Starting phenix.real_space_refine (version: dev) on Wed May 18 05:25:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w21_21521/05_2022/6w21_21521_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w21_21521/05_2022/6w21_21521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w21_21521/05_2022/6w21_21521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w21_21521/05_2022/6w21_21521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w21_21521/05_2022/6w21_21521_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w21_21521/05_2022/6w21_21521_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.001 sd= 0.051 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 48327 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 4419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4419 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4510 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "C" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4510 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "D" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4510 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "E" Number of atoms: 4453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4453 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 18, 'TRANS': 549} Chain breaks: 1 Chain: "F" Number of atoms: 4453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4453 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 18, 'TRANS': 549} Chain breaks: 1 Chain: "X" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "H" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "I" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "J" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "K" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "L" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "M" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "N" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "O" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "P" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "Q" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "R" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "S" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "T" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.93, per 1000 atoms: 0.58 Number of scatterers: 48327 At special positions: 0 Unit cell: (140.112, 144.282, 214.338, 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 252 16.00 P 31 15.00 O 9165 8.00 N 8512 7.00 C 30367 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: 21.52 Conformation dependent library (CDL) restraints added in 7.4 seconds 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11364 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 274 helices and 82 sheets defined 48.0% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 176 through 182 removed outlier: 3.614A pdb=" N VAL A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 220 through 232 removed outlier: 3.630A pdb=" N ALA A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 305 through 312 Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 369 Proline residue: A 363 - end of helix Processing helix chain 'A' and resid 375 through 388 Processing helix chain 'A' and resid 394 through 414 removed outlier: 4.437A pdb=" N ILE A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 423 through 434 Processing helix chain 'A' and resid 445 through 459 removed outlier: 4.236A pdb=" N GLY A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASP A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 478 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'A' and resid 629 through 632 No H-bonds generated for 'chain 'A' and resid 629 through 632' Processing helix chain 'A' and resid 638 through 643 removed outlier: 4.218A pdb=" N ARG A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 676 removed outlier: 4.155A pdb=" N LYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 694 Processing helix chain 'A' and resid 702 through 721 removed outlier: 4.418A pdb=" N ARG A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) Proline residue: A 715 - end of helix Processing helix chain 'B' and resid 176 through 182 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 220 through 232 Processing helix chain 'B' and resid 251 through 254 No H-bonds generated for 'chain 'B' and resid 251 through 254' Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 303 through 312 Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.685A pdb=" N ARG B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 369 Proline residue: B 363 - end of helix Processing helix chain 'B' and resid 375 through 388 Processing helix chain 'B' and resid 394 through 412 removed outlier: 4.640A pdb=" N ILE B 399 " --> pdb=" O PRO B 395 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 434 removed outlier: 3.728A pdb=" N ILE B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 442 No H-bonds generated for 'chain 'B' and resid 440 through 442' Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 464 through 478 Processing helix chain 'B' and resid 501 through 512 removed outlier: 4.116A pdb=" N THR B 505 " --> pdb=" O LYS B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 534 removed outlier: 3.823A pdb=" N ILE B 534 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 571 through 583 removed outlier: 3.530A pdb=" N PHE B 574 " --> pdb=" O PRO B 571 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN B 583 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 612 No H-bonds generated for 'chain 'B' and resid 609 through 612' Processing helix chain 'B' and resid 632 through 635 No H-bonds generated for 'chain 'B' and resid 632 through 635' Processing helix chain 'B' and resid 638 through 643 removed outlier: 4.082A pdb=" N ARG B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 676 removed outlier: 4.423A pdb=" N LYS B 676 " --> pdb=" O GLN B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 693 Processing helix chain 'B' and resid 702 through 721 removed outlier: 4.397A pdb=" N ARG B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS B 714 " --> pdb=" O ASP B 710 " (cutoff:3.500A) Proline residue: B 715 - end of helix Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 220 through 233 removed outlier: 3.928A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 No H-bonds generated for 'chain 'C' and resid 250 through 253' Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 303 through 306 No H-bonds generated for 'chain 'C' and resid 303 through 306' Processing helix chain 'C' and resid 308 through 312 removed outlier: 3.609A pdb=" N SER C 312 " --> pdb=" O LYS C 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 308 through 312' Processing helix chain 'C' and resid 324 through 333 removed outlier: 4.586A pdb=" N GLU C 332 " --> pdb=" O SER C 328 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LYS C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.765A pdb=" N ARG C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 369 Proline residue: C 363 - end of helix Processing helix chain 'C' and resid 375 through 388 Processing helix chain 'C' and resid 394 through 415 removed outlier: 4.340A pdb=" N ILE C 399 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Proline residue: C 413 - end of helix Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 464 through 478 Processing helix chain 'C' and resid 501 through 512 removed outlier: 3.969A pdb=" N THR C 505 " --> pdb=" O LYS C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 524 Processing helix chain 'C' and resid 527 through 534 removed outlier: 3.885A pdb=" N SER C 531 " --> pdb=" O HIS C 528 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 534 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 548 through 555 Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 573 through 583 removed outlier: 3.509A pdb=" N LEU C 578 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN C 583 " --> pdb=" O VAL C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 612 No H-bonds generated for 'chain 'C' and resid 609 through 612' Processing helix chain 'C' and resid 625 through 635 removed outlier: 3.824A pdb=" N ALA C 628 " --> pdb=" O SER C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 643 removed outlier: 3.748A pdb=" N ARG C 643 " --> pdb=" O GLU C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 676 Processing helix chain 'C' and resid 684 through 694 Processing helix chain 'C' and resid 697 through 699 No H-bonds generated for 'chain 'C' and resid 697 through 699' Processing helix chain 'C' and resid 702 through 721 removed outlier: 4.230A pdb=" N LYS C 714 " --> pdb=" O ASP C 710 " (cutoff:3.500A) Proline residue: C 715 - end of helix Processing helix chain 'D' and resid 176 through 181 Processing helix chain 'D' and resid 192 through 203 Processing helix chain 'D' and resid 220 through 233 removed outlier: 4.142A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 262 through 277 Processing helix chain 'D' and resid 287 through 290 Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 324 through 333 removed outlier: 4.677A pdb=" N GLU D 332 " --> pdb=" O SER D 328 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 351 through 369 Proline residue: D 363 - end of helix Processing helix chain 'D' and resid 375 through 388 Processing helix chain 'D' and resid 394 through 414 removed outlier: 3.840A pdb=" N ILE D 399 " --> pdb=" O PRO D 395 " (cutoff:3.500A) Proline residue: D 413 - end of helix Processing helix chain 'D' and resid 423 through 433 Processing helix chain 'D' and resid 444 through 450 Processing helix chain 'D' and resid 452 through 457 Processing helix chain 'D' and resid 464 through 478 Processing helix chain 'D' and resid 501 through 512 removed outlier: 3.921A pdb=" N THR D 505 " --> pdb=" O LYS D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 524 Processing helix chain 'D' and resid 527 through 534 removed outlier: 3.582A pdb=" N VAL D 530 " --> pdb=" O ARG D 527 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 531 " --> pdb=" O HIS D 528 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE D 534 " --> pdb=" O SER D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 548 through 555 Processing helix chain 'D' and resid 566 through 568 No H-bonds generated for 'chain 'D' and resid 566 through 568' Processing helix chain 'D' and resid 571 through 583 Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 625 through 635 Processing helix chain 'D' and resid 638 through 642 Processing helix chain 'D' and resid 655 through 676 removed outlier: 3.521A pdb=" N LYS D 676 " --> pdb=" O GLN D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 694 Processing helix chain 'D' and resid 697 through 699 No H-bonds generated for 'chain 'D' and resid 697 through 699' Processing helix chain 'D' and resid 702 through 722 removed outlier: 3.679A pdb=" N ARG D 706 " --> pdb=" O ARG D 702 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS D 714 " --> pdb=" O ASP D 710 " (cutoff:3.500A) Proline residue: D 715 - end of helix Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 220 through 233 Processing helix chain 'E' and resid 250 through 256 removed outlier: 4.833A pdb=" N GLY E 256 " --> pdb=" O SER E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 277 Processing helix chain 'E' and resid 287 through 290 No H-bonds generated for 'chain 'E' and resid 287 through 290' Processing helix chain 'E' and resid 304 through 311 Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 335 through 338 No H-bonds generated for 'chain 'E' and resid 335 through 338' Processing helix chain 'E' and resid 351 through 369 Proline residue: E 363 - end of helix Processing helix chain 'E' and resid 375 through 387 Processing helix chain 'E' and resid 394 through 411 Processing helix chain 'E' and resid 423 through 433 Processing helix chain 'E' and resid 441 through 444 No H-bonds generated for 'chain 'E' and resid 441 through 444' Processing helix chain 'E' and resid 446 through 449 No H-bonds generated for 'chain 'E' and resid 446 through 449' Processing helix chain 'E' and resid 452 through 459 Processing helix chain 'E' and resid 464 through 478 Processing helix chain 'E' and resid 501 through 511 Processing helix chain 'E' and resid 521 through 524 Processing helix chain 'E' and resid 527 through 534 removed outlier: 4.008A pdb=" N VAL E 530 " --> pdb=" O ARG E 527 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 531 " --> pdb=" O HIS E 528 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE E 534 " --> pdb=" O SER E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 555 Processing helix chain 'E' and resid 566 through 568 No H-bonds generated for 'chain 'E' and resid 566 through 568' Processing helix chain 'E' and resid 571 through 583 removed outlier: 3.928A pdb=" N ASN E 575 " --> pdb=" O PRO E 571 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE E 576 " --> pdb=" O ASP E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 612 No H-bonds generated for 'chain 'E' and resid 610 through 612' Processing helix chain 'E' and resid 625 through 635 removed outlier: 3.680A pdb=" N ILE E 635 " --> pdb=" O ILE E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 641 No H-bonds generated for 'chain 'E' and resid 638 through 641' Processing helix chain 'E' and resid 655 through 676 removed outlier: 3.655A pdb=" N GLN E 675 " --> pdb=" O VAL E 671 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS E 676 " --> pdb=" O GLN E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 693 Processing helix chain 'E' and resid 697 through 699 No H-bonds generated for 'chain 'E' and resid 697 through 699' Processing helix chain 'E' and resid 702 through 722 removed outlier: 4.353A pdb=" N LYS E 714 " --> pdb=" O ASP E 710 " (cutoff:3.500A) Proline residue: E 715 - end of helix Processing helix chain 'E' and resid 724 through 727 removed outlier: 4.380A pdb=" N ASP E 727 " --> pdb=" O SER E 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 724 through 727' Processing helix chain 'F' and resid 176 through 182 Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 220 through 233 removed outlier: 3.581A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 241 No H-bonds generated for 'chain 'F' and resid 238 through 241' Processing helix chain 'F' and resid 250 through 253 No H-bonds generated for 'chain 'F' and resid 250 through 253' Processing helix chain 'F' and resid 260 through 276 Processing helix chain 'F' and resid 287 through 291 Processing helix chain 'F' and resid 307 through 313 Processing helix chain 'F' and resid 324 through 328 Processing helix chain 'F' and resid 335 through 338 No H-bonds generated for 'chain 'F' and resid 335 through 338' Processing helix chain 'F' and resid 351 through 369 Proline residue: F 363 - end of helix Processing helix chain 'F' and resid 375 through 388 removed outlier: 4.409A pdb=" N LYS F 387 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 410 removed outlier: 3.877A pdb=" N ARG F 410 " --> pdb=" O GLY F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 434 Processing helix chain 'F' and resid 447 through 450 No H-bonds generated for 'chain 'F' and resid 447 through 450' Processing helix chain 'F' and resid 452 through 457 Processing helix chain 'F' and resid 464 through 478 Processing helix chain 'F' and resid 501 through 512 Processing helix chain 'F' and resid 521 through 524 Processing helix chain 'F' and resid 527 through 534 removed outlier: 3.989A pdb=" N ARG F 532 " --> pdb=" O HIS F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 548 through 555 Processing helix chain 'F' and resid 566 through 568 No H-bonds generated for 'chain 'F' and resid 566 through 568' Processing helix chain 'F' and resid 571 through 583 Processing helix chain 'F' and resid 609 through 613 Processing helix chain 'F' and resid 629 through 635 Processing helix chain 'F' and resid 638 through 643 Processing helix chain 'F' and resid 655 through 675 Processing helix chain 'F' and resid 684 through 694 Processing helix chain 'F' and resid 702 through 721 removed outlier: 3.660A pdb=" N ALA F 705 " --> pdb=" O ARG F 702 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS F 713 " --> pdb=" O ASP F 710 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS F 714 " --> pdb=" O ASN F 711 " (cutoff:3.500A) Proline residue: F 715 - end of helix removed outlier: 3.559A pdb=" N LEU F 721 " --> pdb=" O ASN F 718 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 67 Processing helix chain 'G' and resid 84 through 96 Processing helix chain 'G' and resid 111 through 118 Processing helix chain 'G' and resid 146 through 171 Processing helix chain 'G' and resid 175 through 181 Processing helix chain 'G' and resid 190 through 196 Processing helix chain 'H' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU H 40 " --> pdb=" O ARG H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 67 Processing helix chain 'H' and resid 84 through 96 Processing helix chain 'H' and resid 111 through 118 Processing helix chain 'H' and resid 146 through 171 Processing helix chain 'H' and resid 175 through 181 Processing helix chain 'H' and resid 190 through 196 Processing helix chain 'I' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU I 40 " --> pdb=" O ARG I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 67 Processing helix chain 'I' and resid 84 through 96 Processing helix chain 'I' and resid 111 through 118 Processing helix chain 'I' and resid 146 through 171 Processing helix chain 'I' and resid 175 through 181 Processing helix chain 'I' and resid 190 through 196 Processing helix chain 'J' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU J 40 " --> pdb=" O ARG J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 67 Processing helix chain 'J' and resid 84 through 96 Processing helix chain 'J' and resid 111 through 118 Processing helix chain 'J' and resid 146 through 171 Processing helix chain 'J' and resid 175 through 181 Processing helix chain 'J' and resid 190 through 196 Processing helix chain 'K' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU K 40 " --> pdb=" O ARG K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 67 Processing helix chain 'K' and resid 84 through 96 Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'K' and resid 146 through 171 Processing helix chain 'K' and resid 175 through 181 Processing helix chain 'K' and resid 190 through 196 Processing helix chain 'L' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU L 40 " --> pdb=" O ARG L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 67 Processing helix chain 'L' and resid 84 through 96 Processing helix chain 'L' and resid 111 through 118 Processing helix chain 'L' and resid 146 through 171 Processing helix chain 'L' and resid 175 through 181 Processing helix chain 'L' and resid 190 through 196 Processing helix chain 'M' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU M 40 " --> pdb=" O ARG M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 67 Processing helix chain 'M' and resid 84 through 96 Processing helix chain 'M' and resid 111 through 118 Processing helix chain 'M' and resid 146 through 171 Processing helix chain 'M' and resid 175 through 181 Processing helix chain 'M' and resid 190 through 196 Processing helix chain 'N' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU N 40 " --> pdb=" O ARG N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 67 Processing helix chain 'N' and resid 84 through 96 Processing helix chain 'N' and resid 111 through 118 Processing helix chain 'N' and resid 146 through 171 Processing helix chain 'N' and resid 175 through 181 Processing helix chain 'N' and resid 190 through 196 Processing helix chain 'O' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU O 40 " --> pdb=" O ARG O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 67 Processing helix chain 'O' and resid 84 through 96 Processing helix chain 'O' and resid 111 through 118 Processing helix chain 'O' and resid 146 through 171 Processing helix chain 'O' and resid 175 through 181 Processing helix chain 'O' and resid 190 through 196 Processing helix chain 'P' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU P 40 " --> pdb=" O ARG P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 67 Processing helix chain 'P' and resid 84 through 96 Processing helix chain 'P' and resid 111 through 118 Processing helix chain 'P' and resid 146 through 171 Processing helix chain 'P' and resid 175 through 181 Processing helix chain 'P' and resid 190 through 196 Processing helix chain 'Q' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU Q 40 " --> pdb=" O ARG Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 67 Processing helix chain 'Q' and resid 84 through 96 Processing helix chain 'Q' and resid 111 through 118 Processing helix chain 'Q' and resid 146 through 171 Processing helix chain 'Q' and resid 175 through 181 Processing helix chain 'Q' and resid 190 through 196 Processing helix chain 'R' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU R 40 " --> pdb=" O ARG R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 67 Processing helix chain 'R' and resid 84 through 96 Processing helix chain 'R' and resid 111 through 118 Processing helix chain 'R' and resid 146 through 171 Processing helix chain 'R' and resid 175 through 181 Processing helix chain 'R' and resid 190 through 196 Processing helix chain 'S' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU S 40 " --> pdb=" O ARG S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 67 Processing helix chain 'S' and resid 84 through 96 Processing helix chain 'S' and resid 111 through 118 Processing helix chain 'S' and resid 146 through 171 Processing helix chain 'S' and resid 175 through 181 Processing helix chain 'S' and resid 190 through 196 Processing helix chain 'T' and resid 33 through 40 removed outlier: 3.824A pdb=" N GLU T 40 " --> pdb=" O ARG T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 Processing helix chain 'T' and resid 84 through 96 Processing helix chain 'T' and resid 111 through 118 Processing helix chain 'T' and resid 146 through 171 Processing helix chain 'T' and resid 175 through 181 Processing helix chain 'T' and resid 190 through 196 Processing sheet with id= A, first strand: chain 'A' and resid 173 through 175 removed outlier: 6.827A pdb=" N ARG A 317 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE A 284 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 319 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 342 through 345 removed outlier: 6.492A pdb=" N GLY A 320 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY A 214 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR A 322 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 646 through 649 removed outlier: 3.546A pdb=" N ASN A 646 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 585 through 587 Processing sheet with id= E, first strand: chain 'A' and resid 679 through 682 Processing sheet with id= F, first strand: chain 'B' and resid 173 through 175 removed outlier: 6.932A pdb=" N ARG B 317 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILE B 284 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 319 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN B 342 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 213 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE B 344 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 646 through 650 removed outlier: 3.811A pdb=" N ASN B 646 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY B 489 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA B 559 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL B 602 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU B 561 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR B 604 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 563 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU B 515 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU B 562 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 517 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASP B 564 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE B 519 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 585 through 587 Processing sheet with id= I, first strand: chain 'B' and resid 679 through 682 removed outlier: 3.564A pdb=" N GLY B 745 " --> pdb=" O THR B 732 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.462A pdb=" N ILE C 281 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU C 248 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE C 283 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER C 321 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN C 342 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL C 213 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE C 344 " --> pdb=" O VAL C 213 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 646 through 649 removed outlier: 3.798A pdb=" N ASN C 646 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 489 " --> pdb=" O VAL C 599 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ALA C 559 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL C 602 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU C 561 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR C 604 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU C 563 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU C 515 " --> pdb=" O VAL C 560 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU C 562 " --> pdb=" O GLU C 515 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU C 517 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP C 564 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE C 519 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 585 through 587 Processing sheet with id= M, first strand: chain 'C' and resid 679 through 682 Processing sheet with id= N, first strand: chain 'D' and resid 173 through 175 removed outlier: 5.142A pdb=" N ASP D 285 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG D 317 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE D 284 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE D 319 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN D 342 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL D 213 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE D 344 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 646 through 650 removed outlier: 3.715A pdb=" N ASN D 646 " --> pdb=" O SER D 490 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY D 489 " --> pdb=" O VAL D 599 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY D 495 " --> pdb=" O THR D 605 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA D 559 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL D 602 " --> pdb=" O ALA D 559 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU D 561 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR D 604 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU D 563 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU D 515 " --> pdb=" O VAL D 560 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU D 562 " --> pdb=" O GLU D 515 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU D 517 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASP D 564 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE D 519 " --> pdb=" O ASP D 564 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 585 through 587 Processing sheet with id= Q, first strand: chain 'D' and resid 680 through 682 removed outlier: 6.441A pdb=" N VAL D 731 " --> pdb=" O GLU D 681 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 173 through 175 removed outlier: 6.401A pdb=" N ILE E 281 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU E 248 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N PHE E 283 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG E 317 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 342 through 345 removed outlier: 5.946A pdb=" N GLY E 320 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 646 through 649 removed outlier: 4.005A pdb=" N GLY E 489 " --> pdb=" O VAL E 599 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA E 559 " --> pdb=" O VAL E 600 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL E 602 " --> pdb=" O ALA E 559 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU E 561 " --> pdb=" O VAL E 602 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR E 604 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU E 563 " --> pdb=" O THR E 604 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU E 515 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU E 562 " --> pdb=" O GLU E 515 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU E 517 " --> pdb=" O LEU E 562 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP E 564 " --> pdb=" O LEU E 517 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE E 519 " --> pdb=" O ASP E 564 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 585 through 587 Processing sheet with id= V, first strand: chain 'E' and resid 678 through 682 removed outlier: 6.593A pdb=" N GLY E 729 " --> pdb=" O SER E 679 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLU E 681 " --> pdb=" O GLY E 729 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL E 731 " --> pdb=" O GLU E 681 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 173 through 175 removed outlier: 6.614A pdb=" N ILE F 281 " --> pdb=" O TYR F 246 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU F 248 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE F 283 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER F 321 " --> pdb=" O ILE F 284 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 646 through 649 removed outlier: 3.504A pdb=" N ASN F 646 " --> pdb=" O SER F 490 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU F 601 " --> pdb=" O PHE F 491 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N PHE F 493 " --> pdb=" O LEU F 601 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N MET F 603 " --> pdb=" O PHE F 493 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 585 through 587 removed outlier: 3.663A pdb=" N LEU F 586 " --> pdb=" O ALA F 594 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA F 594 " --> pdb=" O LEU F 586 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 678 through 682 removed outlier: 5.884A pdb=" N GLY F 729 " --> pdb=" O SER F 679 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLU F 681 " --> pdb=" O GLY F 729 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL F 731 " --> pdb=" O GLU F 681 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 19 through 22 Processing sheet with id= AB, first strand: chain 'G' and resid 42 through 46 removed outlier: 6.220A pdb=" N TYR G 74 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU G 45 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR G 76 " --> pdb=" O LEU G 45 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 126 through 128 removed outlier: 6.681A pdb=" N SER G 201 " --> pdb=" O CYS G 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'G' and resid 133 through 135 Processing sheet with id= AE, first strand: chain 'H' and resid 19 through 22 Processing sheet with id= AF, first strand: chain 'H' and resid 42 through 46 removed outlier: 6.220A pdb=" N TYR H 74 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU H 45 " --> pdb=" O TYR H 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR H 76 " --> pdb=" O LEU H 45 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 126 through 128 removed outlier: 6.680A pdb=" N SER H 201 " --> pdb=" O CYS H 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'H' and resid 133 through 135 Processing sheet with id= AI, first strand: chain 'I' and resid 19 through 22 Processing sheet with id= AJ, first strand: chain 'I' and resid 42 through 46 removed outlier: 6.220A pdb=" N TYR I 74 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU I 45 " --> pdb=" O TYR I 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR I 76 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 126 through 128 removed outlier: 6.681A pdb=" N SER I 201 " --> pdb=" O CYS I 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'I' and resid 133 through 135 Processing sheet with id= AM, first strand: chain 'J' and resid 19 through 22 Processing sheet with id= AN, first strand: chain 'J' and resid 42 through 46 removed outlier: 6.220A pdb=" N TYR J 74 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU J 45 " --> pdb=" O TYR J 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR J 76 " --> pdb=" O LEU J 45 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'J' and resid 126 through 128 removed outlier: 6.682A pdb=" N SER J 201 " --> pdb=" O CYS J 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'J' and resid 133 through 135 Processing sheet with id= AQ, first strand: chain 'K' and resid 19 through 22 Processing sheet with id= AR, first strand: chain 'K' and resid 42 through 46 removed outlier: 6.220A pdb=" N TYR K 74 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU K 45 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR K 76 " --> pdb=" O LEU K 45 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'K' and resid 126 through 128 removed outlier: 6.682A pdb=" N SER K 201 " --> pdb=" O CYS K 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'K' and resid 133 through 135 Processing sheet with id= AU, first strand: chain 'L' and resid 19 through 22 Processing sheet with id= AV, first strand: chain 'L' and resid 42 through 46 removed outlier: 6.219A pdb=" N TYR L 74 " --> pdb=" O ILE L 43 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU L 45 " --> pdb=" O TYR L 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR L 76 " --> pdb=" O LEU L 45 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'L' and resid 126 through 128 removed outlier: 6.682A pdb=" N SER L 201 " --> pdb=" O CYS L 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'L' and resid 133 through 135 Processing sheet with id= AY, first strand: chain 'M' and resid 19 through 22 Processing sheet with id= AZ, first strand: chain 'M' and resid 42 through 46 removed outlier: 6.220A pdb=" N TYR M 74 " --> pdb=" O ILE M 43 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU M 45 " --> pdb=" O TYR M 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR M 76 " --> pdb=" O LEU M 45 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'M' and resid 126 through 128 removed outlier: 6.681A pdb=" N SER M 201 " --> pdb=" O CYS M 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'M' and resid 133 through 135 Processing sheet with id= BC, first strand: chain 'N' and resid 19 through 22 Processing sheet with id= BD, first strand: chain 'N' and resid 42 through 46 removed outlier: 6.220A pdb=" N TYR N 74 " --> pdb=" O ILE N 43 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU N 45 " --> pdb=" O TYR N 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR N 76 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'N' and resid 126 through 128 removed outlier: 6.680A pdb=" N SER N 201 " --> pdb=" O CYS N 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'N' and resid 133 through 135 Processing sheet with id= BG, first strand: chain 'O' and resid 19 through 22 Processing sheet with id= BH, first strand: chain 'O' and resid 42 through 46 removed outlier: 6.220A pdb=" N TYR O 74 " --> pdb=" O ILE O 43 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU O 45 " --> pdb=" O TYR O 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR O 76 " --> pdb=" O LEU O 45 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'O' and resid 126 through 128 removed outlier: 6.681A pdb=" N SER O 201 " --> pdb=" O CYS O 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'O' and resid 133 through 135 Processing sheet with id= BK, first strand: chain 'P' and resid 19 through 22 Processing sheet with id= BL, first strand: chain 'P' and resid 42 through 46 removed outlier: 6.220A pdb=" N TYR P 74 " --> pdb=" O ILE P 43 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU P 45 " --> pdb=" O TYR P 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR P 76 " --> pdb=" O LEU P 45 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'P' and resid 126 through 128 removed outlier: 6.680A pdb=" N SER P 201 " --> pdb=" O CYS P 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'P' and resid 133 through 135 Processing sheet with id= BO, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id= BP, first strand: chain 'Q' and resid 42 through 46 removed outlier: 6.219A pdb=" N TYR Q 74 " --> pdb=" O ILE Q 43 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU Q 45 " --> pdb=" O TYR Q 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR Q 76 " --> pdb=" O LEU Q 45 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'Q' and resid 126 through 128 removed outlier: 6.681A pdb=" N SER Q 201 " --> pdb=" O CYS Q 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BQ Processing sheet with id= BR, first strand: chain 'Q' and resid 133 through 135 Processing sheet with id= BS, first strand: chain 'R' and resid 19 through 22 Processing sheet with id= BT, first strand: chain 'R' and resid 42 through 46 removed outlier: 6.221A pdb=" N TYR R 74 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU R 45 " --> pdb=" O TYR R 74 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR R 76 " --> pdb=" O LEU R 45 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'R' and resid 126 through 128 removed outlier: 6.681A pdb=" N SER R 201 " --> pdb=" O CYS R 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'R' and resid 133 through 135 Processing sheet with id= BW, first strand: chain 'S' and resid 19 through 22 Processing sheet with id= BX, first strand: chain 'S' and resid 42 through 46 removed outlier: 6.220A pdb=" N TYR S 74 " --> pdb=" O ILE S 43 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU S 45 " --> pdb=" O TYR S 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR S 76 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'S' and resid 126 through 128 removed outlier: 6.681A pdb=" N SER S 201 " --> pdb=" O CYS S 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BY Processing sheet with id= BZ, first strand: chain 'S' and resid 133 through 135 Processing sheet with id= CA, first strand: chain 'T' and resid 19 through 22 Processing sheet with id= CB, first strand: chain 'T' and resid 42 through 46 removed outlier: 6.220A pdb=" N TYR T 74 " --> pdb=" O ILE T 43 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU T 45 " --> pdb=" O TYR T 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR T 76 " --> pdb=" O LEU T 45 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'T' and resid 126 through 128 removed outlier: 6.682A pdb=" N SER T 201 " --> pdb=" O CYS T 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= CC Processing sheet with id= CD, first strand: chain 'T' and resid 133 through 135 2054 hydrogen bonds defined for protein. 5820 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: 20.37 Time building geometry restraints manager: 22.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12196 1.33 - 1.45: 8238 1.45 - 1.57: 28122 1.57 - 1.69: 58 1.69 - 1.81: 464 Bond restraints: 49078 Sorted by residual: bond pdb=" C3' ADP A 801 " pdb=" C4' ADP A 801 " ideal model delta sigma weight residual 1.524 1.332 0.192 2.00e-02 2.50e+03 9.17e+01 bond pdb=" C3' ADP F 801 " pdb=" C4' ADP F 801 " ideal model delta sigma weight residual 1.524 1.333 0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C3' ADP A 802 " pdb=" C4' ADP A 802 " ideal model delta sigma weight residual 1.524 1.334 0.190 2.00e-02 2.50e+03 9.07e+01 bond pdb=" C3' ADP F 802 " pdb=" C4' ADP F 802 " ideal model delta sigma weight residual 1.524 1.334 0.190 2.00e-02 2.50e+03 9.04e+01 bond pdb=" C4' ADP F 801 " pdb=" O4' ADP F 801 " ideal model delta sigma weight residual 1.426 1.594 -0.168 2.00e-02 2.50e+03 7.04e+01 ... (remaining 49073 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.79: 1310 106.79 - 114.18: 29650 114.18 - 121.58: 24459 121.58 - 128.97: 10588 128.97 - 136.37: 266 Bond angle restraints: 66273 Sorted by residual: angle pdb=" PB ATP D 801 " pdb=" O3B ATP D 801 " pdb=" PG ATP D 801 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 120.49 19.38 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP C 802 " pdb=" O3B ATP C 802 " pdb=" PG ATP C 802 " ideal model delta sigma weight residual 139.87 120.49 19.38 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 ... (remaining 66268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.22: 28963 28.22 - 56.44: 827 56.44 - 84.66: 90 84.66 - 112.88: 34 112.88 - 141.10: 4 Dihedral angle restraints: 29918 sinusoidal: 12288 harmonic: 17630 Sorted by residual: dihedral pdb=" O1B ADP B 802 " pdb=" O3A ADP B 802 " pdb=" PB ADP B 802 " pdb=" PA ADP B 802 " ideal model delta sinusoidal sigma weight residual 300.00 158.89 141.10 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O2A ADP F 802 " pdb=" O3A ADP F 802 " pdb=" PA ADP F 802 " pdb=" PB ADP F 802 " ideal model delta sinusoidal sigma weight residual 300.00 175.82 124.18 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" O1B ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " pdb=" PA ADP A 802 " ideal model delta sinusoidal sigma weight residual 300.00 178.60 121.39 1 2.00e+01 2.50e-03 3.65e+01 ... (remaining 29915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 6596 0.061 - 0.123: 947 0.123 - 0.184: 32 0.184 - 0.246: 0 0.246 - 0.307: 3 Chirality restraints: 7578 Sorted by residual: chirality pdb=" CA ILE F 620 " pdb=" N ILE F 620 " pdb=" C ILE F 620 " pdb=" CB ILE F 620 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA SER C 442 " pdb=" N SER C 442 " pdb=" C SER C 442 " pdb=" CB SER C 442 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA GLN C 443 " pdb=" N GLN C 443 " pdb=" C GLN C 443 " pdb=" CB GLN C 443 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 7575 not shown) Planarity restraints: 8557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 412 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.71e+00 pdb=" N PRO C 413 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 413 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 413 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 412 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.23e+00 pdb=" N PRO A 413 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 413 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 413 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 394 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO C 395 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 395 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 395 " 0.025 5.00e-02 4.00e+02 ... (remaining 8554 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 649 2.56 - 3.15: 41407 3.15 - 3.73: 81395 3.73 - 4.32: 111957 4.32 - 4.90: 182301 Nonbonded interactions: 417709 Sorted by model distance: nonbonded pdb=" O LYS C 439 " pdb=" O SER C 440 " model vdw 1.978 3.040 nonbonded pdb=" OD1 ASP K 92 " pdb=" ND2 ASN L 130 " model vdw 2.197 2.520 nonbonded pdb=" C GLY C 495 " pdb=" NZ LYS C 501 " model vdw 2.198 3.350 nonbonded pdb=" O GLY E 535 " pdb=" ND2 ASN E 589 " model vdw 2.203 2.520 nonbonded pdb=" OD1 ASP L 92 " pdb=" ND2 ASN M 130 " model vdw 2.208 2.520 ... (remaining 417704 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 169 through 292 or resid 303 through 746)) selection = (chain 'B' and (resid 169 through 292 or resid 303 through 609 or resid 615 thro \ ugh 746)) selection = (chain 'C' and (resid 169 through 292 or resid 303 through 609 or resid 615 thro \ ugh 746)) selection = (chain 'D' and (resid 169 through 292 or resid 303 through 609 or resid 615 thro \ ugh 746)) selection = (chain 'E' and (resid 169 through 609 or resid 615 through 746)) selection = (chain 'F' and (resid 169 through 609 or resid 615 through 746)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 252 5.16 5 C 30367 2.51 5 N 8512 2.21 5 O 9165 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 13.490 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: 0.050 Extract box with map and model: 48.400 Check model and map are aligned: 0.690 Convert atoms to be neutral: 0.390 Process input model: 130.090 Find NCS groups from input model: 3.870 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 200.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 0.192 49078 Z= 0.375 Angle : 0.717 19.396 66273 Z= 0.483 Chirality : 0.041 0.307 7578 Planarity : 0.003 0.060 8557 Dihedral : 13.642 141.103 18554 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.47 % Favored : 97.38 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.10), residues: 6075 helix: -0.20 (0.09), residues: 3067 sheet: -0.82 (0.16), residues: 869 loop : -1.31 (0.13), residues: 2139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 401 time to evaluate : 5.782 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 outliers start: 47 outliers final: 17 residues processed: 429 average time/residue: 0.6721 time to fit residues: 469.1145 Evaluate side-chains 280 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 263 time to evaluate : 6.082 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4217 time to fit residues: 21.5325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 512 optimal weight: 6.9990 chunk 460 optimal weight: 0.0370 chunk 255 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 475 optimal weight: 1.9990 chunk 184 optimal weight: 20.0000 chunk 289 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 551 optimal weight: 5.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN B 233 GLN B 273 GLN B 393 HIS B 590 ASN B 659 HIS C 233 GLN C 528 HIS C 606 ASN C 659 HIS C 709 GLN ** C 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 HIS ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN D 659 HIS D 684 GLN E 288 HIS E 622 GLN E 659 HIS ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 HIS ** F 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN G 152 HIS H 60 GLN H 152 HIS I 60 GLN I 137 GLN J 60 GLN K 60 GLN K 143 GLN L 60 GLN L 152 HIS M 55 ASN M 60 GLN M 152 HIS N 60 GLN N 152 HIS O 60 GLN O 152 HIS P 60 GLN P 152 HIS Q 60 GLN R 60 GLN R 152 HIS R 205 HIS S 60 GLN T 60 GLN T 152 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 49078 Z= 0.317 Angle : 0.589 8.274 66273 Z= 0.297 Chirality : 0.043 0.170 7578 Planarity : 0.004 0.057 8557 Dihedral : 6.320 143.130 6730 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.67 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 6075 helix: 0.87 (0.09), residues: 3077 sheet: -0.96 (0.16), residues: 934 loop : -0.92 (0.13), residues: 2064 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 270 time to evaluate : 6.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 31 residues processed: 314 average time/residue: 0.6057 time to fit residues: 324.6384 Evaluate side-chains 275 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 244 time to evaluate : 6.083 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4029 time to fit residues: 31.3143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 306 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 458 optimal weight: 2.9990 chunk 375 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 552 optimal weight: 2.9990 chunk 596 optimal weight: 3.9990 chunk 491 optimal weight: 4.9990 chunk 547 optimal weight: 0.8980 chunk 188 optimal weight: 0.0030 chunk 443 optimal weight: 0.8980 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 ASN ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 621 HIS ** F 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 ASN N 137 GLN S 137 GLN T 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 49078 Z= 0.189 Angle : 0.516 7.942 66273 Z= 0.258 Chirality : 0.041 0.154 7578 Planarity : 0.003 0.058 8557 Dihedral : 5.969 134.110 6730 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.12 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.11), residues: 6075 helix: 1.26 (0.10), residues: 3079 sheet: -0.80 (0.16), residues: 936 loop : -0.73 (0.14), residues: 2060 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 261 time to evaluate : 8.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 10 residues processed: 291 average time/residue: 0.5719 time to fit residues: 288.5157 Evaluate side-chains 255 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 245 time to evaluate : 5.885 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4145 time to fit residues: 15.8135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 545 optimal weight: 3.9990 chunk 415 optimal weight: 1.9990 chunk 286 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 263 optimal weight: 9.9990 chunk 370 optimal weight: 0.9990 chunk 554 optimal weight: 0.7980 chunk 586 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 525 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 HIS ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN F 356 GLN ** F 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN H 137 GLN I 55 ASN K 55 ASN P 55 ASN R 137 GLN T 48 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 49078 Z= 0.219 Angle : 0.514 7.714 66273 Z= 0.256 Chirality : 0.041 0.214 7578 Planarity : 0.003 0.055 8557 Dihedral : 5.801 126.300 6730 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.11), residues: 6075 helix: 1.40 (0.10), residues: 3097 sheet: -0.72 (0.16), residues: 924 loop : -0.62 (0.14), residues: 2054 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 247 time to evaluate : 6.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 21 residues processed: 288 average time/residue: 0.5644 time to fit residues: 285.6718 Evaluate side-chains 261 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 240 time to evaluate : 6.008 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4264 time to fit residues: 24.9666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 488 optimal weight: 4.9990 chunk 333 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 436 optimal weight: 9.9990 chunk 242 optimal weight: 0.0870 chunk 500 optimal weight: 0.9980 chunk 405 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 299 optimal weight: 9.9990 chunk 526 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS ** B 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 740 ASN C 684 GLN C 688 ASN D 485 HIS ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** F 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN M 55 ASN O 55 ASN Q 137 GLN R 55 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 49078 Z= 0.332 Angle : 0.575 8.835 66273 Z= 0.286 Chirality : 0.042 0.156 7578 Planarity : 0.003 0.053 8557 Dihedral : 5.857 119.493 6730 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.11), residues: 6075 helix: 1.41 (0.10), residues: 3086 sheet: -0.81 (0.16), residues: 926 loop : -0.64 (0.14), residues: 2063 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 243 time to evaluate : 5.941 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 29 residues processed: 293 average time/residue: 0.6350 time to fit residues: 322.8704 Evaluate side-chains 268 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 239 time to evaluate : 5.761 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4884 time to fit residues: 34.7648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 197 optimal weight: 5.9990 chunk 528 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 344 optimal weight: 0.3980 chunk 144 optimal weight: 7.9990 chunk 587 optimal weight: 1.9990 chunk 487 optimal weight: 0.7980 chunk 271 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 308 optimal weight: 40.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 GLN C 688 ASN ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 49078 Z= 0.148 Angle : 0.505 8.732 66273 Z= 0.249 Chirality : 0.040 0.193 7578 Planarity : 0.003 0.054 8557 Dihedral : 5.550 115.311 6730 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.38 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.11), residues: 6075 helix: 1.53 (0.10), residues: 3099 sheet: -0.58 (0.16), residues: 945 loop : -0.57 (0.14), residues: 2031 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 6.