Starting phenix.real_space_refine on Tue Nov 19 13:08:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkn_13473/11_2024/7pkn_13473.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkn_13473/11_2024/7pkn_13473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkn_13473/11_2024/7pkn_13473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkn_13473/11_2024/7pkn_13473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkn_13473/11_2024/7pkn_13473.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkn_13473/11_2024/7pkn_13473.cif" } resolution = 3.2 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1122 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 11925 2.51 5 N 3138 2.21 5 O 3451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18616 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1122 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 138} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3109 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 364} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1064 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 128} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2412 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1325 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 164} Chain: "N" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2613 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "P" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1788 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "Q" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1526 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1365 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 161} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain breaks: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.43, per 1000 atoms: 0.51 Number of scatterers: 18616 At special positions: 0 Unit cell: (95.46, 188.34, 195.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3451 8.00 N 3138 7.00 C 11925 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 2.3 seconds 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 10 sheets defined 62.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'H' and resid 35 through 65 removed outlier: 3.844A pdb=" N ARG H 39 " --> pdb=" O CYS H 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 115 removed outlier: 3.732A pdb=" N ASN H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 182 removed outlier: 4.231A pdb=" N ASN H 129 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS H 138 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER H 170 " --> pdb=" O GLN H 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 362 through 368 removed outlier: 3.731A pdb=" N SER I 365 " --> pdb=" O GLN I 362 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN I 368 " --> pdb=" O SER I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 377 Processing helix chain 'I' and resid 381 through 399 Processing helix chain 'I' and resid 411 through 427 removed outlier: 3.727A pdb=" N THR I 415 " --> pdb=" O GLY I 411 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE I 427 " --> pdb=" O ARG I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 430 No H-bonds generated for 'chain 'I' and resid 428 through 430' Processing helix chain 'I' and resid 432 through 443 removed outlier: 3.688A pdb=" N GLU I 436 " --> pdb=" O PHE I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 461 removed outlier: 3.807A pdb=" N SER I 460 " --> pdb=" O LEU I 456 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TRP I 461 " --> pdb=" O GLN I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 483 Proline residue: I 472 - end of helix removed outlier: 4.834A pdb=" N ASP I 476 " --> pdb=" O PRO I 472 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N HIS I 477 " --> pdb=" O LEU I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 512 removed outlier: 3.791A pdb=" N MET I 510 " --> pdb=" O LEU I 506 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP I 511 " --> pdb=" O TRP I 507 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE I 512 " --> pdb=" O LEU I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 525 through 551 removed outlier: 4.421A pdb=" N SER I 532 " --> pdb=" O GLY I 528 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL I 533 " --> pdb=" O SER I 529 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 569 removed outlier: 3.726A pdb=" N PHE I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) Processing helix chain 'I' and resid 570 through 575 Processing helix chain 'I' and resid 584 through 593 removed outlier: 3.513A pdb=" N PHE I 588 " --> pdb=" O PRO I 584 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU I 593 " --> pdb=" O TYR I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 625 removed outlier: 3.658A pdb=" N LEU I 600 " --> pdb=" O ASP I 596 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS I 619 " --> pdb=" O THR