Starting phenix.real_space_refine on Fri Dec 8 19:32:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj4_33871/12_2023/7yj4_33871.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj4_33871/12_2023/7yj4_33871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj4_33871/12_2023/7yj4_33871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj4_33871/12_2023/7yj4_33871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj4_33871/12_2023/7yj4_33871.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj4_33871/12_2023/7yj4_33871.pdb" } resolution = 3.19 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= -0.003 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5726 2.51 5 N 1538 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 10": "OD1" <-> "OD2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I GLU 290": "OE1" <-> "OE2" Residue "I GLU 309": "OE1" <-> "OE2" Residue "R GLU 100": "OE1" <-> "OE2" Residue "R PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 10": "OE1" <-> "OE2" Residue "T GLU 130": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8985 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 140 Classifications: {'peptide': 20} Modifications used: {'COO': 1} Link IDs: {'TRANS': 19} Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 168 Classifications: {'peptide': 20} Modifications used: {'COO': 1} Link IDs: {'TRANS': 19} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "I" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1662 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 204} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2220 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "T" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Time building chain proxies: 5.39, per 1000 atoms: 0.60 Number of scatterers: 8985 At special positions: 0 Unit cell: (91.035, 119.952, 143.514, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1659 8.00 N 1538 7.00 C 5726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 12 " distance=2.03 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 7 " distance=2.04 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS B 19 " distance=2.03 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 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: 3.31 Conformation dependent library (CDL) restraints added in 1.9 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 38.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.922A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS A 7 " --> pdb=" O LEU A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 7' Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.689A pdb=" N LEU A 20 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 16 through 21' Processing helix chain 'B' and resid 10 through 21 removed outlier: 4.196A pdb=" N VAL B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N CYS B 19 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.892A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.626A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 31 removed outlier: 3.605A pdb=" N ASN I 22 " --> pdb=" O MET I 18 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 53 removed outlier: 3.620A pdb=" N GLN I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET I 53 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 217 removed outlier: 5.271A pdb=" N ILE I 213 " --> pdb=" O LYS I 210 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N HIS I 214 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU I 217 " --> pdb=" O HIS I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 231 No H-bonds generated for 'chain 'I' and resid 229 through 231' Processing helix chain 'I' and resid 242 through 256 Processing helix chain 'I' and resid 271 through 282 removed outlier: 3.989A pdb=" N GLU I 276 " --> pdb=" O LYS I 272 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU I 277 " --> pdb=" O ASP I 273 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS I 278 " --> pdb=" O LEU I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 298 through 311 Processing helix chain 'I' and resid 331 through 352 Processing helix chain 'R' and resid 35 through 39 removed outlier: 3.855A pdb=" N ARG R 39 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 64 removed outlier: 3.643A pdb=" N ILE R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN R 57 " --> pdb=" O GLY R 53 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU R 58 " --> pdb=" O LEU R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 103 removed outlier: 3.949A pdb=" N VAL R 80 " --> pdb=" O SER R 76 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR R 93 " --> pdb=" O GLY R 89 " (cutoff:3.500A) Proline