Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 9 19:39:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cfw_7468/10_2023/6cfw_7468_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cfw_7468/10_2023/6cfw_7468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cfw_7468/10_2023/6cfw_7468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cfw_7468/10_2023/6cfw_7468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cfw_7468/10_2023/6cfw_7468_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cfw_7468/10_2023/6cfw_7468_updated.pdb" } resolution = 3.7 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= 0.008 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 Fe 13 7.16 5 Ni 1 6.56 5 S 105 5.16 5 C 12898 2.51 5 N 3187 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 49": "NH1" <-> "NH2" Residue "H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 440": "NH1" <-> "NH2" Residue "H ARG 457": "NH1" <-> "NH2" Residue "H ARG 487": "NH1" <-> "NH2" Residue "H ARG 494": "NH1" <-> "NH2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "I ARG 36": "NH1" <-> "NH2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 114": "NH1" <-> "NH2" Residue "M ARG 37": "NH1" <-> "NH2" Residue "M TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 127": "NH1" <-> "NH2" Residue "M ARG 225": "NH1" <-> "NH2" Residue "M PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 303": "NH1" <-> "NH2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 23": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 82": "NH1" <-> "NH2" Residue "J ARG 121": "NH1" <-> "NH2" Residue "K ARG 14": "NH1" <-> "NH2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K ARG 35": "NH1" <-> "NH2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 66": "NH1" <-> "NH2" Residue "L ARG 81": "NH1" <-> "NH2" Residue "L ARG 135": "NH1" <-> "NH2" Residue "L ARG 137": "NH1" <-> "NH2" Residue "L TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ARG 170": "NH1" <-> "NH2" Residue "L ARG 180": "NH1" <-> "NH2" Residue "L ARG 201": "NH1" <-> "NH2" Residue "L GLU 250": "OE1" <-> "OE2" Residue "L ARG 258": "NH1" <-> "NH2" Residue "L PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 315": "NH1" <-> "NH2" Residue "L ARG 328": "NH1" <-> "NH2" Residue "L ARG 333": "NH1" <-> "NH2" Residue "L ARG 380": "NH1" <-> "NH2" Residue "N ARG 36": "NH1" <-> "NH2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 68": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 19589 Number of models: 1 Model: "" Number of chains: 17 Chain: "H" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3850 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain: "G" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 866 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "D" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 579 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 811 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "M" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2468 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 15, 'TRANS': 301} Chain: "F" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1073 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "A" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1314 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 10, 'TRANS': 154} Chain: "E" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 732 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "C" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 870 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 622 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "J" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 128} Chain: "K" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1362 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 14, 'TRANS': 151} Chain: "L" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2965 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "N" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 12, 'TRANS': 108} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'NFU': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16169 SG CYS L 71 45.337 75.236 138.924 1.00 60.30 S ATOM 18577 SG CYS L 377 43.936 72.038 136.557 1.00 75.46 S ATOM 16151 SG CYS L 68 46.014 71.530 139.271 1.00 55.16 S ATOM 16169 SG CYS L 71 45.337 75.236 138.924 1.00 60.30 S ATOM 18557 SG CYS L 374 47.889 71.986 136.372 1.00 75.19 S ATOM 18577 SG CYS L 377 43.936 72.038 136.557 1.00 75.46 S Time building chain proxies: 10.05, per 1000 atoms: 0.51 Number of scatterers: 19589 At special positions: 0 Unit cell: (125.12, 109.888, 184.96, 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) Ni 1 28.00 Fe 13 26.01 S 105 16.00 O 3385 8.00 N 3187 7.00 C 12898 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.02 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 J 201 " pdb="FE3 SF4 J 201 " - pdb=" SG CYS J 35 " pdb="FE4 SF4 J 201 " - pdb=" SG CYS J 38 " pdb="FE2 SF4 J 201 " - pdb=" SG CYS J 132 " pdb="FE1 SF4 J 201 " - pdb=" SG CYS J 102 " pdb=" SF4 N 201 " pdb="FE1 SF4 N 201 " - pdb=" SG CYS N 77 " pdb="FE3 SF4 N 201 " - pdb=" SG CYS N 56 " pdb="FE4 SF4 N 201 " - pdb=" SG CYS N 80 " pdb=" SF4 N 202 " pdb="FE1 SF4 N 202 " - pdb=" SG CYS N 87 " pdb="FE4 SF4 N 202 " - pdb=" SG CYS N 52 " pdb="FE3 SF4 N 202 " - pdb=" SG CYS N 46 " Number of angles added : 30 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 