I 615 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN I 620 " --> pdb=" O ALA I 616 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 622 " --> pdb=" O LYS I 618 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL I 623 " --> pdb=" O LYS I 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 633 through 652 removed outlier: 4.088A pdb=" N TYR I 637 " --> pdb=" O SER I 633 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 672 removed outlier: 4.395A pdb=" N LEU I 668 " --> pdb=" O ASP I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 688 through 698 removed outlier: 3.933A pdb=" N GLN I 698 " --> pdb=" O SER I 694 " (cutoff:3.500A) Processing helix chain 'I' and resid 719 through 727 removed outlier: 3.500A pdb=" N GLY I 727 " --> pdb=" O LEU I 723 " (cutoff:3.500A) Processing helix chain 'I' and resid 728 through 740 Processing helix chain 'K' and resid 20 through 43 Processing helix chain 'K' and resid 55 through 77 removed outlier: 3.653A pdb=" N LYS K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 149 removed outlier: 3.801A pdb=" N GLN K 102 " --> pdb=" O GLN K 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 37 Processing helix chain 'L' and resid 60 through 68 Processing helix chain 'L' and resid 88 through 103 Processing helix chain 'L' and resid 167 through 172 removed outlier: 3.843A pdb=" N GLU L 172 " --> pdb=" O ASP L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 205 removed outlier: 3.515A pdb=" N THR L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 228 Processing helix chain 'L' and resid 257 through 269 removed outlier: 3.518A pdb=" N VAL L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 296 removed outlier: 3.674A pdb=" N LEU L 287 " --> pdb=" O PHE L 283 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS L 294 " --> pdb=" O HIS L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 302 Processing helix chain 'L' and resid 327 through 344 removed outlier: 3.553A pdb=" N VAL L 331 " --> pdb=" O TYR L 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 36 removed outlier: 3.520A pdb=" N LEU M 28 " --> pdb=" O GLU M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 85 removed outlier: 4.002A pdb=" N LEU M 78 " --> pdb=" O SER M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 88 No H-bonds generated for 'chain 'M' and resid 86 through 88' Processing helix chain 'M' and resid 89 through 94 removed outlier: 3.871A pdb=" N LEU M 94 " --> pdb=" O SER M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 124 removed outlier: 3.759A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 154 removed outlier: 3.634A pdb=" N THR M 141 " --> pdb=" O GLY M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 20 through 29 Processing helix chain 'N' and resid 32 through 36 Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 62 through 78 removed outlier: 3.886A pdb=" N ALA N 66 " --> pdb=" O SER N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 116 removed outlier: 3.534A pdb=" N LEU N 112 " --> pdb=" O PHE N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 170 removed outlier: 3.828A pdb=" N ARG N 170 " --> pdb=" O MET N 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 167 through 170' Processing helix chain 'N' and resid 171 through 183 Processing helix chain 'N' and resid 197 through 206 Processing helix chain 'N' and resid 241 through 257 Processing helix chain 'N' and resid 305 through 309 Processing helix chain 'N' and resid 325 through 330 Processing helix chain 'O' and resid 17 through 27 removed outlier: 3.828A pdb=" N GLN O 27 " --> pdb=" O ARG O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 110 removed outlier: 3.690A pdb=" N PHE O 110 " --> pdb=" O GLN O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 169 removed outlier: 4.259A pdb=" N ILE O 164 " --> pdb=" O PRO O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 200 Processing helix chain 'O' and resid 261 through 278 removed outlier: 3.845A pdb=" N GLU O 265 " --> pdb=" O SER O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 288 removed outlier: 3.826A pdb=" N VAL O 283 " --> pdb=" O PRO O 279 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE O 284 " --> pdb=" O LEU O 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 75 Processing helix chain 'P' and resid 147 through 161 removed outlier: 3.511A pdb=" N SER P 151 " --> pdb=" O CYS P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 191 removed outlier: 3.547A pdb=" N TYR P 191 " --> pdb=" O LEU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 250 removed outlier: 4.019A pdb=" N LEU P 247 " --> pdb=" O PRO P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 270 removed outlier: 3.528A pdb=" N GLY P 270 " --> pdb=" O VAL P 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 271 through 283 Processing helix chain 'Q' and resid 77 through 97 removed outlier: 3.677A pdb=" N ARG Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 124 