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 278 average time/residue: 0.5855 time to fit residues: 282.5038 Evaluate side-chains 257 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 242 time to evaluate : 6.182 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4367 time to fit residues: 20.4464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 566 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 334 optimal weight: 8.9990 chunk 428 optimal weight: 4.9990 chunk 332 optimal weight: 10.0000 chunk 494 optimal weight: 9.9990 chunk 327 optimal weight: 7.9990 chunk 585 optimal weight: 0.9980 chunk 366 optimal weight: 5.9990 chunk 356 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN J 55 ASN M 55 ASN N 95 GLN Q 55 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 49078 Z= 0.393 Angle : 0.612 9.512 66273 Z= 0.303 Chirality : 0.043 0.223 7578 Planarity : 0.004 0.055 8557 Dihedral : 5.716 116.389 6730 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.20 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.11), residues: 6075 helix: 1.45 (0.10), residues: 3092 sheet: -0.84 (0.16), residues: 944 loop : -0.60 (0.14), residues: 2039 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 239 time to evaluate : 6.284 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 269 average time/residue: 0.5910 time to fit residues: 275.6796 Evaluate side-chains 254 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 236 time to evaluate : 6.473 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4646 time to fit residues: 24.3497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 361 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 349 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 371 optimal weight: 3.9990 chunk 398 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 54 optimal weight: 30.0000 chunk 459 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 528 HIS ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN Q 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 49078 Z= 0.284 Angle : 0.566 9.426 66273 Z= 0.278 Chirality : 0.041 0.213 7578 Planarity : 0.003 0.053 8557 Dihedral : 5.628 112.639 6730 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.28 % Favored : 96.69 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.11), residues: 6075 helix: 1.49 (0.10), residues: 3093 sheet: -0.77 (0.16), residues: 922 loop : -0.59 (0.14), residues: 2060 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 242 time to evaluate : 5.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 259 average time/residue: 0.6046 time to fit residues: 270.4404 Evaluate side-chains 249 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 237 time to evaluate : 5.822 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5369 time to fit residues: 19.1094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 532 optimal weight: 2.9990 chunk 560 optimal weight: 0.0370 chunk 511 optimal weight: 3.9990 chunk 545 optimal weight: 0.8980 chunk 328 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 428 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 492 optimal weight: 0.9980 chunk 515 optimal weight: 0.6980 chunk 543 optimal weight: 5.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 GLN C 688 ASN ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 49078 Z= 0.148 Angle : 0.529 11.464 66273 Z= 0.255 Chirality : 0.041 0.226 7578 Planarity : 0.003 0.053 8557 Dihedral : 5.304 108.578 6730 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.11), residues: 6075 helix: 1.60 (0.10), residues: 3095 sheet: -0.56 (0.16), residues: 944 loop : -0.52 (0.14), residues: 2036 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 248 time to evaluate : 6.127 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 255 average time/residue: 0.6031 time to fit residues: 267.9961 Evaluate side-chains 242 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 238 time to evaluate : 6.001 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4864 time to fit residues: 11.5571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 358 optimal weight: 0.5980 chunk 576 optimal weight: 0.9990 chunk 351 optimal weight: 2.9990 chunk 273 optimal weight: 5.9990 chunk 400 optimal weight: 5.9990 chunk 604 optimal weight: 1.9990 chunk 556 optimal weight: 7.9990 chunk 481 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 371 optimal weight: 6.9990 chunk 295 optimal weight: 0.0870 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 49078 Z= 0.186 Angle : 0.536 11.927 66273 Z= 0.258 Chirality : 0.040 0.223 7578 Planarity : 0.003 0.053 8557 Dihedral : 5.212 106.439 6730 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.11), residues: 6075 helix: 1.64 (0.10), residues: 3097 sheet: -0.52 (0.16), residues: 944 loop : -0.50 (0.14), residues: 2034 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12150 Ramachandran restraints generated. 6075 Oldfield, 0 Emsley, 6075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 240 time to evaluate : 6.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 245 average time/residue: 0.6063 time to fit residues: 259.2187 Evaluate side-chains 240 residues out of total 5163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 238 time to evaluate : 5.992 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.8471 time to fit residues: 10.4846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 382 optimal weight: 0.1980 chunk 512 optimal weight: 0.4980 chunk 147 optimal weight: 4.9990 chunk 444 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 482 optimal weight: 0.7980 chunk 201 optimal weight: 10.0000 chunk 495 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.053392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.037368 restraints weight = 232807.834| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.63 r_work: 0.2967 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work: 0.2950 rms_B_bonded: 3.40 restraints_weight: 0.1250 r_work: 0.2941 rms_B_bonded: 3.43 restraints_weight: 0.0625 r_work: 0.2933 rms_B_bonded: 3.47 restraints_weight: 0.0312 r_work: 0.2924 rms_B_bonded: 3.53 restraints_weight: 0.0156 r_work: 0.2915 rms_B_bonded: 3.60 restraints_weight: 0.0078 r_work: 0.2905 rms_B_bonded: 3.69 restraints_weight: 0.0039 r_work: 0.2896 rms_B_bonded: 3.78 restraints_weight: 0.0020 r_work: 0.2887 rms_B_bonded: 3.89 restraints_weight: 0.0010 r_work: 0.2877 rms_B_bonded: 4.01 restraints_weight: 0.0005 r_work: 0.2867 rms_B_bonded: 4.14 restraints_weight: 0.0002 r_work: 0.2857 rms_B_bonded: 4.28 restraints_weight: 0.0001 r_work: 0.2846 rms_B_bonded: 4.44 restraints_weight: 0.0001 r_work: 0.2835 rms_B_bonded: 4.61 restraints_weight: 0.0000 r_work: 0.2824 rms_B_bonded: 4.80 restraints_weight: 0.0000 r_work: 0.2813 rms_B_bonded: 5.00 restraints_weight: 0.0000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 49078 Z= 0.144 Angle : 0.531 11.681 66273 Z= 0.253 Chirality : 0.040 0.234 7578 Planarity : 0.003 0.053 8557 Dihedral : 5.051 100.250 6730 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.12 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.11), residues: 6075 helix: 1.67 (0.10), residues: 3100 sheet: -0.41 (0.16), residues: 949 loop : -0.50 (0.14), residues: 2026 =============================================================================== Job complete usr+sys time: 9178.46 seconds wall clock time: 169 minutes 46.74 seconds (10186.74 seconds total)