2.00e-02 2.50e+03 pdb=" O4' G7M Z 46 " -0.238 2.00e-02 2.50e+03 pdb=" C3' G7M Z 46 " 0.551 2.00e-02 2.50e+03 pdb=" O3' G7M Z 46 " 0.447 2.00e-02 2.50e+03 pdb=" C2' G7M Z 46 " 0.233 2.00e-02 2.50e+03 pdb=" O2' G7M Z 46 " -0.808 2.00e-02 2.50e+03 pdb=" C1' G7M Z 46 " -0.242 2.00e-02 2.50e+03 pdb=" N9 G7M Z 46 " 0.550 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 4SU Z 8 " -0.284 2.00e-02 2.50e+03 4.43e-01 4.42e+03 pdb=" C4' 4SU Z 8 " 0.402 2.00e-02 2.50e+03 pdb=" O4' 4SU Z 8 " 0.738 2.00e-02 2.50e+03 pdb=" C3' 4SU Z 8 " -0.486 2.00e-02 2.50e+03 pdb=" O3' 4SU Z 8 " -0.090 2.00e-02 2.50e+03 pdb=" C2' 4SU Z 8 " -0.377 2.00e-02 2.50e+03 pdb=" O2' 4SU Z 8 " 0.410 2.00e-02 2.50e+03 pdb=" C1' 4SU Z 8 " 0.279 2.00e-02 2.50e+03 pdb=" N1 4SU Z 8 " -0.593 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC Z 32 " -0.033 2.00e-02 2.50e+03 4.36e-01 4.27e+03 pdb=" C4' OMC Z 32 " 0.401 2.00e-02 2.50e+03 pdb=" O4' OMC Z 32 " 0.407 2.00e-02 2.50e+03 pdb=" C3' OMC Z 32 " -0.561 2.00e-02 2.50e+03 pdb=" O3' OMC Z 32 " -0.305 2.00e-02 2.50e+03 pdb=" C2' OMC Z 32 " -0.298 2.00e-02 2.50e+03 pdb=" O2' OMC Z 32 " 0.702 2.00e-02 2.50e+03 pdb=" C1' OMC Z 32 " 0.259 2.00e-02 2.50e+03 pdb=" N1 OMC Z 32 " -0.571 2.00e-02 2.50e+03 ... (remaining 5224 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 39 2.01 - 2.73: 5769 2.73 - 3.46: 81072 3.46 - 4.18: 188088 4.18 - 4.90: 247672 Nonbonded interactions: 522640 Sorted by model distance: nonbonded pdb=" O LYS X 3 " pdb=" NH1 ARG X 66 " model vdw 1.289 2.520 nonbonded pdb=" OP1 C A 578 " pdb="MG MG A1668 " model vdw 1.364 2.170 nonbonded pdb=" OP2 G A 597 " pdb="MG MG A1634 " model vdw 1.368 2.170 nonbonded pdb=" OP2 A A 195 " pdb="MG MG A1609 " model vdw 1.370 2.170 nonbonded pdb=" OP2 C A 352 " pdb="MG MG A1639 " model vdw 1.416 2.170 ... (remaining 522635 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=0.63 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.030 Extract box with map and model: 5.910 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 159.550 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.008 0.312 59561 Z= 0.502 Angle : 1.439 27.088 88373 Z= 0.958 Chirality : 0.121 1.068 11083 Planarity : 0.016 0.446 5227 Dihedral : 27.089 179.138 33824 Min Nonbonded Distance : 1.289 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 3.75 % Allowed : 12.01 % Favored : 84.24 % Rotamer: Outliers : 25.30 % Allowed : 19.49 % Favored : 55.20 % Cbeta Deviations : 1.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.08 % 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: -2.57 (0.15), residues: 2506 helix: 0.15 (0.14), residues: 986 sheet: -1.89 (0.25), residues: 367 loop : -3.44 (0.14), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP P 59 HIS 0.010 0.002 HIS G 153 PHE 0.019 0.003 PHE R 81 TYR 0.031 0.003 TYR L 120 ARG 0.026 0.002 ARG Q 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1587 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 540 poor density : 1047 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7639 (mt) REVERT: B 51 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7509 (mt) REVERT: B 75 LYS cc_start: 0.8404 (tttt) cc_final: 0.7420 (ptpp) REVERT: B 83 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6906 (ttm) REVERT: B 132 LYS cc_start: 0.6319 (mptt) cc_final: 0.6007 (mmtt) REVERT: B 172 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7992 (mt) REVERT: B 200 ILE cc_start: 0.8003 (mp) cc_final: 0.7718 (mt) REVERT: C 6 HIS cc_start: 0.8405 (t70) cc_final: 0.8136 (t-90) REVERT: C 27 LYS cc_start: 0.8038 (mptt) cc_final: 0.7469 (mmmm) REVERT: C 57 