Processing helix chain 'Q' and resid 133 through 135 No H-bonds generated for 'chain 'Q' and resid 133 through 135' Processing helix chain 'Q' and resid 136 through 197 removed outlier: 3.612A pdb=" N LEU Q 140 " --> pdb=" O ASN Q 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU Q 191 " --> pdb=" O ALA Q 187 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU Q 192 " --> pdb=" O SER Q 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU Q 193 " --> pdb=" O GLU Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 221 removed outlier: 3.725A pdb=" N LEU Q 219 " --> pdb=" O SER Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 223 through 232 removed outlier: 4.008A pdb=" N GLU Q 227 " --> pdb=" O THR Q 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 234 through 248 removed outlier: 4.741A pdb=" N ASP Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE Q 244 " --> pdb=" O LYS Q 240 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 268 Processing helix chain 'U' and resid 253 through 267 removed outlier: 4.153A pdb=" N GLU U 257 " --> pdb=" O ILE U 253 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N HIS U 262 " --> pdb=" O PHE U 258 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU U 263 " --> pdb=" O GLU U 259 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN U 267 " --> pdb=" O LEU U 263 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 369 removed outlier: 4.305A pdb=" N GLN U 318 " --> pdb=" O GLU U 314 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG U 319 " --> pdb=" O LYS U 315 " (cutoff:3.500A) Proline residue: U 332 - end of helix removed outlier: 4.254A pdb=" N GLU U 346 " --> pdb=" O ASP U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 375 Processing helix chain 'U' and resid 383 through 385 No H-bonds generated for 'chain 'U' and resid 383 through 385' Processing helix chain 'U' and resid 386 through 415 removed outlier: 4.830A pdb=" N THR U 396 " --> pdb=" O PHE U 392 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU U 397 " --> pdb=" O LYS U 393 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLU U 401 " --> pdb=" O LEU U 397 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER U 402 " --> pdb=" O LEU U 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 105 removed outlier: 4.203A pdb=" N GLU R 98 " --> pdb=" O GLU R 94 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU R 99 " --> pdb=" O LYS R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 114 removed outlier: 4.194A pdb=" N GLN R 111 " --> pdb=" O LEU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 124 removed outlier: 3.581A pdb=" N GLU R 120 " --> pdb=" O SER R 116 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU R 122 " --> pdb=" O GLU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 150 removed outlier: 4.719A pdb=" N GLU R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU R 142 " --> pdb=" O LYS R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 177 removed outlier: 3.801A pdb=" N ILE R 175 " --> pdb=" O PHE R 171 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN R 177 " --> pdb=" O LYS R 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 47 through 48 removed outlier: 3.518A pdb=" N ARG L 47 " --> pdb=" O VAL L 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 117 through 123 removed outlier: 7.093A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 117 through 123 removed outlier: 7.093A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS L 319 " --> pdb=" O HIS L 315 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU L 304 " --> pdb=" O SER L 242 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N SER L 242 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG L 306 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N LEU N 294 " --> pdb=" O GLU N 272 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N GLU N 272 " --> pdb=" O LEU N 294 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N LYS N 296 " --> pdb=" O LYS N 270 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N LYS N 270 " --> pdb=" O LYS N 296 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N SER N 298 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N GLN N 268 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE N 266 " --> pdb=" O PRO N 300 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU N 264 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N PHE N 334 " --> pdb=" O PHE N 266 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN N 268 " --> pdb=" O PHE N 334 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE N 336 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS N 270 " --> pdb=" O ILE N 336 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'M' and resid 128 through 131 removed outlier: 6.503A pdb=" N ILE M 66 " --> pdb=" O CYS M 98 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU M 100 " --> pdb=" O ILE M 66 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE M 68 " --> pdb=" O LEU M 100 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR M 102 " --> pdb=" O PHE M 68 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL M 70 " --> pdb=" O THR M 102 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N LEU M 65 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR M 17 " --> pdb=" O LEU M 65 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL M 67 " --> pdb=" O THR M 17 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU M 19 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL M 69 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL M 21 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ASN M 71 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N ILE N 238 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL M 46 " --> pdb=" O ILE N 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 120 through 126 removed outlier: 4.809A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR N 155 " --> pdb=" O TYR N 160 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR N 160 " --> pdb=" O TYR N 155 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TRP N 83 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU N 193 " --> pdb=" O TRP N 83 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL N 85 " --> pdb=" O MET N 191 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET N 191 " --> pdb=" O VAL N 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 113 through 117 removed outlier: 3.511A pdb=" N VAL O 122 " --> pdb=" O LEU O 142 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR O 128 " --> pdb=" O ASP O 136 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP O 136 " --> pdb=" O THR O 128 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE O 130 " --> pdb=" O LEU O 134 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU O 134 " --> pdb=" O PHE O 130 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS O 152 " --> pdb=" O ASP O 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 210 through 211 removed outlier: 3.765A pdb=" N SER O 219 " --> pdb=" O GLN O 210 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU O 224 " --> pdb=" O PHE O 231 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE O 231 " --> pdb=" O LEU O 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 77 through 87 removed outlier: 5.007A pdb=" N SER P 108 " --> pdb=" O ARG P 79 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N HIS P 81 " --> pdb=" O ARG P 106 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG P 106 " --> pdb=" O HIS P 81 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS P 83 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG P 104 " --> pdb=" O LYS P 83 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR P 85 " --> pdb=" O LEU P 102 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU P 102 " --> pdb=" O THR P 85 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP P 87 " --> pdb=" O LYS P 100 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LYS P 100 " --> pdb=" O ASP P 87 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN P 117 " --> pdb=" O ILE P 140 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE P 140 " --> pdb=" O GLN P 117 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU P 119 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU P 138 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN P 121 " --> pdb=" O THR P 136 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA P 134 " --> pdb=" O LEU P 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 205 through 210 removed outlier: 3.900A pdb=" N SER P 210 " --> pdb=" O PHE P 216 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE P 216 " --> pdb=" O SER P 210 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU P 217 " --> pdb=" O LYS P 241 " (cutoff:3.500A) 1171 hydrogen bonds defined for protein. 3435 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: 5.78 Time building geometry restraints manager: 5.06 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: 5986 1.34 - 1.46: 4090 1.46 - 1.58: 8725 1.58 - 1.70: 0 1.70 - 1.82: 158 Bond restraints: 18959 Sorted by residual: bond pdb=" CG GLU U 326 " pdb=" CD GLU U 326 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.53e+00 bond pdb=" N PRO P 144 " pdb=" CA PRO P 144 " ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.38e+00 bond pdb=" CA GLU U 331 " pdb=" C GLU U 331 " ideal model delta sigma weight residual 1.521 1.535 -0.014 1.17e-02 7.31e+03 1.38e+00 bond pdb=" CA ILE O 159 " pdb=" CB ILE O 159 " ideal model delta sigma weight residual 1.537 1.523 0.014 1.29e-02 6.01e+03 1.17e+00 bond pdb=" N PRO I 584 " pdb=" CA PRO I 584 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.31e-02 5.83e+03 1.10e+00 ... (remaining 18954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 25127 1.65 - 3.30: 364 3.30 - 4.96: 65 4.96 - 6.61: 22 6.61 - 8.26: 7 Bond angle restraints: 25585 Sorted by residual: angle