residue: R 95 - end of helix removed outlier: 4.202A pdb=" N GLU R 100 " --> pdb=" O PHE R 96 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER R 101 " --> pdb=" O TRP R 97 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 144 removed outlier: 4.267A pdb=" N LEU R 113 " --> pdb=" O PHE R 109 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS R 114 " --> pdb=" O GLY R 110 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU R 118 " --> pdb=" O CYS R 114 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 173 removed outlier: 3.686A pdb=" N TRP R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 180 Processing helix chain 'R' and resid 200 through 213 removed outlier: 3.652A pdb=" N LEU R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 233 Processing helix chain 'R' and resid 240 through 275 removed outlier: 4.309A pdb=" N VAL R 244 " --> pdb=" O ASP R 240 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE R 260 " --> pdb=" O PHE R 256 " (cutoff:3.500A) Proline residue: R 261 - end of helix removed outlier: 4.570A pdb=" N LYS R 273 " --> pdb=" O GLY R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 288 Processing helix chain 'R' and resid 289 through 300 removed outlier: 3.513A pdb=" N VAL R 293 " --> pdb=" O TYR R 289 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU R 297 " --> pdb=" O VAL R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 310 Proline residue: R 306 - end of helix removed outlier: 3.546A pdb=" N TYR R 309 " --> pdb=" O ASN R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 324 removed outlier: 3.723A pdb=" N ARG R 317 " --> pdb=" O ARG R 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN R 318 " --> pdb=" O ARG R 314 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA R 319 " --> pdb=" O GLU R 315 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU R 320 " --> pdb=" O PRO R 316 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY R 322 " --> pdb=" O GLN R 318 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.780A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.664A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.647A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.852A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 25 removed outlier: 3.893A pdb=" N ALA T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU T 12 " --> pdb=" O ARG T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 34 Processing helix chain 'T' and resid 35 through 37 No H-bonds generated for 'chain 'T' and resid 35 through 37' Processing sheet with id=AA1, first strand: chain 'I' and resid 186 through 192 removed outlier: 3.830A pdb=" N ALA I 221 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS I 225 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE I 222 " --> pdb=" O ILE I 266 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE I 268 " --> pdb=" O ILE I 222 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE I 224 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN I 270 " --> pdb=" O PHE I 224 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL I 226 " --> pdb=" O ASN I 270 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N HIS I 323 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU I 267 " --> pdb=" O HIS I 323 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 5 through 7 Processing sheet with id=AA3, first strand: chain 'S' and resid 11 through 12 removed outlier: 7.000A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AA5, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.773A pdb=" N THR S 141 " --> pdb=" O ARG S 160 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 147 through 148 removed outlier: 3.803A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL S 226 " --> pdb=" O GLN S 179 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'T' and resid 46 through 52 removed outlier: 6.695A pdb=" N ILE T 338 " --> pdb=" O ARG T 48 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR T 50 " --> pdb=" O LEU T 336 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU T 336 " --> pdb=" O THR T 50 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE T 335 " --> pdb=" O SER T 331 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER T 331 " --> pdb=" O PHE T 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 58 through 63 removed outlier: 6.761A pdb=" N ALA T 73 " --> pdb=" O TYR T 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET T 61 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL T 71 " --> pdb=" O MET T 61 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP T 63 " --> pdb=" O LEU T 69 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU T 69 " --> pdb=" O TRP T 63 