8 sheets defined 53.5% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'H' and resid 9 through 15 Processing helix chain 'H' and resid 22 through 24 No H-bonds generated for 'chain 'H' and resid 22 through 24' Processing helix chain 'H' and resid 28 through 53 removed outlier: 4.526A pdb=" N ALA H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET H 35 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU H 41 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE H 42 " --> pdb=" O PHE H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 99 removed outlier: 4.144A pdb=" N LEU H 86 " --> pdb=" O LYS H 82 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET H 87 " --> pdb=" O PHE H 83 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR H 92 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE H 93 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL H 94 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER H 95 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE H 96 " --> pdb=" O THR H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 122 Processing helix chain 'H' and resid 127 through 131 Processing helix chain 'H' and resid 137 through 153 removed outlier: 4.012A pdb=" N MET H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER H 146 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL H 153 " --> pdb=" O SER H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 191 removed outlier: 3.801A pdb=" N GLY H 166 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE H 167 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS H 168 " --> pdb=" O GLU H 164 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA H 172 " --> pdb=" O LYS H 168 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU H 175 " --> pdb=" O PHE H 171 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE H 179 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU H 181 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY H 189 " --> pdb=" O ALA H 185 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 removed outlier: 4.080A pdb=" N ALA H 204 " --> pdb=" O ALA H 200 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU H 205 " --> pdb=" O VAL H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 222 removed outlier: 4.198A pdb=" N LEU H 215 " --> pdb=" O ALA H 211 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU H 217 " --> pdb=" O VAL H 213 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE H 218 " --> pdb=" O ALA H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 231 No H-bonds generated for 'chain 'H' and resid 229 through 231' Processing helix chain 'H' and resid 233 through 238 removed outlier: 3.935A pdb=" N ASP H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 249 removed outlier: 3.964A pdb=" N MET H 249 " --> pdb=" O SER H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 268 Processing helix chain 'H' and resid 277 through 297 removed outlier: 3.709A pdb=" N TRP H 282 " --> pdb=" O GLY H 278 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE H 286 " --> pdb=" O TRP H 282 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE H 287 " --> pdb=" O ILE H 283 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU H 292 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE H 293 " --> pdb=" O CYS H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 312 Processing helix chain 'H' and resid 316 through 329 removed outlier: 3.775A pdb=" N ILE H 320 " --> pdb=" O GLN H 316 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N MET H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL H 329 " --> pdb=" O GLY H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 367 removed outlier: 3.765A pdb=" N VAL H 360 " --> pdb=" O LEU H 356 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA H 361 " --> pdb=" O LEU H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 382 No H-bonds generated for 'chain 'H' and resid 379 through 382' Processing helix chain 'H' and resid 384 through 398 removed outlier: 4.119A pdb=" N ILE H 397 " --> pdb=" O GLY H 393 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL H 398 " --> pdb=" O ALA H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 419 removed outlier: 4.227A pdb=" N LEU H 411 " --> pdb=" O ALA H 407 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE H 412 " --> pdb=" O SER H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 421 through 443 removed outlier: 3.985A pdb=" N ALA H 425 " --> pdb=" O PRO H 421 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N CYS H 434 " --> pdb=" O GLY H 430 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR H 435 " --> pdb=" O THR H 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 465 through 479 removed outlier: 3.623A pdb=" N ILE H 469 " --> pdb=" O LEU H 465 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY H 478 " --> pdb=" O ILE H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 481 through 487 removed outlier: 4.276A pdb=" N ASP H 486 " --> pdb=" O TRP H 482 " (cutoff:3.500A) Processing helix chain 'H' and resid 491 through 494 No H-bonds generated for 'chain 'H' and resid 491 through 494' Processing helix chain 'H' and resid 499 through 505 Processing helix chain 'G' and resid 4 through 19 Processing helix chain 'G' and resid 26 through 45 Processing helix chain 'G' and resid 75 through 102 removed outlier: 3.736A pdb=" N ILE G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR G 101 " --> pdb=" O THR G 97 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG G 102 " --> pdb=" O VAL G 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 35 removed outlier: 4.108A pdb=" N ILE D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 59 removed outlier: 3.627A pdb=" N SER D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.674A pdb=" N ALA D 68 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 removed outlier: 4.493A pdb=" N TYR D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 30 removed outlier: 4.377A pdb=" N PHE I 10 " --> pdb=" O PRO I 7 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE I 11 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL I 13 " --> pdb=" O PHE I 10 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR I 22 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU I 24 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS I 29 " --> pdb=" O LEU I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 86 removed outlier: 4.030A pdb=" N THR I 84 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU I 85 " --> pdb=" O PHE I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 113 removed outlier: 3.715A pdb=" N LEU I 113 " --> pdb=" O VAL I 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 36 removed outlier: 4.332A pdb=" N ILE M 8 " --> pdb=" O TYR M 5 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY M 9 " --> pdb=" O GLY M 6 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE M 13 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER M 18 " --> pdb=" O ILE M 15 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER M 21 " --> pdb=" O SER M 18 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU M 22 " --> pdb=" O VAL M 19 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL M 32 " --> pdb=" O ARG M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 55 removed outlier: 4.333A pdb=" N LEU M 51 " --> pdb=" O PHE M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 80 removed outlier: 4.603A pdb=" N LEU M 76 " --> pdb=" O PRO M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 85 No H-bonds generated for 'chain 'M' and resid 83 through 85' Processing helix chain 'M' and resid 101 through 119 removed outlier: 3.885A pdb=" N ALA M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP M 111 " --> pdb=" O LEU M 107 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE M 112 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 140 removed outlier: 3.515A pdb=" N ALA M 131 " --> pdb=" O ARG M 127 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG M 132 " --> pdb=" O ILE M 128 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY M 133 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA M 135 " --> pdb=" O ALA M 131 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU M 136 " --> pdb=" O ARG M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 156 removed outlier: 4.205A pdb=" N GLY M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER M 156 " --> pdb=" O MET M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 170 removed outlier: 3.699A pdb=" N LEU M 169 " --> pdb=" O LEU M 166 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR M 170 " --> pdb=" O SER M 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 166 through 170' Processing helix chain 'M' and resid 174 through 176 No H-bonds generated for 'chain 'M' and resid 174 through 176' Processing helix chain 'M' and resid 179 through 199 removed outlier: 3.932A pdb=" N GLY M 185 " --> pdb=" O TRP M 182 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL M 187 " --> pdb=" O ALA M 184 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE M 192 " --> pdb=" O ILE M 189 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU M 199 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 249 removed outlier: 4.007A pdb=" N SER M 235 " --> pdb=" O LYS M 231 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA M 242 " --> pdb=" O GLU M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 287 removed outlier: 3.821A pdb=" N VAL M 279 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER M 280 " --> pdb=" O VAL M 276 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR M 282 " --> pdb=" O LEU M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 300 removed outlier: 4.163A pdb=" N ASN M 298 " --> pdb=" O SER M 294 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU M 299 " --> pdb=" O GLN M 295 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU M 300 " --> pdb=" O ALA M 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 294 through 300' Processing helix chain 'M' and resid 305 through 318 removed outlier: 3.652A pdb=" N GLY M 318 " --> pdb=" O LEU M 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 29 Proline residue: F 18 - end of helix removed outlier: 3.778A pdb=" N PHE F 23 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 55 removed outlier: 3.821A pdb=" N THR F 44 " --> pdb=" O GLN F 40 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 64 removed outlier: 4.105A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 83 removed outlier: 4.855A pdb=" N GLU F 74 " --> pdb=" O TYR F 70 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY F 75 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL F 80 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 141 removed outlier: 3.762A pdb=" N THR