pdb=" N ILE H 119 " pdb=" CA ILE H 119 " pdb=" C ILE H 119 " ideal model delta sigma weight residual 111.91 106.88 5.03 8.90e-01 1.26e+00 3.19e+01 angle pdb=" N GLU U 326 " pdb=" CA GLU U 326 " pdb=" CB GLU U 326 " ideal model delta sigma weight residual 110.16 115.76 -5.60 1.48e+00 4.57e-01 1.43e+01 angle pdb=" CA MET P 113 " pdb=" CB MET P 113 " pdb=" CG MET P 113 " ideal model delta sigma weight residual 114.10 121.41 -7.31 2.00e+00 2.50e-01 1.34e+01 angle pdb=" N ASN N 332 " pdb=" CA ASN N 332 " pdb=" C ASN N 332 " ideal model delta sigma weight residual 114.56 110.33 4.23 1.27e+00 6.20e-01 1.11e+01 angle pdb=" C THR U 280 " pdb=" N PHE U 281 " pdb=" CA PHE U 281 " ideal model delta sigma weight residual 121.14 115.50 5.64 1.75e+00 3.27e-01 1.04e+01 ... (remaining 25580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 10649 17.50 - 35.00: 790 35.00 - 52.50: 140 52.50 - 70.00: 19 70.00 - 87.50: 13 Dihedral angle restraints: 11611 sinusoidal: 4765 harmonic: 6846 Sorted by residual: dihedral pdb=" CA CYS P 111 " pdb=" C CYS P 111 " pdb=" N HIS P 112 " pdb=" CA HIS P 112 " ideal model delta harmonic sigma weight residual 180.00 154.42 25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLU Q 194 " pdb=" C GLU Q 194 " pdb=" N GLU Q 195 " pdb=" CA GLU Q 195 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA CYS L 245 " pdb=" C CYS L 245 " pdb=" N SER L 246 " pdb=" CA SER L 246 " ideal model delta harmonic sigma weight residual 180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 11608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2055 0.033 - 0.066: 642 0.066 - 0.098: 162 0.098 - 0.131: 84 0.131 - 0.164: 6 Chirality restraints: 2949 Sorted by residual: chirality pdb=" CB ILE K 82 " pdb=" CA ILE K 82 " pdb=" CG1 ILE K 82 " pdb=" CG2 ILE K 82 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA SER L 246 " pdb=" N SER L 246 " pdb=" C SER L 246 " pdb=" CB SER L 246 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA GLU N 128 " pdb=" N GLU N 128 " pdb=" C GLU N 128 " pdb=" CB GLU N 128 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 2946 not shown) Planarity restraints: 3212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS P 111 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" C CYS P 111 " -0.050 2.00e-02 2.50e+03 pdb=" O CYS P 111 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS P 112 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU P 143 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO P 144 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO P 144 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO P 144 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 179 " -0.016 2.00e-02 2.50e+03 1.41e-02 3.98e+00 pdb=" CG TYR P 179 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR P 179 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR P 179 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR P 179 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR P 179 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR P 179 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR P 179 " 0.001 2.00e-02 2.50e+03 ... (remaining 3209 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 179 2.67 - 3.22: 17289 3.22 - 3.78: 27895 3.78 - 4.34: 35575 4.34 - 4.90: 60483 Nonbonded interactions: 141421 Sorted by model distance: nonbonded pdb=" O GLU H 117 " pdb=" OG SER H 120 " model vdw 2.106 3.040 nonbonded pdb=" OG SER H 147 " pdb=" OD1 ASN K 115 " model vdw 2.232 3.040 nonbonded pdb=" O PHE U 258 " pdb=" OG1 THR U 261 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP N 2 " pdb=" OG1 THR N 4 " model vdw 2.242 3.040 nonbonded pdb=" O GLN N 50 " pdb=" ND1 HIS N 54 " model vdw 2.252 3.120 ... (remaining 141416 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 38.480 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.090 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 : 0.002 0.031 18959 Z= 0.153 Angle : 0.553 8.260 25585 Z= 0.319 Chirality : 0.038 0.164 2949 Planarity : 0.003 0.055 3212 Dihedral : 12.625 87.503 7115 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2.14 (0.18), residues: 2260 helix: 2.43 (0.15), residues: 1329 sheet: 1.12 (0.30), residues: 286 loop : -0.66 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 225 HIS 0.005 0.000 HIS M 115 PHE 0.016 0.001 PHE U 281 TYR 0.034 0.001 TYR P 179 ARG 0.010 0.001 ARG O 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 2.215 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: H 38 ASP cc_start: 0.8234 (m-30) cc_final: 0.7873 (m-30) REVERT: H 43 LEU cc_start: 0.9012 (mt) cc_final: 0.8703 (mt) REVERT: H 46 LEU cc_start: 0.8737 (mm) cc_final: 0.8498 (pp) REVERT: H 50 THR cc_start: 0.8775 (m) cc_final: 0.8566 (p) REVERT: H 104 ASP cc_start: 0.9021 (t70) cc_final: 0.8795 (t0) REVERT: I 552 SER cc_start: 0.8672 (m) cc_final: 0.8345 (p) REVERT: I 568 VAL cc_start: 0.6984 (t) cc_final: 0.6705 (t) REVERT: K 43 SER cc_start: 0.8915 (t) cc_final: 