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU T 70 " --> pdb=" O TRP T 82 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER T 74 " --> pdb=" O LYS T 78 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS T 78 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU T 79 " --> pdb=" O ALA T 92 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA T 92 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE T 81 " --> pdb=" O VAL T 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 104 through 105 removed outlier: 6.278A pdb=" N CYS T 121 " --> pdb=" O GLU T 138 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU T 138 " --> pdb=" O CYS T 121 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE T 123 " --> pdb=" O SER T 136 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG T 134 " --> pdb=" O ASN T 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 146 through 151 removed outlier: 6.951A pdb=" N SER T 160 " --> pdb=" O SER T 147 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS T 149 " --> pdb=" O VAL T 158 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL T 158 " --> pdb=" O CYS T 149 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE T 151 " --> pdb=" O GLN T 156 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLN T 156 " --> pdb=" O PHE T 151 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE T 157 " --> pdb=" O TRP T 169 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR T 165 " --> pdb=" O SER T 161 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP T 170 " --> pdb=" O GLN T 176 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN T 176 " --> pdb=" O ASP T 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 191 through 192 removed outlier: 3.622A pdb=" N SER T 201 " --> pdb=" O LYS T 209 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS T 209 " --> pdb=" O SER T 201 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN T 220 " --> pdb=" O LEU T 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 229 through 234 removed outlier: 4.169A pdb=" N SER T 245 " --> pdb=" O THR T 249 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR T 249 " --> pdb=" O SER T 245 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS T 250 " --> pdb=" O TYR T 264 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET T 262 " --> pdb=" O LEU T 252 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP T 254 " --> pdb=" O GLU T 260 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU T 260 " --> pdb=" O ASP T 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 276 through 278 380 hydrogen bonds defined for protein. 1059 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: 2.58 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1449 1.31 - 1.44: 2570 1.44 - 1.57: 5071 1.57 - 1.70: 0 1.70 - 1.83: 86 Bond restraints: 9176 Sorted by residual: bond pdb=" CA THR R 121 " pdb=" C THR R 121 " ideal model delta sigma weight residual 1.524 1.422 0.102 1.24e-02 6.50e+03 6.78e+01 bond pdb=" C THR R 121 " pdb=" N VAL R 122 " ideal model delta sigma weight residual 1.335 1.260 0.075 1.23e-02 6.61e+03 3.74e+01 bond pdb=" CA ASP R 104 " pdb=" C ASP R 104 " ideal model delta sigma weight residual 1.526 1.460 0.067 1.11e-02 8.12e+03 3.64e+01 bond pdb=" CA HIS R 106 " pdb=" C HIS R 106 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.21e-02 6.83e+03 3.07e+01 bond pdb=" C THR R 121 " pdb=" O THR R 121 " ideal model delta sigma weight residual 1.236 1.179 0.058 1.16e-02 7.43e+03 2.46e+01 ... (remaining 9171 not shown) Histogram of bond angle deviations from ideal: 95.67 - 103.36: 76 103.36 - 111.05: 3469 111.05 - 118.75: 3839 118.75 - 126.44: 4910 126.44 - 134.13: 153 Bond angle restraints: 12447 Sorted by residual: angle pdb=" N THR R 323 " pdb=" CA THR R 323 " pdb=" C THR R 323 " ideal model delta sigma weight residual 113.97 100.23 13.74 1.28e+00 6.10e-01 1.15e+02 angle pdb=" N LEU R 267 " pdb=" CA LEU R 267 " pdb=" C LEU R 267 " ideal model delta sigma weight residual 112.23 100.72 11.51 1.26e+00 6.30e-01 8.34e+01 angle pdb=" N TRP R 268 " pdb=" CA TRP R 268 " pdb=" C TRP R 268 " ideal model delta sigma weight residual 111.36 102.25 9.11 1.09e+00 8.42e-01 6.98e+01 angle pdb=" N ASP R 104 " pdb=" CA ASP R 104 " pdb=" C ASP R 104 " ideal model delta sigma weight residual 108.24 95.67 12.57 1.81e+00 3.05e-01 4.82e+01 angle pdb=" N LEU R 103 " pdb=" CA LEU R 103 " pdb=" C LEU R 103 " ideal model delta sigma weight residual 110.53 102.11 8.42 1.29e+00 6.01e-01 4.26e+01 ... (remaining 12442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4836 17.93 - 35.85: 451 35.85 - 53.78: 103 53.78 - 71.70: 18 71.70 - 89.63: 7 Dihedral angle restraints: 5415 sinusoidal: 2082 harmonic: 3333 