Starting phenix.real_space_refine on Tue Dec 12 09:27:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/12_2023/6pvn_20494.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/12_2023/6pvn_20494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/12_2023/6pvn_20494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/12_2023/6pvn_20494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/12_2023/6pvn_20494.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/12_2023/6pvn_20494.pdb" } resolution = 4.07 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= 0.002 sd= 0.014 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: 5 Type Number sf(0) Gaussians S 124 5.16 5 Na 2 4.78 5 C 13560 2.51 5 N 3464 2.21 5 O 3724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 698": "NH1" <-> "NH2" Residue "C ARG 712": "NH1" <-> "NH2" Residue "C ARG 714": "NH1" <-> "NH2" Residue "C PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 698": "NH1" <-> "NH2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D ARG 714": "NH1" <-> "NH2" Residue "D PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 758": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20874 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5218 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 626} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5218 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 626} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5218 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 626} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5218 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 626} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.87, per 1000 atoms: 0.52 Number of scatterers: 20874 At special positions: 0 Unit cell: (143.1, 143.1, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 Na 2 11.00 O 3724 8.00 N 3464 7.00 C 13560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.09 Conformation dependent library (CDL) restraints added in 3.7 seconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 57.9% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 132 through 149 removed outlier: 3.640A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.605A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.858A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.526A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.709A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.518A pdb=" N THR A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.802A pdb=" N ASN A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.669A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.542A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.904A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.667A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.609A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 removed outlier: 3.723A pdb=" N ARG A 371 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N SER A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.592A pdb=" N ILE A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.936A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 459 removed outlier: 3.687A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 505 removed outlier: 3.523A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 535 removed outlier: 3.566A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.925A pdb=" N LEU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 565 Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.809A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 586 through 610 removed outlier: 3.852A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 634 removed outlier: 4.006A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 665 removed outlier: 3.958A pdb=" N PHE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.875A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 704 removed outlier: 3.763A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 132 through 149 removed outlier: 3.640A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.605A pdb=" N PHE B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.858A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.525A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.709A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.518A pdb=" N THR B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.803A pdb=" N ASN B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.670A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.542A pdb=" N ILE B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.903A pdb=" N LEU B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.667A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.608A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 374 removed outlier: 3.723A pdb=" N ARG B 371 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER B 372 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.592A pdb=" N ILE B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.936A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 459 removed outlier: 3.687A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 505 removed outlier: 3.524A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 535 removed outlier: 3.565A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.925A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 565 Processing helix chain 'B' and resid 570 through 576 removed outlier: 3.808A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 586 through 610 removed outlier: 3.852A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 634 removed outlier: 4.005A pdb=" N LEU B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 665 removed outlier: 3.958A pdb=" N PHE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 681 removed outlier: 3.875A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 704 removed outlier: 3.763A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 132 through 149 removed outlier: 3.639A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.605A pdb=" N PHE C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 178 removed outlier: 3.858A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.526A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.709A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.518A pdb=" N THR C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.802A pdb=" N ASN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.670A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.543A pdb=" N ILE C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 3.903A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.668A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.608A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 374 removed outlier: 3.723A pdb=" N ARG C 371 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 removed outlier: 3.592A pdb=" N ILE C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.937A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 459 removed outlier: 3.688A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 454 " --> pdb=" O PHE C 450 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 505 removed outlier: 3.523A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 501 " --> pdb=" O ILE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 535 removed outlier: 3.565A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.925A pdb=" N LEU C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 565 Processing helix chain 'C' and resid 570 through 576 removed outlier: 3.810A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 586 Processing helix chain 'C' and resid 586 through 610 removed outlier: 3.853A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 634 removed outlier: 4.006A pdb=" N LEU C 632 " --> pdb=" O ALA C 628 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 665 removed outlier: 3.958A pdb=" N PHE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 681 removed outlier: 3.875A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 704 removed outlier: 3.763A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 132 through 149 removed outlier: 3.639A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.605A pdb=" N PHE D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.858A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.526A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.709A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.518A pdb=" N THR D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 272 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.803A pdb=" N ASN D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.669A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.543A pdb=" N ILE D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER D 328 " --> pdb=" O ILE D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 3.904A pdb=" N LEU D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.667A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.608A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 374 removed outlier: 3.723A pdb=" N ARG D 371 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER D 372 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 374 " --> pdb=" O ARG D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.592A pdb=" N ILE D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.936A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 459 removed outlier: 3.688A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 454 " --> pdb=" O PHE D 450 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 505 removed outlier: 3.523A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 501 " --> pdb=" O ILE D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 535 removed outlier: 3.565A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.926A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 565 Processing helix chain 'D' and resid 570 through 576 removed outlier: 3.809A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 Processing helix chain 'D' and resid 586 through 610 removed outlier: 3.853A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 634 removed outlier: 4.006A pdb=" N LEU D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 665 removed outlier: 3.958A pdb=" N PHE D 656 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 681 removed outlier: 3.875A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 704 removed outlier: 3.763A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA2, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AA3, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AA4, first strand: chain 'D' and resid 387 through 388 764 hydrogen bonds defined for protein. 2244 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: 5.74 Time building geometry restraints manager: 7.78 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: 6542 1.34 - 1.46: 5002 1.46 - 1.58: 9576 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 21324 Sorted by residual: bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.80e+00 bond pdb=" C VAL D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.66e+00 bond pdb=" C VAL C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.66e+00 bond pdb=" C VAL A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.66e+00 bond pdb=" C ASP D 752 " pdb=" N PRO D 753 " ideal model delta sigma weight residual 1.328 1.360 -0.032 1.25e-02 6.40e+03 6.44e+00 ... (remaining 21319 not shown) Histogram of bond angle deviations from ideal: 98.95 - 106.10: 358 106.10 - 113.26: 11441 113.26 - 120.42: 8775 120.42 - 127.58: 8090 127.58 - 134.74: 208 Bond angle restraints: 28872 Sorted by residual: angle pdb=" N ILE B 652 " pdb=" CA ILE B 652 " pdb=" C ILE B 652 " ideal model delta sigma weight residual 112.29 105.14 7.15 9.40e-01 1.13e+00 5.78e+01 angle pdb=" N ILE A 652 " pdb=" CA ILE A 652 " pdb=" C ILE A 652 " ideal model delta sigma weight residual 112.29 105.19 7.10 9.40e-01 1.13e+00 5.70e+01 angle pdb=" N ILE C 652 " pdb=" CA ILE C 652 " pdb=" C ILE C 652 " ideal model delta sigma weight residual 112.29 105.19 7.10 9.40e-01 1.13e+00 5.70e+01 angle pdb=" N ILE D 652 " pdb=" CA ILE D 652 " pdb=" C ILE D 652 " ideal model delta sigma weight residual 112.29 105.22 7.07 9.40e-01 1.13e+00 5.65e+01 angle pdb=" N LYS D 686 " pdb=" CA LYS D 686 " pdb=" C LYS D 686 " ideal model delta sigma weight residual 114.39 105.24 9.15 1.45e+00 4.76e-01 3.98e+01 ... (remaining 28867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 11599 15.63 - 31.27: 853 31.27 - 46.90: 244 46.90 - 62.54: 28 62.54 - 78.17: 28 Dihedral angle restraints: 12752 sinusoidal: 5152 harmonic: 7600 Sorted by residual: dihedral pdb=" CA SER A 648 " pdb=" C SER A 648 " pdb=" N THR A 649 " pdb=" CA THR A 649 " ideal model delta harmonic sigma weight residual -180.00 -131.59 -48.41 0 5.00e+00 4.00e-02 9.37e+01 dihedral pdb=" CA SER D 648 " pdb=" C SER D 648 " pdb=" N THR D 649 " pdb=" CA THR D 649 " ideal model delta harmonic sigma weight residual -180.00 -131.62 -48.38 0 5.00e+00 4.00e-02 9.36e+01 dihedral pdb=" CA SER B 648 " pdb=" C SER B 648 " pdb=" N THR B 649 " pdb=" CA THR B 649 " ideal model delta harmonic sigma weight residual -180.00 -131.66 -48.34 0 5.00e+00 4.00e-02 9.35e+01 ... (remaining 12749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2310 0.051 - 0.103: 710 0.103 - 0.154: 190 0.154 - 0.205: 74 0.205 - 0.257: 24 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CB THR D 740 " pdb=" CA THR D 740 " pdb=" OG1 THR D 740 " pdb=" CG2 THR D 740 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR C 740 " pdb=" CA THR C 740 " pdb=" OG1 THR C 740 " pdb=" CG2 THR C 740 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR A 740 " pdb=" CA THR A 740 " pdb=" OG1 THR A 740 " pdb=" CG2 THR A 740 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3305 not shown) Planarity restraints: 3608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 754 " -0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO B 755 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 755 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 755 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 754 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.72e+00 pdb=" N PRO A 755 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 755 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 755 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 754 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO D 755 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 755 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 755 " -0.042 5.00e-02 4.00e+02 ... (remaining 3605 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 5115 2.78 - 3.31: 19004 3.31 - 3.84: 31607 3.84 - 4.37: 36282 4.37 - 4.90: 61241 Nonbonded interactions: 153249 Sorted by model distance: nonbonded pdb=" NH2 ARG C 464 " pdb=" O GLU C 467 " model vdw 2.256 2.520 nonbonded pdb=" NH2 ARG A 464 " pdb=" O GLU A 467 " model vdw 2.256 2.520 nonbonded pdb=" NH2 ARG B 464 " pdb=" O GLU B 467 " model vdw 2.256 2.520 nonbonded pdb=" NH2 ARG D 464 " pdb=" O GLU D 467 " model vdw 2.256 2.520 nonbonded pdb=" OE2 GLU A 751 " pdb=" NZ LYS B 174 " model vdw 2.298 2.520 ... (remaining 153244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 115 through 758) selection = (chain 'B' and resid 115 through 758) selection = chain 'C' selection = chain 'D' } 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: 0.570 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: 0.020 Extract box with map and model: 3.030 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 51.000 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.006 0.065 21324 Z= 0.398 Angle : 1.328 14.338 28872 Z= 0.769 Chirality : 0.060 0.257 3308 Planarity : 0.007 0.078 3608 Dihedral : 12.870 78.173 7816 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.21 % Favored : 85.32 % Rotamer: Outliers : 1.23 % Allowed : 8.11 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.44 % 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: -6.84 (0.09), residues: 2568 helix: -4.54 (0.06), residues: 1420 sheet: None (None), residues: 0 loop : -4.50 (0.13), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 692 HIS 0.012 0.002 HIS B 301 PHE 0.043 0.003 PHE D 542 TYR 0.036 0.002 TYR D 213 ARG 0.011 0.001 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 848 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 8 residues processed: 868 average time/residue: 0.3235 time to fit residues: 437.8297 Evaluate side-chains 474 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 466 time to evaluate : 2.578 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1844 time to fit residues: 6.1903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 232 optimal weight: 9.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 HIS A 426 HIS A 483 GLN A 570 GLN A 585 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 HIS B 426 HIS B 483 GLN B 570 GLN B 585 HIS ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS C 426 HIS C 483 GLN C 570 GLN C 585 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS D 426 HIS D 483 GLN D 570 GLN D 585 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21324 Z= 0.298 Angle : 0.846 13.244 28872 Z= 0.443 Chirality : 0.046 0.231 3308 Planarity : 0.006 0.070 3608 Dihedral : 7.718 44.121 2804 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.56 % Favored : 85.24 % Rotamer: Outliers : 0.18 % Allowed : 4.98 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: -4.89 (0.13), residues: 2568 helix: -2.44 (0.11), residues: 1460 sheet: None (None), residues: 0 loop : -4.43 (0.14), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 739 HIS 0.005 0.001 HIS B 160 PHE 0.032 0.002 PHE A 249 TYR 0.022 0.002 TYR D 213 ARG 0.004 0.001 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 650 time to evaluate : 2.283 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 654 average time/residue: 0.2981 time to fit residues: 304.8932 Evaluate side-chains 445 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 441 time to evaluate : 2.199 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1772 time to fit residues: 4.3545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 232 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 256 HIS A 523 HIS A 585 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS C 585 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS D 297 ASN D 523 HIS D 585 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21324 Z= 0.320 Angle : 0.822 8.617 28872 Z= 0.426 Chirality : 0.047 0.226 3308 Planarity : 0.005 0.070 3608 Dihedral : 7.186 37.279 2804 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.11 % Favored : 84.70 % Rotamer: Outliers : 0.18 % Allowed : 6.13 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.80 % 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: -4.01 (0.14), residues: 2568 helix: -1.57 (0.12), residues: 1480 sheet: None (None), residues: 0 loop : -4.31 (0.14), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 739 HIS 0.007 0.001 HIS D 523 PHE 0.037 0.002 PHE B 249 TYR 0.019 0.002 TYR A 213 ARG 0.004 0.001 ARG D 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 540 time to evaluate : 2.344 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 outliers start: 4 outliers final: 4 residues processed: 544 average time/residue: 0.2928 time to fit residues: 258.4287 Evaluate side-chains 393 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 389 time to evaluate : 2.346 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1770 time to fit residues: 4.7089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.8627 > 50: distance: 29 - 56: 18.462 distance: 38 - 66: 29.953 distance: 42 - 48: 33.777 distance: 48 - 49: 47.084 distance: 49 - 52: 33.926 distance: 50 - 51: 19.117 distance: 50 - 56: 32.779 distance: 52 - 53: 52.899 distance: 53 - 54: 33.205 distance: 53 - 55: 36.539 distance: 56 - 57: 42.194 distance: 57 - 58: 41.284 distance: 57 - 60: 44.535 distance: 58 - 59: 58.374 distance: 58 - 66: 49.929 distance: 60 - 61: 61.308 distance: 61 - 62: 44.341 distance: 61 - 63: 56.058 distance: 62 - 64: 60.002 distance: 63 - 65: 55.315 distance: 66 - 67: 17.020 distance: 67 - 68: 10.337 distance: 67 - 70: 48.126 distance: 68 - 69: 16.260 distance: 68 - 74: 37.687 distance: 69 - 98: 14.188 distance: 70 - 71: 42.080 distance: 71 - 72: 44.614 distance: 71 - 73: 43.937 distance: 74 - 75: 39.321 distance: 75 - 76: 43.714 distance: 75 - 78: 22.815 distance: 76 - 77: 11.696 distance: 76 - 81: 23.002 distance: 77 - 109: 16.690 distance: 78 - 79: 33.909 distance: 78 - 80: 46.604 distance: 81 - 82: 56.190 distance: 82 - 83: 25.754 distance: 82 - 85: 43.931 distance: 83 - 84: 50.361 distance: 83 - 89: 24.096 distance: 85 - 86: 15.621 distance: 86 - 87: 36.924 distance: 86 - 88: 30.195 distance: 89 - 90: 46.082 distance: 90 - 91: 22.219 distance: 90 - 93: 28.773 distance: 91 - 92: 23.282 distance: 91 - 98: 38.376 distance: 93 - 94: 30.714 distance: 94 - 95: 26.317 distance: 95 - 96: 27.409 distance: 96 - 97: 26.153 distance: 98 - 99: 38.812 distance: 99 - 100: 22.406 distance: 99 - 102: 40.495 distance: 100 - 101: 19.196 distance: 100 - 109: 24.728 distance: 101 - 135: 35.820 distance: 102 - 103: 37.649 distance: 103 - 104: 22.569 distance: 103 - 105: 16.544 distance: 104 - 106: 20.604 distance: 105 - 107: 32.183 distance: 106 - 108: 17.773 distance: 107 - 108: 15.010 distance: 109 - 110: 35.302 distance: 110 - 111: 18.981 distance: 110 - 113: 17.249 distance: 111 - 112: 15.243 distance: 111 - 117: 45.160 distance: 112 - 144: 28.460 distance: 113 - 114: 28.719 distance: 114 - 115: 54.250 distance: 114 - 116: 32.662 distance: 117 - 118: 26.717 distance: 118 - 119: 35.124 distance: 118 - 121: 9.175 distance: 119 - 120: 23.540 distance: 119 - 128: 29.581 distance: 121 - 122: 31.744 distance: 122 - 123: 15.087 distance: 122 - 124: 41.804 distance: 123 - 125: 10.837 distance: 124 - 126: 33.937 distance: 125 - 127: 6.360 distance: 126 - 127: 6.627 distance: 128 - 129: 35.489 distance: 129 - 130: 20.922 distance: 129 - 132: 30.479 distance: 130 - 131: 40.840 distance: 130 - 135: 34.102 distance: 131 - 158: 30.263 distance: 132 - 133: 9.310 distance: 132 - 134: 38.210