Starting phenix.real_space_refine on Mon Aug 5 17:10:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/08_2024/7cq7_30438.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/08_2024/7cq7_30438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/08_2024/7cq7_30438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/08_2024/7cq7_30438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/08_2024/7cq7_30438.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/08_2024/7cq7_30438.cif" } resolution = 3.55 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 92 5.16 5 Cl 3 4.86 5 C 8926 2.51 5 N 2304 2.21 5 O 2481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 526": "NH1" <-> "NH2" Residue "C ARG 639": "NH1" <-> "NH2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 526": "NH1" <-> "NH2" Residue "D ARG 640": "NH1" <-> "NH2" Residue "D ARG 707": "NH1" <-> "NH2" Residue "D ARG 712": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13810 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1630 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1637 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5194 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 28, 'TRANS': 647} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 5236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5236 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CL': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CL': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.39, per 1000 atoms: 0.61 Number of scatterers: 13810 At special positions: 0 Unit cell: (136.14, 111.986, 132.846, 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) Cl 3 17.00 S 92 16.00 P 4 15.00 O 2481 8.00 N 2304 7.00 C 8926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.04 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 438 " - pdb=" SG CYS D 454 " 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=5, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG E 1 " - " ASN A 263 " " NAG F 1 " - " ASN B 263 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.95 Conformation dependent library (CDL) restraints added in 5.8 seconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3312 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 10 sheets defined 63.9% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 81 through 105 removed outlier: 3.783A pdb=" N GLU A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.750A pdb=" N GLN A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 183 through 203 removed outlier: 3.684A pdb=" N ASN A 203 " --> pdb=" O CYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.923A pdb=" N CYS A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 222' Processing helix chain 'A' and resid 224 through 245 removed outlier: 3.813A pdb=" N TYR A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 Processing helix chain 'A' and resid 281 through 294 removed outlier: 4.260A pdb=" N VAL A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'B' and resid 81 through 105 removed outlier: 4.311A pdb=" N GLU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N PHE B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 removed outlier: 3.710A pdb=" N ILE B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.983A pdb=" N ALA B 149 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP B 150 " --> pdb=" O LEU B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 150' Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 185 through 203 removed outlier: 3.586A pdb=" N ASN B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.841A pdb=" N CYS B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing helix chain 'B' and resid 224 through 246 removed outlier: 4.223A pdb=" N THR B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.540A pdb=" N ALA B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.625A pdb=" N VAL B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 306 Proline residue: B 296 - end of helix removed outlier: 3.610A pdb=" N SER B 303 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 122 through 167 removed outlier: 3.596A pdb=" N ARG C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 196 removed outlier: 4.301A pdb=" N SER C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 removed outlier: 3.863A pdb=" N CYS C 211 " --> pdb=" O PRO C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.682A pdb=" N ILE C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 250 through 263 removed outlier: 3.956A pdb=" N GLN C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 removed outlier: 3.879A pdb=" N ARG C 280 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 302 removed outlier: 3.698A pdb=" N ARG C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 312 removed outlier: 3.734A pdb=" N