Sorted by residual: dihedral pdb=" CB CYS A 21 " pdb=" SG CYS A 21 " pdb=" SG CYS B 19 " pdb=" CB CYS B 19 " ideal model delta sinusoidal sigma weight residual 93.00 163.18 -70.18 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CD ARG B 23 " pdb=" NE ARG B 23 " pdb=" CZ ARG B 23 " pdb=" NH1 ARG B 23 " ideal model delta sinusoidal sigma weight residual 0.00 -59.47 59.47 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS A 8 " pdb=" SG CYS A 8 " pdb=" SG CYS B 7 " pdb=" CB CYS B 7 " ideal model delta sinusoidal sigma weight residual 93.00 54.62 38.38 1 1.00e+01 1.00e-02 2.07e+01 ... (remaining 5412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1286 0.077 - 0.154: 129 0.154 - 0.230: 2 0.230 - 0.307: 2 0.307 - 0.384: 3 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA THR R 121 " pdb=" N THR R 121 " pdb=" C THR R 121 " pdb=" CB THR R 121 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA PHE R 105 " pdb=" N PHE R 105 " pdb=" C PHE R 105 " pdb=" CB PHE R 105 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA THR B 14 " pdb=" N THR B 14 " pdb=" C THR B 14 " pdb=" CB THR B 14 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 1419 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 23 " 0.947 9.50e-02 1.11e+02 4.24e-01 1.09e+02 pdb=" NE ARG B 23 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG B 23 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 23 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 23 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 102 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C ALA R 102 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA R 102 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU R 103 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 266 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C THR R 266 " 0.041 2.00e-02 2.50e+03 pdb=" O THR R 266 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU R 267 " -0.014 2.00e-02 2.50e+03 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 402 2.72 - 3.27: 9102 3.27 - 3.81: 14279 3.81 - 4.35: 17413 4.35 - 4.90: 30077 Nonbonded interactions: 71273 Sorted by model distance: nonbonded pdb=" OG SER T 331 " pdb=" OD1 ASP T 333 " model vdw 2.175 2.440 nonbonded pdb=" O TYR R 284 " pdb=" OG1 THR R 288 " model vdw 2.212 2.440 nonbonded pdb=" OG SER T 97 " pdb=" OD2 ASP T 118 " model vdw 2.220 2.440 nonbonded pdb=" OG SER T 161 " pdb=" OD1 ASP T 163 " model vdw 2.222 2.440 nonbonded pdb=" O ILE T 58 " pdb=" OG SER T 316 " model vdw 2.228 2.440 ... (remaining 71268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.100 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.290 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 0.102 9176 Z= 0.265 Angle : 0.669 13.743 12447 Z= 0.398 Chirality : 0.047 0.384 1422 Planarity : 0.011 0.424 1569 Dihedral : 14.733 89.630 3248 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.49 % Favored : 94.42 % Rotamer: Outliers : 1.55 % Allowed : 0.62 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.26), residues: 1130 helix: 0.51 (0.28), residues: 360 sheet: -0.94 (0.32), residues: 275 loop : -0.82 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 200 HIS 0.002 0.001 HIS R 106 PHE 0.012 0.001 PHE T 234 TYR 0.024 0.001 TYR T 59 ARG 0.009 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 260 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 272 average time/residue: 0.2747 time to fit residues: 98.5324 Evaluate side-chains 196 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0822 time to fit residues: 1.6212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 189 HIS I 196 HIS I 305 GLN R 82 ASN R 106 HIS R 232 GLN R 263 HIS R 305 ASN S 3 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN T 110 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9176 Z= 0.215 Angle : 0.606 8.582 12447 Z= 0.313 Chirality : 0.044 0.185 1422 Planarity : 0.004 0.047 1569 Dihedral : 4.500 61.627 1248 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.24 % Allowed : 11.55 % Favored : 87.22 % 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: -0.52 (0.25), residues: 1130 helix: 0.76 (0.28), residues: 358 sheet: -0.60 (0.32), residues: 277 loop : -0.92 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 279 HIS 0.004 0.001 HIS R 263 PHE 0.018 0.002 PHE S 68 TYR 0.016 0.002 TYR B 11 ARG 0.006 0.001 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 214 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 220 average time/residue: 0.2401 time to fit residues: 70.9010 Evaluate side-chains 191 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0901 time to fit residues: 2.6332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 205 