ILE cc_start: 0.8967 (mt) cc_final: 0.8557 (mm) REVERT: C 94 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7914 (tt) REVERT: C 107 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6878 (pp30) REVERT: C 111 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8630 (tp) REVERT: C 119 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6474 (ttm110) REVERT: C 139 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7762 (tp-100) REVERT: D 4 TYR cc_start: 0.7246 (t80) cc_final: 0.6218 (t80) REVERT: D 13 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6692 (mtp85) REVERT: D 42 GLN cc_start: 0.8467 (mt0) cc_final: 0.8075 (tt0) REVERT: D 77 ASN cc_start: 0.8554 (m-40) cc_final: 0.8354 (m110) REVERT: D 81 GLU cc_start: 0.7041 (tt0) cc_final: 0.6765 (tt0) REVERT: D 205 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7637 (mt-10) REVERT: E 12 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8880 (tp) REVERT: E 13 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8317 (pt) REVERT: E 20 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7342 (tp40) REVERT: E 66 MET cc_start: 0.7961 (mmm) cc_final: 0.6879 (mmt) REVERT: E 121 LYS cc_start: 0.9302 (tptt) cc_final: 0.9063 (tptm) REVERT: E 129 ILE cc_start: 0.9080 (mp) cc_final: 0.8862 (mp) REVERT: E 130 ASN cc_start: 0.8257 (m-40) cc_final: 0.8041 (m-40) REVERT: E 136 MET cc_start: 0.8564 (mmm) cc_final: 0.8251 (mmm) REVERT: E 137 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7919 (tm-30) REVERT: E 142 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8435 (mt) REVERT: F 11 ASN cc_start: 0.8871 (t0) cc_final: 0.7325 (t0) REVERT: F 39 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8027 (ptpp) REVERT: F 77 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7814 (ttt-90) REVERT: F 88 VAL cc_start: 0.8548 (t) cc_final: 0.8334 (t) REVERT: F 89 MET cc_start: 0.7873 (ttt) cc_final: 0.7627 (ttp) REVERT: F 98 LEU cc_start: 0.7870 (mt) cc_final: 0.7178 (pp) REVERT: G 33 ASP cc_start: 0.8006 (m-30) cc_final: 0.7498 (m-30) REVERT: G 60 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8263 (ptmm) REVERT: G 75 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.7867 (m) REVERT: G 137 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7782 (tptp) REVERT: G 151 TYR cc_start: 0.8518 (m-80) cc_final: 0.8158 (m-80) REVERT: G 156 TRP cc_start: 0.6831 (t-100) cc_final: 0.5829 (t-100) REVERT: H 2 LEU cc_start: 0.8171 (tt) cc_final: 0.7531 (tt) REVERT: H 9 MET cc_start: 0.8393 (ttp) cc_final: 0.7718 (tmm) REVERT: H 10 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9204 (mt) REVERT: H 29 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8400 (p) REVERT: H 85 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8018 (tmt-80) REVERT: H 87 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8561 (p) REVERT: H 92 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7821 (mtt90) REVERT: H 103 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7848 (p) REVERT: H 134 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7385 (pt) REVERT: I 4 TYR cc_start: 0.7695 (m-80) cc_final: 0.7246 (m-80) REVERT: I 36 TYR cc_start: 0.8233 (t80) cc_final: 0.7769 (t80) REVERT: I 48 GLU cc_start: 0.6559 (tp30) cc_final: 0.5532 (mm-30) REVERT: I 88 TYR cc_start: 0.7024 (t80) cc_final: 0.6751 (t80) REVERT: I 91 ASP cc_start: 0.8013 (m-30) cc_final: 0.7631 (m-30) REVERT: I 111 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7074 (ttt-90) REVERT: I 118 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7963 (pttp) REVERT: I 124 GLN cc_start: 0.9245 (tm130) cc_final: 0.8519 (tm-30) REVERT: I 125 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7725 (p90) REVERT: I 128 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7467 (ptm-80) REVERT: J 4 ILE cc_start: 0.8508 (mp) cc_final: 0.7988 (mp) REVERT: J 9 ARG cc_start: 0.7998 (ptp-110) cc_final: 0.7776 (mtm-85) REVERT: J 19 SER cc_start: 0.9125 (t) cc_final: 0.8786 (t) REVERT: J 47 PHE cc_start: 0.8905 (m-80) cc_final: 0.8633 (m-80) REVERT: J 54 PHE cc_start: 0.8899 (t80) cc_final: 0.8636 (t80) REVERT: J 57 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6591 (tptp) REVERT: J 85 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5934 (mt) REVERT: K 48 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.8612 (mp) REVERT: K 54 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8071 (mtm-85) REVERT: K 62 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: K 95 ILE cc_start: 0.8497 (mt) cc_final: 0.8202 (mt) REVERT: L 7 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9057 (mp) REVERT: L 8 ASN cc_start: 0.7998 (t0) cc_final: 0.7546 (t0) REVERT: L 17 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7429 (ttmt) REVERT: L 67 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8966 (p) REVERT: L 86 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7871 (ttp80) REVERT: L 98 TYR cc_start: 0.8957 (m-80) cc_final: 0.8537 (m-10) REVERT: L 114 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7972 (mptt) REVERT: M 15 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8104 (t) REVERT: M 40 ASN cc_start: 0.8259 (t0) cc_final: 0.7602 (p0) REVERT: M 48 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7527 (mt) REVERT: M 54 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8238 (p) REVERT: M 74 VAL cc_start: 0.8723 (t) cc_final: 0.8487 (p) REVERT: M 102 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8303 (ptm160) REVERT: N 18 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8857 (t) REVERT: O 84 LYS cc_start: 0.7885 (tttt) cc_final: 0.7434 (mtpp) REVERT: P 23 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8250 (p0) REVERT: P 33 ILE cc_start: 0.8881 (mp) cc_final: 0.8585 (mt) REVERT: P 42 ARG cc_start: 0.8315 (mtm110) cc_final: 0.8110 (mtp85) REVERT: Q 2 PRO cc_start: 0.7510 (Cg_endo) cc_final: 0.7173 (Cg_exo) REVERT: Q 7 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8295 (p) REVERT: Q 34 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9136 (pttt) REVERT: Q 38 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7868 (ttm-80) REVERT: Q 46 ASP cc_start: 0.7426 (t0) cc_final: 0.7179 (p0) REVERT: Q 51 TYR cc_start: 0.7799 (m-80) cc_final: 0.7171 (m-80) REVERT: Q 63 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8291 (ptt90) REVERT: Q 71 PHE cc_start: 0.8878 (m-80) cc_final: 0.8661 (m-80) REVERT: Q 75 ARG cc_start: 0.7576 (ptt90) cc_final: 0.6156 (ptt90) REVERT: Q 88 TYR cc_start: 0.8291 (t80) cc_final: 0.7950 (t80) REVERT: S 13 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6928 (p0) REVERT: S 70 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7678 (mptt) REVERT: S 74 PHE cc_start: 0.8197 (m-80) cc_final: 0.7868 (m-10) REVERT: S 79 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8814 (m) REVERT: T 56 MET cc_start: 0.7479 (tmm) cc_final: 0.7268 (tmm) REVERT: T 71 THR cc_start: 0.8737 (m) cc_final: 0.8479 (m) REVERT: T 75 ASN cc_start: 0.7087 (OUTLIER) cc_final: 0.6525 (t0) REVERT: V 3 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8488 (mmtm) REVERT: V 13 ILE cc_start: 0.8889 (mt) cc_final: 0.8626 (mt) REVERT: V 25 LYS cc_start: 0.5577 (OUTLIER) cc_final: 0.5299 (ptpt) REVERT: X 24 LYS cc_start: 0.1938 (OUTLIER) cc_final: 0.1648 (mtmt) REVERT: X 64 LYS cc_start: 0.1241 (OUTLIER) cc_final: 0.0737 (ptpp) outliers start: 540 outliers final: 108 residues processed: 1309 average time/residue: 0.6846 time to fit residues: 1386.5013 Evaluate side-chains 847 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 683 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 125 TYR Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 116 HIS Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 59 ARG Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain L residue 114 LYS Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 69 GLU Chi-restraints excluded: chain M residue 102 ARG Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 41 ARG Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 34 LYS Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain R residue 19 LYS Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 29 ARG Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 75 ASN Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain V residue 3 LYS Chi-restraints excluded: chain V residue 25 LYS Chi-restraints excluded: chain X residue 24 LYS Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 64 LYS Chi-restraints excluded: chain X residue 101 THR Chi-restraints excluded: chain X residue 150 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 62.4516 > 50: distance: 14 - 135: 31.067 distance: 17 - 132: 20.498 distance: 56 - 61: 17.115 distance: 61 - 62: 29.356 distance: 62 - 63: 28.540 distance: 63 - 64: 38.646 distance: 63 - 65: 42.219 distance: 65 - 66: 25.216 distance: 66 - 67: 15.247 distance: 66 - 69: 22.850 distance: 67 - 68: 36.916 distance: 67 - 75: 41.858 distance: 69 - 70: 41.154 distance: 70 - 71: 18.952 distance: 70 - 72: 19.867 distance: 71 - 73: 18.806 distance: 72 - 74: 8.003 distance: 73 - 74: 12.901 distance: 75 - 76: 55.886 distance: 76 - 77: 31.224 distance: 76 - 79: 35.739 distance: 77 - 78: 30.631 distance: 77 - 83: 37.975 distance: 79 - 80: 21.097 distance: 80 - 81: 26.578 distance: 80 - 82: 32.480 distance: 83 - 84: 47.273 distance: 84 - 85: 24.689 distance: 84 - 87: 53.624 distance: 85 - 86: 57.933 distance: 85 - 91: 37.359 distance: 87 - 88: 61.076 distance: 88 - 89: 38.805 distance: 88 - 90: 44.333 distance: 91 - 92: 28.157 distance: 92 - 93: 28.345 distance: 92 - 95: 36.095 distance: 93 - 94: 44.373 distance: 93 - 100: 62.452 distance: 95 - 96: 27.042 distance: 96 - 97: 28.111 distance: 97 - 98: 9.212 distance: 97 - 99: 11.473 distance: 100 - 101: 30.027 distance: 101 - 102: 31.301 distance: 101 - 104: 33.702 distance: 102 - 103: 22.173 distance: 102 - 109: 18.466 distance: 104 - 105: 27.029 distance: 105 - 106: 16.051 distance: 106 - 107: 12.255 distance: 106 - 108: 6.148 distance: 109 - 110: 12.767 distance: 110 - 111: 9.475 distance: 110 - 113: 17.793 distance: 111 - 112: 14.650 distance: 111 - 119: 14.198 distance: 113 - 114: 17.448 distance: 114 - 115: 9.334 distance: 114 - 116: 14.713 distance: 115 - 117: 6.201 distance: 116 - 118: 7.544 distance: 117 - 118: 5.797 distance: 119 - 120: 20.072 distance: 120 - 121: 20.675 distance: 120 - 123: 14.027 distance: 121 - 122: 33.740 distance: 121 - 125: 35.138 distance: 123 - 124: 8.004 distance: 125 - 126: 17.411 distance: 126 - 127: 30.910 distance: 126 - 129: 30.340 distance: 127 - 128: 44.130 distance: 127 - 132: 22.348 distance: 129 - 130: 42.037 distance: 129 - 131: 35.590 distance: 132 - 133: 30.802 distance: 133 - 134: 27.528 distance: 133 - 136: 24.494 distance: 134 - 135: 23.121 distance: 134 - 139: 20.593 distance: 136 - 137: 12.881 distance: 136 - 138: 22.731