0.8684 (p) REVERT: K 62 MET cc_start: 0.8999 (mtp) cc_final: 0.8345 (mtp) REVERT: K 66 CYS cc_start: 0.9320 (m) cc_final: 0.9009 (m) REVERT: K 87 ASP cc_start: 0.8248 (p0) cc_final: 0.8043 (t0) REVERT: K 129 LEU cc_start: 0.7490 (tp) cc_final: 0.7194 (tp) REVERT: L 173 THR cc_start: 0.9442 (p) cc_final: 0.9161 (t) REVERT: L 284 MET cc_start: 0.8963 (mmm) cc_final: 0.8283 (mmt) REVERT: M 8 ASP cc_start: 0.7909 (m-30) cc_final: 0.7589 (p0) REVERT: M 59 ASN cc_start: 0.7973 (t0) cc_final: 0.7590 (p0) REVERT: M 106 ARG cc_start: 0.7612 (mtm-85) cc_final: 0.7220 (mtm-85) REVERT: O 168 TYR cc_start: 0.8393 (m-80) cc_final: 0.8065 (m-80) REVERT: O 172 ASN cc_start: 0.7653 (t0) cc_final: 0.7332 (t0) REVERT: O 183 TYR cc_start: 0.8840 (m-80) cc_final: 0.8535 (m-10) REVERT: O 192 TYR cc_start: 0.8223 (t80) cc_final: 0.7968 (t80) REVERT: O 276 CYS cc_start: 0.8680 (t) cc_final: 0.8350 (p) REVERT: P 112 HIS cc_start: 0.6189 (t-170) cc_final: 0.5781 (t-170) REVERT: P 113 MET cc_start: 0.6682 (mmp) cc_final: 0.6460 (mmm) REVERT: P 117 GLN cc_start: 0.7507 (tp-100) cc_final: 0.7230 (mp-120) REVERT: P 142 MET cc_start: 0.6302 (mmp) cc_final: 0.6062 (tpp) REVERT: P 162 ASP cc_start: 0.6618 (t0) cc_final: 0.5691 (t70) REVERT: P 227 ASP cc_start: 0.7238 (p0) cc_final: 0.6553 (p0) REVERT: Q 165 MET cc_start: 0.8492 (ttt) cc_final: 0.8048 (ptt) REVERT: Q 168 THR cc_start: 0.9081 (m) cc_final: 0.8877 (m) REVERT: Q 183 ILE cc_start: 0.8950 (pt) cc_final: 0.8475 (pt) REVERT: U 298 MET cc_start: 0.4924 (ppp) cc_final: 0.4515 (ppp) REVERT: U 343 GLU cc_start: 0.8737 (pp20) cc_final: 0.8355 (pp20) REVERT: R 98 GLU cc_start: 0.6034 (mp0) cc_final: 0.5468 (mp0) REVERT: R 101 MET cc_start: 0.1273 (mpp) cc_final: 0.0802 (tpp) REVERT: R 135 GLU cc_start: 0.5114 (tp30) cc_final: 0.4720 (mt-10) REVERT: R 141 GLU cc_start: 0.4385 (pm20) cc_final: 0.4165 (tm-30) REVERT: R 170 GLU cc_start: 0.5454 (pp20) cc_final: 0.4554 (mm-30) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.3346 time to fit residues: 204.8941 Evaluate side-chains 225 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 30.0000 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 177 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 206 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 602 GLN K 63 GLN L 294 HIS M 80 ASN N 118 ASN P 77 ASN U 284 ASN U 324 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18959 Z= 0.279 Angle : 0.635 11.094 25585 Z= 0.322 Chirality : 0.041 0.184 2949 Planarity : 0.004 0.047 3212 Dihedral : 3.872 30.673 2446 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.10 % Allowed : 9.87 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.82 (0.18), residues: 2260 helix: 2.15 (0.14), residues: 1355 sheet: 0.96 (0.30), residues: 286 loop : -0.80 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 542 HIS 0.014 0.001 HIS U 403 PHE 0.029 0.002 PHE O 287 TYR 0.020 0.002 TYR P 191 ARG 0.007 0.001 ARG O 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 104 ASP cc_start: 0.9196 (t70) cc_final: 0.8914 (t0) REVERT: K 43 SER cc_start: 0.9023 (t) cc_final: 0.8822 (p) REVERT: K 87 ASP cc_start: 0.8373 (p0) cc_final: 0.8063 (t0) REVERT: M 59 ASN cc_start: 0.8208 (t0) cc_final: 0.7769 (p0) REVERT: M 106 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7831 (mtm-85) REVERT: N 118 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.7576 (t0) REVERT: O 136 ASP cc_start: 0.8287 (t0) cc_final: 0.8014 (t0) REVERT: O 172 ASN cc_start: 0.7440 (t0) cc_final: 0.7185 (t0) REVERT: O 181 CYS cc_start: 0.8664 (m) cc_final: 0.7657 (t) REVERT: P 112 HIS cc_start: 0.6127 (t-170) cc_final: 0.5640 (t-170) REVERT: P 117 GLN cc_start: 0.7556 (tp-100) cc_final: 0.7286 (tp40) REVERT: P 142 MET cc_start: 0.6250 (mmp) cc_final: 0.6037 (tpp) REVERT: P 162 ASP cc_start: 0.6645 (t0) cc_final: 0.5942 (t70) REVERT: U 298 MET cc_start: 0.4749 (ppp) cc_final: 0.4470 (ppp) REVERT: U 306 ASN cc_start: 0.6944 (OUTLIER) cc_final: 0.6619 (t0) outliers start: 23 outliers final: 15 residues processed: 237 average time/residue: 0.3093 time to fit residues: 113.0665 Evaluate side-chains 203 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain I residue 459 VAL Chi-restraints excluded: chain I residue 508 LEU Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 118 ASN Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 303 LEU Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain Q residue 257 PHE Chi-restraints excluded: chain Q residue 258 ILE Chi-restraints excluded: chain U residue 306 ASN Chi-restraints excluded: chain R residue 118 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 206 optimal weight: 50.0000 chunk 223 optimal weight: 0.5980 chunk 183 optimal weight: 7.9990 chunk 204 optimal weight: 30.0000 chunk 70 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 50 GLN O 151 HIS P 121 GLN ** Q 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3381 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: