Starting phenix.real_space_refine on Thu Nov 16 09:37:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy9_11555/11_2023/6zy9_11555_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy9_11555/11_2023/6zy9_11555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy9_11555/11_2023/6zy9_11555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy9_11555/11_2023/6zy9_11555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy9_11555/11_2023/6zy9_11555_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy9_11555/11_2023/6zy9_11555_updated.pdb" } resolution = 3.3 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= 0.004 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 9647 2.51 5 N 2513 2.21 5 O 2736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 7": "OE1" <-> "OE2" Residue "I PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 74": "OD1" <-> "OD2" Residue "I TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 95": "OD1" <-> "OD2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 132": "OD1" <-> "OD2" Residue "I ASP 145": "OD1" <-> "OD2" Residue "J TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 70": "OD1" <-> "OD2" Residue "J TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 87": "OE1" <-> "OE2" Residue "J ASP 95": "OD1" <-> "OD2" Residue "K TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 95": "OD1" <-> "OD2" Residue "K ASP 132": "OD1" <-> "OD2" Residue "K ASP 136": "OD1" <-> "OD2" Residue "K ASP 145": "OD1" <-> "OD2" Residue "K TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 136": "OD1" <-> "OD2" Residue "L PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B ASP 63": "OD1" <-> "OD2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F ASP 61": "OD1" <-> "OD2" Residue "F PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 25": "OD1" <-> "OD2" Residue "G ARG 33": "NH1" <-> "NH2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G ASP 176": "OD1" <-> "OD2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G ASP 220": "OD1" <-> "OD2" Residue "G ASP 249": "OD1" <-> "OD2" Residue "G ARG 255": "NH1" <-> "NH2" Residue "G ASP 260": "OD1" <-> "OD2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ASP 138": "OD1" <-> "OD2" Residue "E ASP 198": "OD1" <-> "OD2" Residue "E ASP 223": "OD1" <-> "OD2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 196": "NH1" <-> "NH2" Residue "H ASP 198": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 14973 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 966 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 801 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 957 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 2 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "J" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1041 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 966 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 925 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 712 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} 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: "C" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1954 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 240} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1971 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1927 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "H" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1946 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 251} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.80, per 1000 atoms: 0.52 Number of scatterers: 14973 At special positions: 0 Unit cell: (99.372, 130.806, 147.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 6 15.00 Mg 2 11.99 O 2736 8.00 N 2513 7.00 C 9647 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: 5.19 Conformation dependent library (CDL) restraints added in 2.6 seconds 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 21 sheets defined 33.6% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 4 through 23 removed outlier: 4.079A pdb=" N ILE A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'D' and resid 5 through 16 removed outlier: 3.693A pdb=" N TRP D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY D 11 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE D 12 " --> pdb=" O ILE D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 151 No H-bonds generated for 'chain 'D' and resid 148 through 151' Processing helix chain 'I' and resid 6 through 23 removed outlier: 3.547A pdb=" N VAL I 10 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 146 No H-bonds generated for 'chain 'I' and resid 143 through 146' Processing helix chain 'J' and resid 6 through 28 removed outlier: 3.712A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA J 17 " --> pdb=" O PHE J 13 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS J 27 " --> pdb=" O PHE J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 151 removed outlier: 3.518A pdb=" N LEU J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 23 removed outlier: 3.636A pdb=" N LEU K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 150 No H-bonds generated for 'chain 'K' and resid 147 through 150' Processing helix chain 'L' and resid 6 through 18 removed outlier: 3.840A pdb=" N VAL L 10 " --> pdb=" O ASN L 6 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY L 11 " --> pdb=" O GLU L 7 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA L 17 " --> pdb=" O PHE L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 151 Processing helix chain 'B' and resid 26 through 29 No H-bonds generated for 'chain 'B' and resid 26 through 29' Processing helix chain 'B' and resid 52 through 59 removed outlier: 4.358A pdb=" N LEU B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 removed outlier: 3.839A pdb=" N LYS B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 29 No H-bonds generated for 'chain 'C' and resid 26 through 29' Processing helix chain 'C' and resid 52 through 68 removed outlier: 3.670A pdb=" N LEU C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 83 No H-bonds generated for 'chain 'C' and resid 80 through 83' Processing helix chain 'F' and resid 48 through 55 removed outlier: 3.534A pdb=" N ARG F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 53 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 118 through 121 No H-bonds generated for 'chain 'F' and resid 118 through 121' Processing helix chain 'F' and resid 123 through 126 No H-bonds generated for 'chain 'F' and resid 123 through 126' Processing helix chain 'F' and resid 129 through 132 No H-bonds generated for 'chain 'F' and resid 129 through 132' Processing helix chain 'F' and resid 147 through 158 removed outlier: 3.911A pdb=" N ARG F 151 " --> pdb=" O GLY F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 192 removed outlier: 3.580A pdb=" N VAL F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 184 " --> pdb=" O MET F 180 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS F 185 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN F 191 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 208 No H-bonds generated for 'chain 'F' and resid 205 through 208' Processing helix chain 'F' and resid 240 through 243 No H-bonds generated for 'chain 'F' and resid 240 through 243' Processing helix chain 'G' and resid 48 through 55 removed outlier: 3.663A pdb=" N ARG G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 48 through 55' Processing helix chain 'G' and resid 77 through 80 No H-bonds generated for 'chain 'G' and resid 77 through 80' Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 102 through 106 removed outlier: 3.553A pdb=" N VAL G 106 " --> pdb=" O VAL G 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 102 through 106' Processing helix chain 'G' and resid 118 through 132 removed outlier: 3.709A pdb=" N SER G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL G 125 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET G 126 " --> pdb=" O HIS G 122 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 144 No H-bonds generated for 'chain 'G' and resid 142 through 144' Processing helix chain 'G' and resid 147 through 158 removed outlier: 4.088A pdb=" N ARG G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 188 removed outlier: 3.848A pdb=" N VAL G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 208 No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 240 through 243 No H-bonds generated for 'chain 'G' and resid 240 through 243' Processing helix chain 'E' and resid 11 through 29 removed outlier: 3.781A pdb=" N LYS E 15 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU E 17 " --> pdb=" O GLY E 13 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY E 24 " --> pdb=" O PHE E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 47 removed outlier: 3.969A pdb=" N VAL E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 47' Processing helix chain 'E' and resid 49 through 52 No H-bonds generated for 'chain 'E' and resid 49 through 52' Processing helix chain 'E' and resid 57 through 79 removed outlier: 3.675A pdb=" N SER E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.979A pdb=" N GLY E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 removed outlier: 4.358A pdb=" N MET E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 135 removed outlier: 3.657A pdb=" N MET E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 145 through 148 No H-bonds generated for 'chain 'E' and resid 145 through 148' Processing helix chain 'E' and resid 154 through 168 removed outlier: 3.804A pdb=" N VAL E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY E 166 " --> pdb=" O PHE E 162 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 No H-bonds generated for 'chain 'E' and resid 170 through 173' Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.628A pdb=" N SER E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA E 188 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET E 189 " --> pdb=" O PHE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 220 removed outlier: 3.699A pdb=" N THR E 212 " --> pdb=" O VAL E 208 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE E 216 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE E 219 " --> pdb=" O TRP E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 246 removed outlier: 3.648A pdb=" N SER E 232 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 245 " --> pdb=" O HIS E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 251 No H-bonds generated for 'chain 'E' and resid 248 through 251' Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'H' and resid 4 through 29 removed outlier: 3.867A pdb=" N SER H 8 " --> pdb=" O ASN H 4 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 9 " --> pdb=" O ALA H 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS H 11 " --> pdb=" O ALA H 7 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY H 24 " --> pdb=" O PHE H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 49 removed outlier: 3.856A pdb=" N VAL H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 60 removed outlier: 4.385A pdb=" N LEU H 57 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE H 58 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL H 60 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 77 removed outlier: 3.566A pdb=" N MET H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU H 70 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 97 removed outlier: 4.475A pdb=" N GLY H 88 " --> pdb=" O THR H 85 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA H 92 " --> pdb=" O MET H 89 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU H 93 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER H 94 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU H 95 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG H 97 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 125 removed outlier: 3.625A pdb=" N LEU H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY H 113 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER H 114 " --> pdb=" O GLY H 110 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA H 115 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU H 122 " --> pdb=" O ALA H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 175 removed outlier: 3.717A pdb=" N GLY H 151 " --> pdb=" O ARG H 147 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE H 153 " --> pdb=" O TRP H 149 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU H 155 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Proline residue: H 156 - end of helix removed outlier: 3.794A pdb=" N VAL H 160 " --> pdb=" O PRO H 156 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE H 167 " --> pdb=" O VAL H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 190 removed outlier: 3.686A pdb=" N TRP H 186 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER H 187 " --> pdb=" O GLY H 183 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET H 189 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 222 removed outlier: 3.528A pdb=" N VAL H 208 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE H 211 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR H 212 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE H 216 " --> pdb=" O THR H 212 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR H 222 " --> pdb=" O LEU H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 254 removed outlier: 3.541A pdb=" N THR H 238 " --> pdb=" O ALA H 234 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL H 239 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL H 240 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU H 249 " --> pdb=" O ALA H 245 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE H 251 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL H 252 " --> pdb=" O GLY H 248 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 40 through 45 removed outlier: 3.529A pdb=" N LEU A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 103 removed outlier: 3.668A pdb=" N SER A 100 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 40 through 45 removed outlier: 4.042A pdb=" N TYR D 40 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 86 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR D 72 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP D 70 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU D 85 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL D 68 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL D 63 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL D 58 " --> pdb=" O VAL D 65 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.872A pdb=" N SER D 98 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 41 through 45 removed outlier: 3.540A pdb=" N LEU I 84 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP I 70 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL I 68 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 98 through 103 removed outlier: 3.742A pdb=" N ARG I 102 " --> pdb=" O TYR I 111 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 57 through 60 removed outlier: 3.689A pdb=" N GLY I 66 " --> pdb=" O VAL I 58 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE I 60 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL I 64 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 42 through 45 Processing sheet with id= I, first strand: chain 'J' and resid 99 through 103 Processing sheet with id= J, first strand: chain 'J' and resid 58 through 60 removed outlier: 4.044A pdb=" N GLY J 66 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE J 60 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 39 through 41 removed outlier: 3.574A pdb=" N TYR K 40 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE K 86 " --> pdb=" O TYR K 40 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'K' and resid 71 through 73 Processing sheet with id= M, first strand: chain 'K' and resid 97 through 104 removed outlier: 4.566A pdb=" N GLU K 109 " --> pdb=" O SER K 104 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 43 through 45 removed outlier: 3.802A pdb=" N ALA L 44 " --> pdb=" O VAL L 82 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU L 79 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'L' and resid 84 through 86 removed outlier: 3.549A pdb=" N ARG L 67 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL L 58 " --> pdb=" O VAL L 65 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 99 through 103 removed outlier: 3.560A pdb=" N SER L 100 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.756A pdb=" N CYS B 41 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR B 73 " --> pdb=" O ILE B 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 41 through 43 removed outlier: 7.225A pdb=" N THR C 73 " --> pdb=" O ILE C 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.213A pdb=" N HIS F 214 " --> pdb=" O ALA F 38 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N MET F 40 " --> pdb=" O HIS F 214 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TRP F 216 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA F 225 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA F 219 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 165 through 167 removed outlier: 6.487A pdb=" N THR F 197 " --> pdb=" O ILE F 166 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'G' and resid 214 through 218 removed outlier: 3.853A pdb=" N HIS G 214 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N CYS G 198 " --> pdb=" O THR G 37 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE G 39 " --> pdb=" O CYS G 198 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL G 200 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY G 41 " --> pdb=" O VAL G 200 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1014 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4778 1.34 - 1.46: 3228 1.46 - 1.58: 7089 1.58 - 1.70: 10 1.70 - 1.81: 126 Bond restraints: 15231 Sorted by residual: bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" O3A ANP G 401 " pdb=" PB ANP G 401 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" N3B ANP G 401 " pdb=" PG ANP G 401 " ideal model delta sigma weight residual 1.795 1.694 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O5' ANP G 401 " pdb=" PA ANP G 401 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 15226 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.03: 465 107.03 - 113.78: 8752 113.78 - 120.53: 5808 120.53 - 127.28: 5535 127.28 - 134.04: 166 Bond angle restraints: 20726 Sorted by residual: angle pdb=" C ASP G 204 " pdb=" N VAL G 205 " pdb=" CA VAL G 205 " ideal model delta sigma weight residual 120.33 124.73 -4.40 8.00e-01 1.56e+00 3.03e+01 angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 110.71 16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" PB ANP G 401 " pdb=" N3B ANP G 401 " pdb=" PG ANP G 401 " ideal model delta sigma weight residual 126.95 110.72 16.23 3.00e+00 1.11e-01 2.93e+01 angle pdb=" C ASP G 10 " pdb=" N MET G 11 " pdb=" CA MET G 11 " ideal model delta sigma weight residual 122.46 129.52 -7.06 1.41e+00 5.03e-01 2.50e+01 angle pdb=" C ASP F 204 " pdb=" N VAL F 205 " pdb=" CA VAL F 205 " ideal model delta sigma weight residual 120.33 124.27 -3.94 8.00e-01 1.56e+00 2.42e+01 ... (remaining 20721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 8212 16.92 - 33.83: 635 33.83 - 50.75: 143 50.75 - 67.67: 24 67.67 - 84.58: 5 Dihedral angle restraints: 9019 sinusoidal: 3368 harmonic: 5651 Sorted by residual: dihedral pdb=" CA GLN C 68 " pdb=" C GLN C 68 " pdb=" N GLY C 69 " pdb=" CA GLY C 69 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLN C 22 " pdb=" C GLN C 22 " pdb=" N ASP C 23 " pdb=" CA ASP C 23 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ASP C 93 " pdb=" CB ASP C 93 " pdb=" CG ASP C 93 " pdb=" OD1 ASP C 93 " ideal model delta sinusoidal sigma weight residual -30.00 -90.53 60.53 1 2.00e+01 2.50e-03 1.22e+01 ... (remaining 9016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2123 0.060 - 0.119: 352 0.119 - 0.179: 56 0.179 - 0.238: 3 0.238 - 0.298: 4 Chirality restraints: 2538 Sorted by residual: chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C3' ANP G 401 " pdb=" C2' ANP G 401 " pdb=" C4' ANP G 401 " pdb=" O3' ANP G 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2535 not shown) Planarity restraints: 2570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 176 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO G 177 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 177 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 177 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 118 " 0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO G 119 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 119 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 119 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 155 " -0.035 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO H 156 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO H 156 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 156 " -0.029 5.00e-02 4.00e+02 ... (remaining 2567 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 469 2.72 - 3.26: 13489 3.26 - 3.81: 22772 3.81 - 4.35: 28322 4.35 - 4.90: 46551 Nonbonded interactions: 111603 Sorted by model distance: nonbonded pdb=" OG1 THR G 48 " pdb="MG MG G 402 " model vdw 2.174 2.170 nonbonded pdb=" OG1 THR F 48 " pdb="MG MG F 402 " model vdw 2.259 2.170 nonbonded pdb=" OH TYR J 40 " pdb=" OD1 ASN J 91 " model vdw 2.319 2.440 nonbonded pdb=" O SER H 86 " pdb=" OG SER H 86 " model vdw 2.331 2.440 nonbonded pdb=" O ALA E 234 " pdb=" OG1 THR E 238 " model vdw 2.338 2.440 ... (remaining 111598 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 4 through 24 or resid 40 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 69 or (resid \ 70 through 71 and (name N or name CA or name C or name O or name CB )) or resid \ 72 through 80 or (resid 81 and (name N or name CA or name C or name O or name C \ B )) or resid 82 through 88 or (resid 89 and (name N or name CA or name C or nam \ e O or name CB )) or resid 90 or (resid 91 and (name N or name CA or name C or n \ ame O or name CB )) or resid 92 through 94 or (resid 95 and (name N or name CA o \ r name C or name O or name CB )) or resid 96 through 115 or (resid 127 through 1 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 133 or (resid 134 through 135 and (name N or name CA or name C or name O or nam \ e CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C \ or name O or name CB )) or resid 139 through 142 or (resid 143 through 145 and ( \ name N or name CA or name C or name O or name CB )) or resid 146 or (resid 147 a \ nd (name N or name CA or name C or name O or name CB )) or resid 148 through 150 \ or (resid 151 and (name N or name CA or name C or name O or name CB )) or resid \ 152)) selection = (chain 'I' and (resid 4 through 24 or resid 40 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 72 or (resid \ 73 and (name N or name CA or name C or name O or name CB )) or resid 74 through \ 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or res \ id 77 through 94 or (resid 95 and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 98 or (resid 99 and (name N or name CA or name C or n \ ame O or name CB )) or resid 100 through 106 or (resid 107 and (name N or name C \ A or name C or name O or name CB )) or resid 108 through 115 or (resid 127 throu \ gh 130 and (name N or name CA or name C or name O or name CB )) or resid 131 thr \ ough 134 or (resid 135 and (name N or name CA or name C or name O or name CB )) \ or resid 136 through 142 or (resid 143 through 145 and (name N or name CA or nam \ e C or name O or name CB )) or resid 146 or (resid 147 and (name N or name CA or \ name C or name O or name CB )) or resid 148 through 150 or (resid 151 and (name \ N or name CA or name C or name O or name CB )) or resid 152)) selection = (chain 'J' and (resid 4 through 24 or resid 40 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 54 or (resid \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or res \ id 68 through 69 or (resid 70 through 71 and (name N or name CA or name C or nam \ e O or name CB )) or resid 72 or (resid 73 and (name N or name CA or name C or n \ ame O or name CB )) or resid 74 through 75 or (resid 76 and (name N or name CA o \ r name C or name O or name CB )) or resid 77 through 80 or (resid 81 and (name N \ or name CA or name C or name O or name CB )) or resid 82 through 84 or (resid 8 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 86 or (resid \ 87 and (name N or name CA or name C or name O or name CB )) or resid 88 or (res \ id 89 and (name N or name CA or name C or name O or name CB )) or resid 90 or (r \ esid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thr \ ough 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or \ resid 96 through 98 or (resid 99 and (name N or name CA or name C or name O or \ name CB )) or resid 100 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or (resid 109 and (name N or name CA or \ name C or name O or name CB )) or resid 110 through 115 or (resid 127 through 13 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 133 or (resid 134 through 135 and (name N or name CA or name C or name O or name \ CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 142 or (resid 143 through 145 and (n \ ame N or name CA or name C or name O or name CB )) or resid 146 or (resid 147 an \ d (name N or name CA or name C or name O or name CB )) or resid 148 through 150 \ or (resid 151 and (name N or name CA or name C or name O or name CB )) or resid \ 152)) selection = (chain 'K' and (resid 4 through 24 or resid 40 through 52 or (resid 53 through 5 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 56 through 6 \ 6 or (resid 67 and (name N or name CA or name C or name O or name CB )) or resid \ 68 through 69 or (resid 70 through 71 and (name N or name CA or name C or name \ O or name CB )) or resid 72 or (resid 73 and (name N or name CA or name C or nam \ e O or name CB )) or resid 74 through 80 or (resid 81 and (name N or name CA or \ name C or name O or name CB )) or resid 82 through 84 or (resid 85 and (name N o \ r name CA or name C or name O or name CB )) or resid 86 or (resid 87 and (name N \ or name CA or name C or name O or name CB )) or resid 88 or (resid 89 and (name \ N or name CA or name C or name O or name CB )) or resid 90 or (resid 91 and (na \ me N or name CA or name C or name O or name CB )) or resid 92 through 94 or (res \ id 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throu \ gh 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or r \ esid 100 through 106 or (resid 107 and (name N or name CA or name C or name O or \ name CB )) or resid 108 or (resid 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 through 115 or (resid 127 through 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 133 or (resid 1 \ 34 through 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 137 or (resid 138 and (name N or name CA or name C or name O or nam \ e CB )) or resid 139 through 142 or (resid 143 through 145 and (name N or name C \ A or name C or name O or name CB )) or resid 146 or (resid 147 and (name N or na \ me CA or name C or name O or name CB )) or resid 148 through 150 or (resid 151 a \ nd (name N or name CA or name C or name O or name CB )) or resid 152)) selection = (chain 'L' and (resid 4 through 24 or resid 40 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 72 or (resid \ 73 and (name N or name CA or name C or name O or name CB )) or resid 74 through \ 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or res \ id 77 through 88 or (resid 89 and (name N or name CA or name C or name O or name \ CB )) or resid 90 or (resid 91 and (name N or name CA or name C or name O or na \ me CB )) or resid 92 through 98 or (resid 99 and (name N or name CA or name C or \ name O or name CB )) or resid 100 through 127 or (resid 128 through 130 and (na \ me N or name CA or name C or name O or name CB )) or resid 131 through 133 or (r \ esid 134 through 135 and (name N or name CA or name C or name O or name CB )) or \ resid 136 through 137 or (resid 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 152)) } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 5 through 96 or (resid 97 and (name N or name CA or name C \ or name O or name CB )))) } ncs_group { reference = (chain 'E' and (resid 2 through 97 or (resid 98 and (name N or name CA or name C \ or name O or name CB )) or resid 99 through 257)) selection = (chain 'H' and resid 2 through 257) } ncs_group { reference = (chain 'F' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 264 or resid 401 through 402)) selection = (chain 'G' and (resid 7 through 129 or (resid 130 through 131 and (name N or nam \ e CA or name C or name O or name CB )) or resid 132 through 259 or (resid 260 an \ d (name N or name CA or name C or name O or name CB )) or resid 261 through 264 \ or resid 401 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.260 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 38.300 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 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 : 0.004 0.142 15231 Z= 0.233 Angle : 0.806 16.239 20726 Z= 0.403 Chirality : 0.047 0.298 2538 Planarity : 0.005 0.063 2570 Dihedral : 12.811 84.584 5383 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.25 % Allowed : 7.53 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.76 (0.13), residues: 1935 helix: -4.94 (0.05), residues: 713 sheet: -2.09 (0.32), residues: 220 loop : -3.37 (0.15), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 375 time to evaluate : 1.754 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 377 average time/residue: 0.3054 time to fit residues: 161.6746 Evaluate side-chains 263 residues out of total 1646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 1.700 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1231 time to fit residues: 2.7518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 ASN I 135 GLN J 91 ASN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 GLN C 9 GLN F 7 ASN F 175 GLN F 191 ASN G 57 GLN G 175 GLN E 11 HIS E 191 ASN H 241 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15231 Z= 0.277 Angle : 0.650 8.502 20726 Z= 0.325 Chirality : 0.044 0.164 2538 Planarity : 0.005 0.073 2570 Dihedral : 4.443 41.394 2108 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.34 % Allowed : 17.78 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.15), residues: 1935 helix: -3.31 (0.13), residues: 739 sheet: -1.74 (0.33), residues: 233 loop : -2.87 (0.16), residues: 963 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 265 time to evaluate : 1.707 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 27 residues processed: 292 average time/residue: 0.2770 time to fit residues: 117.2875 Evaluate side-chains 258 residues out of total 1646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 231 time to evaluate : 1.669 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.1295 time to fit residues: 8.9302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN K 91 ASN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN F 191 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15231 Z= 0.163 Angle : 0.520 7.044 20726 Z= 0.260 Chirality : 0.040 0.142 2538 Planarity : 0.004 0.059 2570 Dihedral : 4.063 40.690 2108 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.09 % Allowed : 18.92 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.17), residues: 1935 helix: -1.83 (0.17), residues: 753 sheet: -1.46 (0.33), residues: 235 loop : -2.63 (0.17), residues: 947 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 245 time to evaluate : 1.604 Fit side-chains outliers start: 33 outliers final: 14 residues processed: 256 average time/residue: 0.2649 time to fit residues: 99.3720 Evaluate side-chains 250 residues out of total 1646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 236 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1803 time to fit residues: 6.3611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 70.0669 > 50: distance: 33 - 38: 35.184 distance: 39 - 40: 17.137 distance: 40 - 41: 39.270 distance: 40 - 50: 16.801 distance: 43 - 44: 5.689 distance: 43 - 45: 26.428 distance: 45 - 47: 16.787 distance: 46 - 48: 50.363 distance: 47 - 48: 23.441 distance: 48 - 49: 40.915 distance: 50 - 51: 33.055 distance: 51 - 52: 9.386 distance: 51 - 54: 36.406 distance: 52 - 53: 12.881 distance: 52 - 57: 39.940 distance: 57 - 58: 14.620 distance: 58 - 61: 27.553 distance: 59 - 65: 39.949 distance: 61 - 62: 11.453 distance: 62 - 63: 19.734 distance: 62 - 64: 5.221 distance: 65 - 66: 34.719 distance: 66 - 69: 34.876 distance: 67 - 68: 3.983 distance: 67 - 70: 15.731 distance: 70 - 71: 14.430 distance: 71 - 72: 28.646 distance: 71 - 74: 12.281 distance: 72 - 79: 39.815 distance: 75 - 76: 19.689 distance: 76 - 77: 39.415 distance: 77 - 78: 56.916 distance: 80 - 83: 11.357 distance: 81 - 82: 13.965 distance: 81 - 87: 25.427 distance: 83 - 84: 39.655 distance: 84 - 86: 36.478 distance: 87 - 88: 42.725 distance: 88 - 91: 40.215 distance: 89 - 90: 60.385 distance: 92 - 93: 39.573 distance: 93 - 95: 23.029 distance: 95 - 97: 16.896 distance: 96 - 97: 56.008 distance: 97 - 98: 40.104 distance: 99 - 100: 39.696 distance: 100 - 101: 55.385 distance: 100 - 103: 56.838 distance: 101 - 102: 4.891 distance: 101 - 107: 42.571 distance: 103 - 104: 36.591 distance: 104 - 105: 44.498 distance: 104 - 106: 27.250 distance: 107 - 108: 29.440 distance: 108 - 109: 28.707 distance: 108 - 111: 52.203 distance: 109 - 110: 29.924 distance: 109 - 115: 38.932 distance: 111 - 112: 6.166 distance: 112 - 113: 41.134 distance: 115 - 116: 42.742 distance: 115 - 121: 41.255 distance: 116 - 119: 40.274 distance: 117 - 122: 35.612 distance: 119 - 120: 5.945 distance: 120 - 121: 39.419