F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 17 removed outlier: 3.952A pdb=" N LEU A 13 " --> pdb=" O TRP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 54 through 57 Processing helix chain 'A' and resid 59 through 87 removed outlier: 3.845A pdb=" N ILE A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 3.926A pdb=" N LYS A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.983A pdb=" N LEU A 112 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 114 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 115 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'E' and resid 2 through 20 Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 41 through 54 removed outlier: 3.697A pdb=" N GLY E 50 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE E 51 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU E 52 " --> pdb=" O GLU E 48 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU E 53 " --> pdb=" O HIS E 49 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 63 No H-bonds generated for 'chain 'E' and resid 60 through 63' Processing helix chain 'E' and resid 69 through 88 Processing helix chain 'C' and resid 5 through 22 removed outlier: 3.719A pdb=" N LEU C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 63 removed outlier: 4.361A pdb=" N LYS C 40 " --> pdb=" O HIS C 36 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 48 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS C 60 " --> pdb=" O HIS C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 99 removed outlier: 3.841A pdb=" N MET C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA C 79 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'B' and resid 5 through 22 removed outlier: 3.648A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 21 " --> pdb=" O THR B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 51 removed outlier: 4.383A pdb=" N VAL B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 80 removed outlier: 3.619A pdb=" N ILE B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 68 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TYR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 22 No H-bonds generated for 'chain 'J' and resid 20 through 22' Processing helix chain 'J' and resid 38 through 43 Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.632A pdb=" N LEU J 80 " --> pdb=" O ASN J 77 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU J 81 " --> pdb=" O GLN J 78 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG J 82 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL J 83 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL J 86 " --> pdb=" O VAL J 83 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR J 87 " --> pdb=" O LYS J 84 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU J 88 " --> pdb=" O LEU J 85 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN J 89 " --> pdb=" O VAL J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 121 No H-bonds generated for 'chain 'J' and resid 119 through 121' Processing helix chain 'J' and resid 136 through 154 Processing helix chain 'K' and resid 7 through 14 removed outlier: 3.611A pdb=" N ARG K 14 " --> pdb=" O LYS K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 51 removed outlier: 4.144A pdb=" N ARG K 49 " --> pdb=" O MET K 45 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU K 50 " --> pdb=" O LYS K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 120 removed outlier: 3.923A pdb=" N GLU K 116 " --> pdb=" O GLN K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 168 No H-bonds generated for 'chain 'K' and resid 166 through 168' Processing helix chain 'L' and resid 48 through 52 Processing helix chain 'L' and resid 57 through 63 removed outlier: 3.776A pdb=" N MET L 61 " --> pdb=" O TYR L 57 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR L 62 " --> pdb=" O VAL L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 67 No H-bonds generated for 'chain 'L' and resid 65 through 67' Processing helix chain 'L' and resid 74 through 87 removed outlier: 3.826A pdb=" N TYR L 79 " --> pdb=" O HIS L 75 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL L 80 " --> pdb=" O ASN L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 120 removed outlier: 3.756A pdb=" N GLU L 104 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS L 109 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU L 113 " --> pdb=" O HIS L 109 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY L 119 " --> pdb=" O LEU L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 145 removed outlier: 4.641A pdb=" N GLU L 136 " --> pdb=" O TRP L 132 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG L 137 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 181 removed outlier: 3.924A pdb=" N ASP L 174 " --> pdb=" O ARG L 170 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N MET L 175 " --> pdb=" O LEU L 171 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE L 176 " --> pdb=" O ILE L 172 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS L 177 " --> pdb=" O LEU L 173 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU L 181 " --> pdb=" O LYS L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 191 removed outlier: 3.534A pdb=" N PHE L 190 " --> pdb=" O ILE L 186 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 198 No H-bonds generated for 'chain 'L' and resid 196 through 198' Processing