VAL C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 346 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 374 through 407 removed outlier: 3.749A pdb=" N ALA C 380 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG C 405 " --> pdb=" O MET C 401 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR C 406 " --> pdb=" O PHE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 434 removed outlier: 3.805A pdb=" N ALA C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 469 through 480 removed outlier: 3.549A pdb=" N SER C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 504 removed outlier: 4.084A pdb=" N PHE C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 531 removed outlier: 3.647A pdb=" N LEU C 527 " --> pdb=" O ALA C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 536 Processing helix chain 'C' and resid 543 through 560 removed outlier: 3.890A pdb=" N LEU C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 573 Processing helix chain 'C' and resid 576 through 578 No H-bonds generated for 'chain 'C' and resid 576 through 578' Processing helix chain 'C' and resid 579 through 596 removed outlier: 3.783A pdb=" N VAL C 596 " --> pdb=" O ILE C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 608 Processing helix chain 'C' and resid 645 through 652 Processing helix chain 'C' and resid 681 through 690 removed outlier: 3.628A pdb=" N HIS C 690 " --> pdb=" O VAL C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 713 removed outlier: 3.720A pdb=" N ASP C 713 " --> pdb=" O ASP C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 724 Processing helix chain 'C' and resid 753 through 763 removed outlier: 3.838A pdb=" N LYS C 759 " --> pdb=" O PRO C 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.706A pdb=" N ARG D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 166 removed outlier: 3.618A pdb=" N LYS D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 196 removed outlier: 3.673A pdb=" N LEU D 178 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.565A pdb=" N ALA D 202 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.547A pdb=" N ASN D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 239 Processing helix chain 'D' and resid 248 through 262 removed outlier: 4.423A pdb=" N HIS D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 302 Processing helix chain 'D' and resid 303 through 314 Processing helix chain 'D' and resid 320 through 346 removed outlier: 3.915A pdb=" N HIS D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 374 through 406 removed outlier: 4.230A pdb=" N ALA D 390 " --> pdb=" O GLY D 386 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 434 removed outlier: 3.644A pdb=" N ALA D 417 " --> pdb=" O GLN D 413 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 418 " --> pdb=" O VAL D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 466 Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.601A pdb=" N SER D 473 " --> pdb=" O THR D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 504 removed outlier: 4.601A pdb=" N PHE D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 536 removed outlier: 3.509A pdb=" N ALA D 523 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY D 529 " --> pdb=" O GLY D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 560 removed outlier: 3.608A pdb=" N TYR D 547 " --> pdb=" O ASP D 543 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 removed outlier: 4.004A pdb=" N THR D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 578 No H-bonds generated for 'chain 'D' and resid 576 through 578' Processing helix chain 'D' and resid 579 through 596 Processing helix chain 'D' and resid 600 through 608 Processing helix chain 'D' and resid 646 through 652 removed outlier: 3.596A pdb=" N SER D 652 " --> pdb=" O VAL D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 685 Processing helix chain 'D' and resid 685 through 690 Processing helix chain 'D' and resid 753 through 762 removed outlier: 3.902A pdb=" N LYS D 759 " --> pdb=" O PRO D 755 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 265 through 266 Processing sheet with id=AA2, first strand: chain 'C' and resid 438 through 440 Processing sheet with id=AA3, first strand: chain 'C' and resid 638 through 639 Processing sheet with id=AA4, first strand: chain 'C' and resid 642 through 643 removed outlier: 4.231A pdb=" N GLU C 642 " --> pdb=" O MET C 735 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET C 735 " --> pdb=" O GLU C 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 747 through 748 removed outlier: 5.691A pdb=" N VAL C 748 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU C 769 " --> pdb=" O LEU C 781 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU C 781 " --> pdb=" O LEU C 769 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL C 771 " --> pdb=" O VAL C 779 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.946A pdb=" N GLU D 95 " --> pdb=" O LYS D 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 438 through 439 Processing sheet with id=AA8, first strand: chain 'D' and resid 638 through 639 removed outlier: 3.714A pdb=" N GLY D 677 " --> pdb=" O VAL D 663 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 641 through 643 removed outlier: 3.632A pdb=" N GLU D 642 " --> pdb=" O MET D 735 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 747 through 749 removed outlier: 6.471A pdb=" N VAL D 748 " --> pdb=" O VAL D 772 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 758 hydrogen bonds defined for protein. 