GLN ** R 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9176 Z= 0.361 Angle : 0.634 8.659 12447 Z= 0.329 Chirality : 0.046 0.207 1422 Planarity : 0.004 0.049 1569 Dihedral : 4.753 56.169 1248 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.06 % Allowed : 15.46 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1130 helix: 0.99 (0.28), residues: 347 sheet: -0.74 (0.31), residues: 287 loop : -1.02 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 36 HIS 0.008 0.001 HIS R 263 PHE 0.029 0.002 PHE R 130 TYR 0.018 0.002 TYR B 17 ARG 0.006 0.001 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 203 average time/residue: 0.2356 time to fit residues: 64.1631 Evaluate side-chains 193 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0866 time to fit residues: 2.8336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 299 HIS ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9176 Z= 0.295 Angle : 0.603 8.174 12447 Z= 0.314 Chirality : 0.044 0.167 1422 Planarity : 0.004 0.051 1569 Dihedral : 4.747 53.998 1248 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.16 % Allowed : 17.42 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1130 helix: 0.85 (0.28), residues: 358 sheet: -0.67 (0.31), residues: 285 loop : -1.03 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 36 HIS 0.004 0.001 HIS R 263 PHE 0.021 0.002 PHE R 130 TYR 0.015 0.002 TYR B 17 ARG 0.006 0.000 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 206 average time/residue: 0.2376 time to fit residues: 66.3856 Evaluate side-chains 192 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 185 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1310 time to fit residues: 2.8715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 196 HIS R 263 HIS R 299 HIS ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN T 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9176 Z= 0.223 Angle : 0.579 8.063 12447 Z= 0.300 Chirality : 0.042 0.145 1422 Planarity : 0.004 0.049 1569 Dihedral : 4.581 53.738 1248 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.93 % Allowed : 18.25 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1130 helix: 0.78 (0.27), residues: 371 sheet: -0.62 (0.31), residues: 280 loop : -1.00 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP R 107 HIS 0.003 0.001 HIS T 91 PHE 0.024 0.002 PHE S 68 TYR 0.013 0.001 TYR B 17 ARG 0.006 0.000 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 195 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 201 average time/residue: 0.2359 time to fit residues: 64.1881 Evaluate side-chains 189 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0903 time to fit residues: 2.0346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 HIS ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN T 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9176 Z= 0.224 Angle : 0.584 10.200 12447 Z= 0.301 Chirality : 0.042 0.152 1422 Planarity : 0.004 0.050 1569 Dihedral : 4.622 54.050 1248 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.86 % Allowed : 18.56 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1130 helix: 1.04 (0.28), residues: 352 sheet: -0.59 (0.32), residues: 280 loop : -0.99 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 107 HIS 0.003 0.001 HIS T 91 PHE 0.019 0.001 PHE S 68 TYR 0.013 0.001 TYR I 303 ARG 0.007 0.000 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 191 average time/residue: 0.2346 time to fit residues: 60.6292 Evaluate side-chains 192 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 181 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1141 time to fit residues: 3.5229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 108 optimal weight: 0.0030 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.0070 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 overall best weight: 0.5410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 301 ASN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9176 Z= 0.183 Angle : 0.578 9.732 12447 Z= 0.296 Chirality : 0.042 0.155 1422 Planarity : 0.004 0.049 1569 Dihedral : 4.536 54.645 1248 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.52 % Allowed : 19.18 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1130 helix: 0.90 (0.28), residues: 359 sheet: -0.51 (0.32), residues: 274 loop : -1.00 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 339 HIS 0.004 0.001 HIS R 263 PHE 0.017 0.001 PHE S 68 TYR 0.011 0.001 TYR S 59 ARG 0.007 0.000 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 189 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 191 average time/residue: 0.2311 time to fit residues: 59.8216 Evaluate side-chains 181 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0832 time to fit residues: 1.5451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.3980 chunk 32 optimal weight: 0.0570 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 301 ASN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9176 Z= 0.212 Angle : 0.608 12.008 12447 Z= 0.308 Chirality : 0.042 0.165 1422 Planarity : 0.004 0.050 1569 Dihedral : 4.479 55.134 1248 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.03 % Allowed : 20.31 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1130 helix: 0.81 (0.28), residues: 358 sheet: -0.44 (0.32), residues: 278 loop : -0.97 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 97 HIS 0.005 0.001 HIS R 263 PHE 0.016 0.001 PHE S 68 TYR 0.011 0.001 TYR S 59 ARG 0.007 0.000 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 182 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 184 average time/residue: 0.2341 time to fit residues: 58.5880 Evaluate side-chains 184 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0860 time to fit residues: 2.5434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 52 GLN I 348 ASN R 152 HIS ** R 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 301 ASN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9176 Z= 0.256 Angle : 0.624 9.292 12447 Z= 0.314 Chirality : 0.043 0.163 1422 Planarity : 0.004 0.051 1569 Dihedral : 4.544 55.372 1248 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.62 % Allowed : 20.31 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.25), residues: 1130 helix: 0.85 (0.28), residues: 358 sheet: -0.51 (0.32), residues: 272 loop : -0.97 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 97 HIS 0.005 0.001 HIS R 263 PHE 0.017 0.001 PHE S 68 TYR 0.013 0.001 TYR S 59 ARG 0.009 0.000 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 186 average time/residue: 0.2349 time to fit residues: 59.4360 Evaluate side-chains 179 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0978 time to fit residues: 1.6142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 56.0727 > 50: distance: 37 - 53: 6.576 distance: 41 - 61: 10.307 distance: 45 - 68: 14.077 distance: 48 - 53: 5.866 distance: 49 - 73: 10.766 distance: 53 - 54: 4.458 distance: 54 - 55: 3.665 distance: 54 - 57: 6.962 distance: 55 - 56: 5.774 distance: 55 - 61: 7.787 distance: 56 - 79: 5.015 distance: 57 - 58: 6.584 distance: 58 - 60: 4.949 distance: 61 - 62: 6.429 distance: 62 - 63: 6.893 distance: 62 - 65: 11.109 distance: 63 - 64: 9.998 distance: 63 - 68: 20.153 distance: 64 - 90: 12.964 distance: 65 - 66: 9.592 distance: 65 - 67: 3.826 distance: 68 - 69: 8.323 distance: 69 - 70: 18.376 distance: 69 - 72: 13.049 distance: 70 - 71: 7.779 distance: 70 - 73: 5.453 distance: 71 - 101: 26.780 distance: 73 - 74: 6.524 distance: 74 - 77: 17.286 distance: 75 - 76: 6.110 distance: 75 - 79: 6.443 distance: 76 - 109: 5.835 distance: 77 - 78: 27.178 distance: 79 - 80: 3.573 distance: 80 - 81: 11.853 distance: 80 - 83: 9.747 distance: 81 - 82: 12.097 distance: 81 - 90: 10.410 distance: 82 - 115: 9.777 distance: 83 - 84: 9.109 distance: 84 - 85: 4.512 distance: 84 - 86: 8.253 distance: 85 - 87: 4.475 distance: 86 - 88: 4.162 distance: 87 - 89: 8.319 distance: 88 - 89: 5.282 distance: 90 - 91: 11.123 distance: 91 - 92: 7.528 distance: 91 - 94: 15.041 distance: 92 - 93: 6.685 distance: 92 - 101: 7.019 distance: 94 - 95: 6.699 distance: 95 - 96: 17.596 distance: 95 - 97: 18.926 distance: 96 - 98: 10.204 distance: 97 - 99: 7.817 distance: 98 - 100: 17.615 distance: 99 - 100: 13.741 distance: 101 - 102: 8.713 distance: 102 - 103: 6.655 distance: 102 - 105: 8.372 distance: 103 - 104: 4.042 distance: 103 - 109: 5.369 distance: 105 - 106: 8.644 distance: 106 - 107: 9.154 distance: 106 - 108: 8.655 distance: 109 - 110: 5.171 distance: 110 - 111: 27.028 distance: 110 - 113: 26.388 distance: 111 - 112: 5.358 distance: 111 - 115: 32.306 distance: 113 - 114: 6.408 distance: 115 - 116: 3.520 distance: 116 - 117: 15.594 distance: 116 - 119: 22.320 distance: 117 - 118: 8.438 distance: 117 - 129: 15.428 distance: 119 - 120: 13.951 distance: 120 - 121: 16.670 distance: 120 - 122: 9.004 distance: 121 - 123: 9.375 distance: 122 - 124: 25.070 distance: 122 - 125: 20.525 distance: 123 - 124: 3.471 distance: 124 - 126: 9.490 distance: 125 - 127: 12.444 distance: 126 - 128: 18.564 distance: 127 - 128: 21.384 distance: 129 - 130: 11.176 distance: 130 - 131: 8.071 distance: 130 - 133: 9.609 distance: 131 - 132: 11.844 distance: 131 - 140: 13.879 distance: 132 - 162: 12.241 distance: 133 - 134: 7.351 distance: 134 - 135: 14.970 distance: 134 - 136: 13.319 distance: 135 - 137: 16.897 distance: 136 - 138: 8.830 distance: 137 - 139: 16.093 distance: 138 - 139: 7.269