helix chain 'L' and resid 208 through 213 Processing helix chain 'L' and resid 219 through 224 removed outlier: 4.284A pdb=" N SER L 224 " --> pdb=" O THR L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 242 No H-bonds generated for 'chain 'L' and resid 240 through 242' Processing helix chain 'L' and resid 249 through 252 No H-bonds generated for 'chain 'L' and resid 249 through 252' Processing helix chain 'L' and resid 262 through 281 removed outlier: 3.878A pdb=" N LEU L 272 " --> pdb=" O ARG L 268 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP L 277 " --> pdb=" O TRP L 273 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU L 280 " --> pdb=" O LEU L 276 " (cutoff:3.500A) Processing helix chain 'L' and resid 345 through 355 removed outlier: 3.987A pdb=" N ALA L 353 " --> pdb=" O LEU L 349 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS L 354 " --> pdb=" O PHE L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 363 through 371 removed outlier: 3.644A pdb=" N SER L 370 " --> pdb=" O VAL L 366 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE L 371 " --> pdb=" O ALA L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 375 through 377 No H-bonds generated for 'chain 'L' and resid 375 through 377' Processing helix chain 'N' and resid 7 through 15 removed outlier: 4.119A pdb=" N PHE N 15 " --> pdb=" O ILE N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 25 No H-bonds generated for 'chain 'N' and resid 23 through 25' Processing helix chain 'N' and resid 52 through 55 No H-bonds generated for 'chain 'N' and resid 52 through 55' Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 115 through 121 Processing sheet with id= A, first strand: chain 'H' and resid 58 through 60 Processing sheet with id= B, first strand: chain 'A' and resid 95 through 99 Processing sheet with id= C, first strand: chain 'J' and resid 68 through 71 removed outlier: 6.649A pdb=" N ILE J 95 " --> pdb=" O LEU J 69 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL J 71 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE J 97 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL J 127 " --> pdb=" O ALA J 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'K' and resid 21 through 24 Processing sheet with id= E, first strand: chain 'L' and resid 8 through 10 removed outlier: 3.508A pdb=" N VAL L 8 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE L 10 " --> pdb=" O ILE L 27 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE L 27 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS L 24 " --> pdb=" O LYS L 40 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN L 36 " --> pdb=" O THR L 28 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP L 30 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE L 34 " --> pdb=" O ASP L 30 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 313 through 317 removed outlier: 3.666A pdb=" N VAL L 324 " --> pdb=" O ARG L 342 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'N' and resid 39 through 41 Processing sheet with id= H, first strand: chain 'N' and resid 61 through 63 removed outlier: 3.767A pdb=" N VAL N 62 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR N 71 " --> pdb=" O VAL N 62 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 776 hydrogen bonds defined for protein. 2133 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: 5.07 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.45: 8921 1.45 - 1.75: 10934 1.75 - 2.04: 166 2.04 - 2.34: 36 2.34 - 2.64: 1 Bond restraints: 20058 Sorted by residual: bond pdb=" C2 NFU L 401 " pdb="FE NFU L 401 " ideal model delta sigma weight residual 1.940 1.826 0.114 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C1 NFU L 401 " pdb="FE NFU L 401 " ideal model delta sigma weight residual 1.939 1.825 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C ALA M 71 " pdb=" N PRO M 72 " ideal model delta sigma weight residual 1.334 1.368 -0.034 8.40e-03 1.42e+04 1.67e+01 bond pdb=" N ALA J 151 " pdb=" CA ALA J 151 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" C THR A 119 " pdb=" N PRO A 120 " ideal model delta sigma weight residual 1.334 1.407 -0.073 2.34e-02 1.83e+03 9.78e+00 ... (remaining 20053 not shown) Histogram of bond angle deviations from ideal: 70.29 - 92.22: 36 92.22 - 114.16: 12223 114.16 - 136.10: 15045 136.10 - 158.03: 0 158.03 - 179.97: 2 Bond angle restraints: 27306 Sorted by residual: angle pdb=" N PRO I 56 " pdb=" CA PRO I 56 " pdb=" CB PRO I 56 " ideal model delta sigma weight residual 103.25 110.56 -7.31 1.05e+00 9.07e-01 4.85e+01 angle pdb=" N HIS F 100 " pdb=" CA HIS F 100 " pdb=" C HIS F 100 " ideal model delta sigma weight residual 109.71 101.22 8.49 1.41e+00 5.03e-01 3.63e+01 angle pdb=" N PRO I 51 " pdb=" CA PRO I 51 " pdb=" CB PRO I 51 " ideal model delta sigma weight residual 103.25 109.49 -6.24 1.05e+00 9.07e-01 3.53e+01 angle pdb=" CA LEU H 4 " pdb=" CB LEU H 4 " pdb=" CG LEU H 4 " ideal model delta sigma weight residual 116.30 135.77 -19.47 3.50e+00 8.16e-02 3.10e+01 angle pdb=" N ASN L 298 " pdb=" CA ASN L 298 " pdb=" C ASN L 298 " ideal model delta sigma weight residual 113.43 106.43 7.00 1.26e+00 6.30e-01 3.08e+01 ... (remaining 27301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 10956 17.65 - 35.29: 675 35.29 - 52.94: 121 52.94 - 70.58: 17 70.58 - 88.23: 6 Dihedral angle restraints: 11775 sinusoidal: 4536 harmonic: 7239 Sorted