2235 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: 4.77 Time building geometry restraints manager: 6.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4350 1.34 - 1.47: 3464 1.47 - 1.59: 6154 1.59 - 1.71: 6 1.71 - 1.83: 140 Bond restraints: 14114 Sorted by residual: bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 ADP D 901 " pdb=" C6 ADP D 901 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 ADP C 901 " pdb=" C6 ADP C 901 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CB VAL C 586 " pdb=" CG1 VAL C 586 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 ... (remaining 14109 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.81: 318 105.81 - 112.94: 7623 112.94 - 120.07: 5412 120.07 - 127.20: 5654 127.20 - 134.33: 178 Bond angle restraints: 19185 Sorted by residual: angle pdb=" C THR A 282 " pdb=" N VAL A 283 " pdb=" CA VAL A 283 " ideal model delta sigma weight residual 120.24 125.32 -5.08 6.30e-01 2.52e+00 6.50e+01 angle pdb=" N GLN D 722 " pdb=" CA GLN D 722 " pdb=" C GLN D 722 " ideal model delta sigma weight residual 114.75 105.85 8.90 1.26e+00 6.30e-01 4.99e+01 angle pdb=" C ARG B 271 " pdb=" N THR B 272 " pdb=" CA THR B 272 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C ARG A 271 " pdb=" N THR A 272 " pdb=" CA THR A 272 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" N ILE D 724 " pdb=" CA ILE D 724 " pdb=" C ILE D 724 " ideal model delta sigma weight residual 110.62 115.92 -5.30 1.14e+00 7.69e-01 2.16e+01 ... (remaining 19180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 8213 22.84 - 45.68: 182 45.68 - 68.52: 10 68.52 - 91.36: 8 91.36 - 114.20: 1 Dihedral angle restraints: 8414 sinusoidal: 3299 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASP C 282 " pdb=" C ASP C 282 " pdb=" N THR C 283 " pdb=" CA THR C 283 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" C5' ADP D 901 " pdb=" O5' ADP D 901 " pdb=" PA ADP D 901 " pdb=" O2A ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 -174.20 114.20 1 2.00e+01 2.50e-03 3.38e+01 dihedral pdb=" CA ARG A 107 " pdb=" C ARG A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta harmonic sigma weight residual 180.00 152.58 27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 8411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1658 0.060 - 0.120: 513 0.120 - 0.180: 68 0.180 - 0.240: 11 0.240 - 0.301: 2 Chirality restraints: 2252 Sorted by residual: chirality pdb=" CB ILE D 721 " pdb=" CA ILE D 721 " pdb=" CG1 ILE D 721 " pdb=" CG2 ILE D 721 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE C 724 " pdb=" CA ILE C 724 " pdb=" CG1 ILE C 724 " pdb=" CG2 ILE C 724 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB ILE D 275 " pdb=" CA ILE D 275 " pdb=" CG1 ILE D 275 " pdb=" CG2 ILE D 275 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2249 not shown) Planarity restraints: 2399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 179 " 0.028 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP C 179 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP C 179 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 179 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 179 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 179 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 179 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 179 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 179 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 179 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 783 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C THR C 783 " 0.048 2.00e-02 2.50e+03 pdb=" O THR C 783 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG C 784 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 349 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C MET D 349 " -0.044 2.00e-02 2.50e+03 pdb=" O MET D 349 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP D 350 " 0.015 2.00e-02 2.50e+03 ... (remaining 2396 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 75 2.51 - 3.11: 10133 3.11 - 3.71: 21215 3.71 - 4.30: 29202 4.30 - 4.90: 49468 