by residual: dihedral pdb=" CA ASP J 92 " pdb=" C ASP J 92 " pdb=" N PRO J 93 " pdb=" CA PRO J 93 " ideal model delta harmonic sigma weight residual -180.00 -109.40 -70.60 0 5.00e+00 4.00e-02 1.99e+02 dihedral pdb=" CA ALA J 117 " pdb=" C ALA J 117 " pdb=" N PRO J 118 " pdb=" CA PRO J 118 " ideal model delta harmonic sigma weight residual -180.00 -110.58 -69.42 0 5.00e+00 4.00e-02 1.93e+02 dihedral pdb=" CA VAL K 154 " pdb=" C VAL K 154 " pdb=" N PRO K 155 " pdb=" CA PRO K 155 " ideal model delta harmonic sigma weight residual 180.00 123.71 56.29 0 5.00e+00 4.00e-02 1.27e+02 ... (remaining 11772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3085 0.143 - 0.286: 110 0.286 - 0.429: 15 0.429 - 0.572: 2 0.572 - 0.715: 6 Chirality restraints: 3218 Sorted by residual: chirality pdb="FE3 SF4 J 201 " pdb=" S1 SF4 J 201 " pdb=" S2 SF4 J 201 " pdb=" S4 SF4 J 201 " both_signs ideal model delta sigma weight residual False -10.55 -9.84 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb="FE1 SF4 N 201 " pdb=" S2 SF4 N 201 " pdb=" S3 SF4 N 201 " pdb=" S4 SF4 N 201 " both_signs ideal model delta sigma weight residual False -10.55 -9.88 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb="FE4 SF4 J 201 " pdb=" S1 SF4 J 201 " pdb=" S2 SF4 J 201 " pdb=" S3 SF4 J 201 " both_signs ideal model delta sigma weight residual False 10.55 9.93 0.63 2.00e-01 2.50e+01 9.77e+00 ... (remaining 3215 not shown) Planarity restraints: 3363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J 150 " 0.029 2.00e-02 2.50e+03 5.62e-02 3.16e+01 pdb=" C LEU J 150 " -0.097 2.00e-02 2.50e+03 pdb=" O LEU J 150 " 0.036 2.00e-02 2.50e+03 pdb=" N ALA J 151 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS J 102 " -0.088 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO J 103 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO J 103 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO J 103 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 141 " -0.086 5.00e-02 4.00e+02 1.31e-01 2.74e+01 pdb=" N PRO M 142 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO M 142 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO M 142 " -0.070 5.00e-02 4.00e+02 ... (remaining 3360 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 96 2.55 - 3.14: 14778 3.14 - 3.73: 28765 3.73 - 4.31: 37966 4.31 - 4.90: 63864 Nonbonded interactions: 145469 Sorted by model distance: nonbonded pdb=" O GLU L 250 " pdb=" O GLY L 254 " model vdw 1.968 3.040 nonbonded pdb=" N GLU L 255 " pdb=" OE1 GLU L 255 " model vdw 2.103 2.520 nonbonded pdb=" CD2 LEU L 19 " pdb=" O GLU L 21 " model vdw 2.110 3.460 nonbonded pdb=" O SER H 272 " pdb=" OG SER H 272 " model vdw 2.243 2.440 nonbonded pdb=" OG SER C 22 " pdb=" OG1 THR B 17 " model vdw 2.261 2.440 ... (remaining 145464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 5.820 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 51.130 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.010 0.114 20058 Z= 0.658 Angle : 1.270 19.474 27306 Z= 0.662 Chirality : 0.075 0.715 3218 Planarity : 0.011 0.132 3363 Dihedral : 12.048 88.231 7151 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.67 % Favored : 88.97 % Rotamer: Outliers : 1.60 % Allowed : 8.36 % Favored : 90.03 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 6.30 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.93 (0.13), residues: 2502 helix: -2.70 (0.11), residues: 1363 sheet: -2.16 (0.46), residues: 128 loop : -4.19 (0.15), residues: 1011 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 534 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 11 residues processed: 564 average time/residue: 0.3259 time to fit residues: 274.5484 Evaluate side-chains 328 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 317 time to evaluate : 2.246 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1798 time to fit residues: 6.7782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 0.7980 chunk 187 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 350 HIS G 99 ASN ** I 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 GLN M 253 GLN F 12 ASN C 26 HIS B 38 ASN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN K 25 ASN L 109 HIS L 151 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20058 Z= 0.195 Angle : 0.696 11.772 27306 Z= 0.351 Chirality : 0.043 0.215 3218 Planarity : 0.007 0.106 3363 Dihedral : 6.185 58.679 2724 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.27 % Favored : 91.53 % Rotamer: Outliers : 3.94 % Allowed : 14.83 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.17 % 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 (0.15), residues: 2502 helix: -1.05 (0.13), residues: 1349 sheet: -1.92 (0.48), residues: 119 loop : -3.79 (0.16), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 418 time to evaluate : 2.321 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 28 residues processed: 469 average time/residue: 0.2795 time to fit residues: 208.7990 Evaluate side-chains 365 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 337 time to evaluate : 2.176 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1807 time to fit residues: 12.5541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 222 optimal weight: 0.0030 chunk 76 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 89 HIS M 253 GLN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN K 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20058 Z= 0.180 Angle : 0.650 14.902 27306 Z= 0.324 Chirality : 0.042 0.361 3218 Planarity : 0.006 0.100 3363 Dihedral : 5.518 56.585 2724 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.39 % Favored : 91.45 % Rotamer: Outliers : 2.72 % Allowed : 17.74 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.16), residues: 2502 helix: -0.33 (0.14), residues: 1342 sheet: -1.94 (0.47), residues: 116 loop : -3.57 (0.17), residues: 1044 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 359 time to evaluate : 2.267 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 19 residues processed: 402 average time/residue: 0.2830 time to fit residues: 181.8491 Evaluate side-chains 349 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 330 time to evaluate : 2.167 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1782 time to fit residues: 9.4358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 225 optimal weight: 0.3980 chunk 238 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 89 HIS ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN K 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20058 Z= 0.211 Angle : 0.647 13.020 27306 Z= 0.323 Chirality : 0.043 0.396 3218 Planarity : 0.006 0.104 3363 Dihedral : 5.345 57.296 2724 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.83 % Favored : 91.05 % Rotamer: Outliers : 3.16 % Allowed : 19.49 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.94 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.17), residues: 2502 helix: -0.05 (0.14), residues: 1356 sheet: -1.71 (0.49), residues: 112 loop : -3.52 (0.17), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 353 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 31 residues processed: 395 average time/residue: 0.2837 time to fit residues: 178.7862 Evaluate side-chains 353 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 322 time to evaluate : 2.151 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1900 time to fit residues: 14.0509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 9.9990 chunk 135 optimal weight: 0.0170 chunk 3 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 165 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 89 HIS ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN L 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 20058 Z= 0.163 Angle : 0.626 13.745 27306 Z= 0.308 Chirality : 0.042 0.387 3218 Planarity : 0.006 0.110 3363 Dihedral : 5.081 55.362 2724 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.19 % Favored : 91.69 % Rotamer: Outliers : 1.56 % Allowed : 20.81 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.94 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.17), residues: 2502 helix: 0.28 (0.15), residues: 1347 sheet: -1.82 (0.47), residues: 118 loop : -3.48 (0.17), residues: 1037 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 374 time to evaluate : 2.163 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 9 residues processed: 400 average time/residue: 0.2736 time to fit residues: 176.4208 Evaluate side-chains 345 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 336 time to evaluate : 2.076 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2216 time to fit residues: 6.3185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 0.3980 chunk 215 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN J 89 GLN K 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20058 Z= 0.241 Angle : 0.658 10.876 27306 Z= 0.325 Chirality : 0.043 0.305 3218 Planarity : 0.006 0.114 3363 Dihedral : 5.098 55.991 2724 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.63 % Favored : 91.21 % Rotamer: Outliers : 1.99 % Allowed : 21.68 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.94 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.17), residues: 2502 helix: 0.32 (0.15), residues: 1359 sheet: -1.64 (0.48), residues: 112 loop : -3.38 (0.17), residues: 1031 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 341 time to evaluate : 2.427 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 21 residues processed: 366 average time/residue: 0.2814 time to fit residues: 166.7671 Evaluate side-chains 350 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 329 time to evaluate : 2.195 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1873 time to fit residues: 10.2354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 5 GLN ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 20058 Z= 0.380 Angle : 0.750 10.746 27306 Z= 0.376 Chirality : 0.047 0.268 3218 Planarity : 0.007 0.120 3363 Dihedral : 5.566 58.274 2724 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.19 % Favored : 89.57 % Rotamer: Outliers : 1.80 % Allowed : 22.12 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.17), residues: 2502 helix: 0.17 (0.14), residues: 1365 sheet: -1.56 (0.50), residues: 110 loop : -3.38 (0.17), residues: 1027 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 332 time to evaluate : 2.326 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 22 residues processed: 350 average time/residue: 0.2793 time to fit residues: 157.1181 Evaluate side-chains 327 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 305 time to evaluate : 2.218 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1864 time to fit residues: 10.7088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 162 