Nonbonded interactions: 110093 Sorted by model distance: nonbonded pdb=" OD2 ASP D 786 " pdb=" O2' ADP D 901 " model vdw 1.915 3.040 nonbonded pdb=" O MET C 368 " pdb=" OH TYR C 579 " model vdw 2.236 3.040 nonbonded pdb=" CG HIS C 658 " pdb=" N7 ADP C 901 " model vdw 2.251 2.672 nonbonded pdb=" O MET D 368 " pdb=" OH TYR D 579 " model vdw 2.261 3.040 nonbonded pdb=" NH2 ARG D 767 " pdb=" O2B ADP D 901 " model vdw 2.261 3.120 ... (remaining 110088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 73 through 306) selection = (chain 'B' and (resid 73 through 130 or resid 142 through 245 or resid 253 throu \ gh 306)) } ncs_group { reference = (chain 'C' and (resid 94 through 115 or (resid 116 and (name N or name CA or nam \ e C or name O or name CB )) or resid 121 through 652 or (resid 653 through 656 a \ nd (name N or name CA or name C or name O or name CB )) or resid 657 through 664 \ or resid 673 through 693 or resid 706 through 789 or (resid 790 and (name N or \ name CA or name C or name O or name CB )) or resid 901 through 902)) selection = (chain 'D' and (resid 94 through 116 or resid 121 through 366 or (resid 367 and \ (name N or name CA or name C or name O or name CB )) or resid 368 through 619 or \ (resid 620 and (name N or name CA or name C or name O or name CB )) or resid 62 \ 1 through 642 or (resid 643 and (name N or name CA or name C or name O or name C \ B )) or resid 644 through 690 or (resid 691 and (name N or name CA or name C or \ name O or name CB )) or resid 692 or (resid 693 and (name N or name CA or name C \ or name O or name CB )) or resid 706 through 707 or (resid 708 and (name N or n \ ame CA or name C or name O or name CB )) or resid 709 through 716 or (resid 717 \ and (name N or name CA or name C or name O or name CB )) or resid 718 or (resid \ 719 and (name N or name CA or name C or name O or name CB )) or resid 720 throug \ h 724 or (resid 725 through 732 and (name N or name CA or name C or name O or na \ me CB )) or resid 733 through 790 or resid 901 through 902)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.570 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 45.000 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4342 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 14114 Z= 0.511 Angle : 1.069 10.899 19185 Z= 0.570 Chirality : 0.056 0.301 2252 Planarity : 0.008 0.063 2397 Dihedral : 10.352 114.200 5066 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.15), residues: 1734 helix: -2.46 (0.12), residues: 1046 sheet: None (None), residues: 0 loop : -3.68 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP C 179 HIS 0.020 0.002 HIS D 725 PHE 0.031 0.003 PHE D 279 TYR 0.022 0.002 TYR D 370 ARG 0.011 0.001 ARG D 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 468 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 VAL cc_start: 0.5320 (t) cc_final: 0.4732 (m) REVERT: C 588 MET cc_start: 0.4373 (mtp) cc_final: 0.4139 (ppp) REVERT: D 227 LEU cc_start: 0.6605 (tp) cc_final: 0.6105 (tt) REVERT: D 275 ILE cc_start: 0.5375 (tp) cc_final: 0.5134 (mp) REVERT: D 513 VAL cc_start: 0.7961 (p) cc_final: 0.7596 (p) outliers start: 1 outliers final: 0 residues processed: 469 average time/residue: 0.2735 time to fit residues: 181.7631 Evaluate side-chains 250 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 158 optimal weight: 0.0050 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN A 202 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 173 ASN C 183 ASN C 220 HIS C 468 ASN C 774 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS D 396 ASN D 623 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4998 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14114 Z= 0.240 Angle : 0.829 10.522 19185 Z= 0.412 Chirality : 0.045 0.270 2252 Planarity : 0.006 0.048 2397 Dihedral : 6.696 108.300 1996 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.22 % Allowed : 11.61 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.37 (0.19), residues: 1734 helix: -0.44 (0.15), residues: 1068 sheet: None (None), residues: 0 loop : -3.53 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 179 HIS 0.010 0.001 HIS C 658 PHE 0.036 0.002 PHE A 294 TYR 0.021 0.002 TYR C 547 ARG 0.007 0.001 ARG D 526 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 291 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6853 (tpp) cc_final: 0.5269 (tpp) REVERT: B 192 LEU cc_start: 0.8414 (tp) cc_final: 0.7848 (mp) REVERT: C 323 LEU cc_start: 0.4278 (OUTLIER) cc_final: 0.3233 (mt) REVERT: C 599 GLU cc_start: 0.3859 (OUTLIER) cc_final: 0.2677 (pm20) REVERT: C 659 ASN cc_start: 0.3950 (m-40) cc_final: 0.3133 (m110) REVERT: D 132 LEU cc_start: 0.7194 (mt) cc_final: 0.6994 (mt) REVERT: D 143 PHE cc_start: 0.7222 (t80) cc_final: 0.5861 (m-10) outliers start: 48 outliers final: 20 residues processed: 320 average time/residue: 0.2158 time to fit residues: 106.0359 Evaluate side-chains 251 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 229 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 517 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 HIS ** D 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5402 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 14114 Z= 0.244 Angle : 0.768 11.322 19185 Z= 0.378 Chirality : 0.046 0.361 2252 Planarity : 0.005 0.044 2397 Dihedral : 6.093 89.324 1996 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.83 % Allowed : 13.83 % Favored : 82.35 % 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: -1.49 (0.20), residues: 1734 helix: 0.30 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -3.22 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 166 HIS 0.011 0.001 HIS C 658 PHE 0.035 0.002 PHE A 294 TYR 0.018 0.002 TYR D 579 ARG 0.006 0.001 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 264 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6852 (tpp) cc_final: 0.5202 (tpp) REVERT: A 168 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6312 (tm-30) REVERT: B 192 LEU cc_start: 0.8025 (tp) cc_final: 0.7605 (mp) REVERT: C 323 LEU cc_start: 0.5492 (OUTLIER) cc_final: 0.4866 (mt) REVERT: C 599 GLU cc_start: 0.4362 (OUTLIER) cc_final: 0.3598 (pm20) REVERT: C 781 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6746 (pt) REVERT: D 143 PHE cc_start: 0.7199 (t80) cc_final: 0.5579 (m-10) REVERT: D 407 ILE cc_start: 0.5952 (mp) cc_final: 0.4669 (mt) REVERT: D 615 HIS cc_start: 0.5457 (t-90) cc_final: 0.5044 (t-90) REVERT: D 741 MET cc_start: 0.7093 (ppp) cc_final: 0.6835 (tmm) REVERT: D 766 LEU cc_start: 0.3236 (mt) cc_final: 0.1801 (mp) outliers start: 57 outliers final: 24 residues processed: 297 average time/residue: 0.2109 time to fit residues: 97.0373 Evaluate side-chains 256 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 0.0980 chunk 150 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN C 683 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN D 396 ASN D 451 GLN D 605 HIS D 623 HIS ** D 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.6616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14114 Z= 0.242 Angle : 0.764 9.995 19185 Z= 0.382 Chirality : 0.045 0.225 2252 Planarity : 0.004 0.045 2397 Dihedral : 5.596 64.204 1996 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.83 % Allowed : 15.50 % Favored : 80.67 % 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: -1.22 (0.20), residues: 1734 helix: 0.48 (0.16), residues: 1077 sheet: -2.55 (1.32), residues: 14 loop : -3.12 (0.21), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 166 HIS 0.008 0.001 HIS C 658 PHE 0.034 0.002 PHE D 613 TYR 0.018 0.002 TYR D 99 ARG 0.010 0.001 ARG C 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 288 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7037 (tpp) cc_final: 0.5461 (tpp) REVERT: B 192 LEU cc_start: 0.7930 (tp) cc_final: 0.7487 (mp) REVERT: C 95 GLU cc_start: 0.4685 (mp0) cc_final: 0.4359 (tt0) REVERT: C 556 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6201 (mt) REVERT: C 599 GLU cc_start: 0.5329 (OUTLIER) cc_final: 0.4506 (pm20) REVERT: D 301 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6401 (t80) REVERT: D 407 ILE cc_start: 0.7085 (mp) cc_final: 0.6720 (mt) REVERT: D 606 ILE cc_start: 0.6250 (OUTLIER) cc_final: 0.5911 (mt) REVERT: D 741 MET cc_start: 0.7031 (ppp) cc_final: 0.6820 (tmm) REVERT: D 766 LEU cc_start: 0.3988 (OUTLIER) cc_final: 0.3168 (mp) outliers start: 57 outliers final: 30 residues processed: 325 average time/residue: 0.2241 time to fit residues: 110.5528 Evaluate side-chains 283 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 248 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 766 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 HIS C 659 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 HIS D 658 HIS D 768 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.7700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14114 Z= 0.215 Angle : 0.750 10.295 19185 Z= 0.366 Chirality : 0.045 0.442 2252 Planarity : 0.004 0.050 2397 Dihedral : 5.606 56.591 1996 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.16 % Allowed : 16.58 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.93 (0.20), residues: 1734 helix: 0.69 (0.16), residues: 1080 sheet: -3.31 (1.00), residues: 19 loop : -2.94 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 269 HIS 0.014 0.001 HIS B 202 PHE 0.036 0.002 PHE A 193 TYR 0.022 0.002 TYR D 99 ARG 0.008 0.001 ARG D 641 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 302 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7313 (tpp) cc_final: 0.6191 (tpp) REVERT: A 168 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6848 (tm-30) REVERT: B 229 LYS cc_start: 0.6859 (tttm) cc_final: 0.6659 (tmmt) REVERT: C 433 TYR cc_start: 0.6680 (OUTLIER) cc_final: 0.5963 (m-80) REVERT: C 505 TYR cc_start: 0.7186 (t80) cc_final: 0.6803 (t80) REVERT: C 556 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6586 (mt) REVERT: C 599 GLU cc_start: 0.5517 (OUTLIER) cc_final: 0.4822 (pm20) REVERT: D 739 GLU cc_start: 0.7294 (mp0) cc_final: 0.7064 (mp0) REVERT: D 741 MET cc_start: 0.7059 (ppp) cc_final: 0.6760 (tmm) REVERT: D 756 ARG cc_start: 0.6727 (mmp80) cc_final: 0.6201 (mtt180) REVERT: D 766 LEU cc_start: 0.4420 (OUTLIER) cc_final: 0.3893 (mt) outliers start: 62 outliers final: 31 residues processed: 336 average time/residue: 0.2144 time to fit residues: 111.0202 Evaluate side-chains 303 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 268 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 659 ASN Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 168 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 162 optimal weight: 0.0170 overall best weight: 1.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 203 ASN C 393 ASN D 101 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN D 623 HIS D 768 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.9183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 14114 Z= 0.269 Angle : 0.785 14.531 19185 Z= 0.389 Chirality : 0.046 0.239 2252 Planarity : 0.005 0.063 2397 Dihedral : 5.538 53.472 1996 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.22 % Allowed : 18.93 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.86 (0.20), residues: 1734 helix: 0.71 (0.16), residues: 1078 sheet: -3.43 (3.01), residues: 5 loop : -2.87 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP A 269 HIS 0.011 0.001 HIS C 658 PHE 0.032 0.002 PHE A 193 TYR 0.026 0.002 TYR D 448 ARG 0.007 0.001 ARG D 436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 338 time to evaluate : 1.482 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6761 (p0) REVERT: A 152 MET cc_start: 0.7816 (tpp) cc_final: 0.6632 (tpp) REVERT: A 167 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7642 (mm-40) REVERT: C 433 TYR cc_start: 0.7108 (OUTLIER) cc_final: 0.6314 (m-80) REVERT: C 505 TYR cc_start: 0.7502 (t80) cc_final: 0.6809 (t80) REVERT: C 556 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7615 (tp) REVERT: C 599 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5731 (pm20) REVERT: D 739 GLU cc_start: 0.7386 (mp0) cc_final: 0.7149 (mp0) REVERT: D 756 ARG cc_start: 0.7319 (mmp80) cc_final: 0.6638 (mtt180) outliers start: 48 outliers final: 25 residues processed: 371 average time/residue: 0.2107 time to fit residues: 120.3498 Evaluate side-chains 313 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 284 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 630 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 65.4607 > 50: distance: 6 - 10: 7.587 distance: 10 - 11: 14.743 distance: 11 - 12: 10.506 distance: 11 - 14: 15.062 distance: 12 - 13: 17.239 distance: 12 - 21: 3.428 distance: 14 - 15: 19.111 distance: 15 - 16: 31.724 distance: 16 - 17: 24.106 distance: 17 - 18: 22.940 distance: 18 - 19: 14.743 distance: 18 - 20: 4.001 distance: 21 - 22: 14.524 distance: 22 - 23: 24.488 distance: 22 - 25: 26.266 distance: 23 - 24: 48.985 distance: 23 - 29: 17.502 distance: 25 - 26: 7.912 distance: 26 - 27: 9.307 distance: 26 - 28: 33.220 distance: 30 - 31: 57.227 distance: 30 - 33: 8.837 distance: 31 - 32: 55.629 distance: 33 - 34: 15.729 distance: 34 - 100: 27.830 distance: 35 - 36: 9.964 distance: 35 - 115: 37.017 distance: 36 - 37: 44.746 distance: 36 - 39: 28.814 distance: 37 - 38: 22.464 distance: 37 - 44: 17.628 distance: 38 - 112: 25.856 distance: 39 - 40: 28.766 distance: 40 - 41: 23.526 distance: 41 - 42: 25.078 distance: 41 - 43: 34.126 distance: 44 - 45: 38.209 distance: 44 - 50: 13.087 distance: 45 - 46: 31.802 distance: 45 - 48: 26.181 distance: 46 - 47: 22.656 distance: 46 - 51: 43.179 distance: 48 - 49: 41.785 distance: 49 - 50: 24.678 distance: 51 - 52: 36.113 distance: 52 - 53: 8.156 distance: 52 - 55: 43.259 distance: 53 - 54: 10.965 distance: 53 - 59: 46.820 distance: 55 - 56: 23.459 distance: 56 - 57: 32.887 distance: 56 - 58: 35.979 distance: 59 - 60: 14.797 distance: 60 - 61: 15.800 distance: 60 - 63: 8.797 distance: 61 - 62: 50.024 distance: 61 - 68: 16.286 distance: 63 - 64: 45.104 distance: 64 - 65: 29.509 distance: 65 - 66: 29.896 distance: 65 - 67: 24.578 distance: 68 - 69: 48.599 distance: 69 - 70: 14.985 distance: 70 - 71: 16.480 distance: 70 - 72: 32.906 distance: 72 - 73: 31.552 distance: 73 - 74: 34.919 distance: 74 - 75: 34.275 distance: 74 - 76: 36.749 distance: 76 - 77: 17.823 distance: 77 - 80: 40.383 distance: 78 - 79: 15.516 distance: 78 - 82: 34.590 distance: 80 - 81: 6.194