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN L 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20058 Z= 0.198 Angle : 0.670 12.772 27306 Z= 0.332 Chirality : 0.043 0.283 3218 Planarity : 0.006 0.109 3363 Dihedral : 5.210 58.989 2724 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.59 % Favored : 91.25 % Rotamer: Outliers : 0.63 % Allowed : 23.63 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.17), residues: 2502 helix: 0.45 (0.14), residues: 1347 sheet: -1.53 (0.48), residues: 115 loop : -3.32 (0.17), residues: 1040 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 339 time to evaluate : 2.243 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 349 average time/residue: 0.2861 time to fit residues: 160.2174 Evaluate side-chains 317 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 312 time to evaluate : 2.219 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1776 time to fit residues: 4.6068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 209 optimal weight: 0.0980 chunk 145 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN K 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20058 Z= 0.243 Angle : 0.689 11.822 27306 Z= 0.343 Chirality : 0.044 0.249 3218 Planarity : 0.006 0.113 3363 Dihedral : 5.197 63.133 2724 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.27 % Favored : 90.49 % Rotamer: Outliers : 0.88 % Allowed : 24.06 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.17), residues: 2502 helix: 0.47 (0.14), residues: 1360 sheet: -1.44 (0.50), residues: 110 loop : -3.30 (0.17), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 319 time to evaluate : 2.184 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 331 average time/residue: 0.2776 time to fit residues: 147.3166 Evaluate side-chains 316 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 309 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1946 time to fit residues: 5.3343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 151 optimal weight: 20.0000 chunk 120 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 5 GLN A 80 ASN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20058 Z= 0.191 Angle : 0.661 12.390 27306 Z= 0.326 Chirality : 0.042 0.249 3218 Planarity : 0.006 0.109 3363 Dihedral : 5.011 58.582 2724 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.71 % Favored : 91.13 % Rotamer: Outliers : 0.15 % Allowed : 24.60 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.15 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.17), residues: 2502 helix: 0.63 (0.15), residues: 1356 sheet: -1.41 (0.47), residues: 118 loop : -3.31 (0.17), residues: 1028 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 329 time to evaluate : 2.368 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 331 average time/residue: 0.2896 time to fit residues: 155.5533 Evaluate side-chains 311 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 2.241 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1780 time to fit residues: 3.3468 ------------------------------------------------------------------------------- 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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 57.4526 > 50: distance: 13 - 33: 15.158 distance: 21 - 26: 8.402 distance: 22 - 38: 22.292 distance: 26 - 27: 5.183 distance: 27 - 30: 15.773 distance: 28 - 29: 19.238 distance: 28 - 33: 10.615 distance: 29 - 49: 27.024 distance: 30 - 31: 16.775 distance: 30 - 32: 10.956 distance: 33 - 34: 8.859 distance: 34 - 35: 7.677 distance: 34 - 37: 28.910 distance: 35 - 36: 9.982 distance: 35 - 38: 3.778 distance: 36 - 57: 8.567 distance: 38 - 39: 6.760 distance: 39 - 40: 27.290 distance: 39 - 42: 19.850 distance: 40 - 41: 28.884 distance: 40 - 49: 45.598 distance: 42 - 43: 14.045 distance: 43 - 44: 21.937 distance: 44 - 45: 23.859 distance: 45 - 46: 22.397 distance: 46 - 47: 16.206 distance: 49 - 50: 30.007 distance: 50 - 51: 19.360 distance: 50 - 53: 25.345 distance: 51 - 52: 9.581 distance: 51 - 57: 29.781 distance: 53 - 54: 17.160 distance: 54 - 55: 17.238 distance: 55 - 56: 29.317 distance: 57 - 58: 9.778 distance: 58 - 59: 15.195 distance: 58 - 61: 16.184 distance: 59 - 60: 16.878 distance: 59 - 66: 16.142 distance: 61 - 62: 19.518 distance: 62 - 63: 21.589 distance: 63 - 64: 4.165 distance: 63 - 65: 22.272 distance: 66 - 67: 21.115 distance: 67 - 68: 23.117 distance: 67 - 70: 19.846 distance: 68 - 69: 6.745 distance: 68 - 77: 27.327 distance: 70 - 71: 32.905 distance: 71 - 72: 23.038 distance: 72 - 73: 27.068 distance: 73 - 74: 17.753 distance: 74 - 75: 28.802 distance: 74 - 76: 27.269 distance: 77 - 78: 19.782 distance: 78 - 79: 34.677 distance: 78 - 81: 10.772 distance: 79 - 80: 16.497 distance: 79 - 88: 33.500 distance: 81 - 82: 7.619 distance: 82 - 83: 14.054 distance: 83 - 84: 14.120 distance: 84 - 85: 9.839 distance: 85 - 86: 14.991 distance: 85 - 87: 8.558 distance: 88 - 89: 13.579 distance: 89 - 90: 20.332 distance: 89 - 92: 27.337 distance: 90 - 91: 14.356 distance: 90 - 96: 31.192 distance: 92 - 93: 46.123 distance: 92 - 94: 27.753 distance: 93 - 95: 51.193 distance: 96 - 97: 22.814 distance: 97 - 98: 15.633 distance: 98 - 99: 14.450 distance: 98 - 100: 13.949 distance: 100 - 101: 18.950 distance: 100 - 106: 23.931 distance: 101 - 102: 17.709 distance: 101 - 104: 21.335 distance: 102 - 103: 21.964 distance: 102 - 107: 14.227 distance: 104 - 105: 36.635 distance: 105 - 106: 25.032