Starting phenix.real_space_refine on Sat Mar 23 03:56:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpa_30149/03_2024/7bpa_30149_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpa_30149/03_2024/7bpa_30149.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/7bpa_30149/03_2024/7bpa_30149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpa_30149/03_2024/7bpa_30149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpa_30149/03_2024/7bpa_30149_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpa_30149/03_2024/7bpa_30149_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 180 5.16 5 C 22086 2.51 5 N 6282 2.21 5 O 6792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B GLU 712": "OE1" <-> "OE2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B GLU 756": "OE1" <-> "OE2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 578": "OE1" <-> "OE2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C GLU 712": "OE1" <-> "OE2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C GLU 756": "OE1" <-> "OE2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D GLU 281": "OE1" <-> "OE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 635": "NH1" <-> "NH2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D GLU 712": "OE1" <-> "OE2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "D GLU 723": "OE1" <-> "OE2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D GLU 756": "OE1" <-> "OE2" Residue "D ARG 766": "NH1" <-> "NH2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E ARG 338": "NH1" <-> "NH2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E GLU 402": "OE1" <-> "OE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 635": "NH1" <-> "NH2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "E GLU 704": "OE1" <-> "OE2" Residue "E ARG 711": "NH1" <-> "NH2" Residue "E GLU 712": "OE1" <-> "OE2" Residue "E ARG 713": "NH1" <-> "NH2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "E GLU 756": "OE1" <-> "OE2" Residue "E ARG 766": "NH1" <-> "NH2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "F TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F GLU 578": "OE1" <-> "OE2" Residue "F ARG 635": "NH1" <-> "NH2" Residue "F GLU 689": "OE1" <-> "OE2" Residue "F ARG 711": "NH1" <-> "NH2" Residue "F GLU 712": "OE1" <-> "OE2" Residue "F ARG 713": "NH1" <-> "NH2" Residue "F ARG 733": "NH1" <-> "NH2" Residue "F GLU 756": "OE1" <-> "OE2" Residue "F ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35370 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5913 Chain: "B" Number of atoms: 5837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5913 Chain: "C" Number of atoms: 5837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5913 Chain: "D" Number of atoms: 5837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5913 Chain: "E" Number of atoms: 5837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5913 Chain: "F" Number of atoms: 5837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5913 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} 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, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AASP A 592 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A 592 " occ=0.50 residue: pdb=" N AASP B 592 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP B 592 " occ=0.50 residue: pdb=" N AASP C 592 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP C 592 " occ=0.50 residue: pdb=" N AASP D 592 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP D 592 " occ=0.50 residue: pdb=" N AASP E 592 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP E 592 " occ=0.50 residue: pdb=" N AASP F 592 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP F 592 " occ=0.50 Time building chain proxies: 33.30, per 1000 atoms: 0.94 Number of scatterers: 35370 At special positions: 0 Unit cell: (172.753, 183.483, 100.862, 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 180 16.00 P 30 15.00 O 6792 8.00 N 6282 7.00 C 22086 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.83 Conformation dependent library (CDL) restraints added in 12.5 seconds 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 206 helices and 38 sheets defined 40.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.11 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 131 through 138 removed outlier: 4.817A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 271 through 274 No H-bonds generated for 'chain 'A' and resid 271 through 274' Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.815A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 320 through 335 removed outlier: 3.939A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 removed outlier: 3.686A pdb=" N VAL A 559 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 563 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 663 removed outlier: 3.964A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 712 removed outlier: 3.685A pdb=" N THR A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A 692 " --> pdb=" O THR A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.218A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 762 Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 131 through 138 removed outlier: 4.862A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 271 through 274 No H-bonds generated for 'chain 'B' and resid 271 through 274' Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.760A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 320 through 335 removed outlier: 3.901A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 removed outlier: 3.668A pdb=" N VAL B 559 " --> pdb=" O GLU B 556 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG B 560 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE B 563 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 650 through 663 removed outlier: 3.972A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 712 removed outlier: 3.668A pdb=" N THR B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.195A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 762 Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 131 through 138 removed outlier: 4.849A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 228 through 231 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 271 through 274 No H-bonds generated for 'chain 'C' and resid 271 through 274' Processing helix chain 'C' and resid 279 through 295 removed outlier: 3.795A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 320 through 335 removed outlier: 3.907A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 408 through 425 Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 494 Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.681A pdb=" N VAL C 559 " --> pdb=" O GLU C 556 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG C 560 " --> pdb=" O ALA C 557 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE C 563 " --> pdb=" O ARG C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 650 through 663 removed outlier: 3.973A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 687 through 712 removed outlier: 4.048A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN C 692 " --> pdb=" O THR C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.200A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 762 Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 131 through 138 removed outlier: 4.819A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 228 through 231 Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 271 through 274 No H-bonds generated for 'chain 'D' and resid 271 through 274' Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.816A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 335 removed outlier: 3.947A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 494 Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.686A pdb=" N VAL D 559 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG D 560 " --> pdb=" O ALA D 557 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE D 563 " --> pdb=" O ARG D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 650 through 663 removed outlier: 3.963A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LYS D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 712 removed outlier: 3.682A pdb=" N THR D 688 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU D 689 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN D 692 " --> pdb=" O THR D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.219A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 762 Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 131 through 138 removed outlier: 4.863A pdb=" N LYS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 271 through 274 No H-bonds generated for 'chain 'E' and resid 271 through 274' Processing helix chain 'E' and resid 279 through 295 removed outlier: 3.787A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 335 removed outlier: 3.905A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 494 Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 525 through 534 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 removed outlier: 3.670A pdb=" N VAL E 559 " --> pdb=" O GLU E 556 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG E 560 " --> pdb=" O ALA E 557 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE E 563 " --> pdb=" O ARG E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 650 through 663 removed outlier: 3.973A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 712 removed outlier: 3.668A pdb=" N THR E 688 " --> pdb=" O GLY E 684 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU E 689 " --> pdb=" O ALA E 685 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN E 692 " --> pdb=" O THR E 688 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 742 removed outlier: 4.191A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 762 Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 131 through 138 removed outlier: 4.854A pdb=" N LYS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 228 through 231 Processing helix chain 'F' and resid 251 through 261 Processing helix chain 'F' and resid 271 through 274 No H-bonds generated for 'chain 'F' and resid 271 through 274' Processing helix chain 'F' and resid 279 through 295 removed outlier: 3.794A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 335 removed outlier: 3.909A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 401 Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 494 Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 525 through 534 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.682A pdb=" N VAL F 559 " --> pdb=" O GLU F 556 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG F 560 " --> pdb=" O ALA F 557 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE F 563 " --> pdb=" O ARG F 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 650 through 663 removed outlier: 3.987A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 687 through 712 removed outlier: 4.051A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN F 692 " --> pdb=" O THR F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 742 removed outlier: 4.207A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 762 Processing sheet with id= A, first strand: chain 'A' and resid 27 through 29 Processing sheet with id= B, first strand: chain 'A' and resid 39 through 42 Processing sheet with id= C, first strand: chain 'A' and resid 66 through 70 Processing sheet with id= D, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.846A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 151 through 156 removed outlier: 6.802A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.993A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 642 through 645 removed outlier: 8.236A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE A 645 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR A 517 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 27 through 29 Processing sheet with id= I, first strand: chain 'B' and resid 38 through 42 removed outlier: 8.193A pdb=" N VAL B 39 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 144 through 147 removed outlier: 3.856A pdb=" N ARG B 144 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.791A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 365 through 368 removed outlier: 9.013A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 642 through 645 removed outlier: 8.243A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE B 645 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR B 517 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 27 through 29 Processing sheet with id= O, first strand: chain 'C' and resid 38 through 42 removed outlier: 8.192A pdb=" N VAL C 39 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.850A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.814A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.969A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 642 through 645 removed outlier: 8.252A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE C 645 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TYR C 517 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 27 through 29 Processing sheet with id= U, first strand: chain 'D' and resid 39 through 42 Processing sheet with id= V, first strand: chain 'D' and resid 66 through 70 Processing sheet with id= W, first strand: chain 'D' and resid 144 through 147 removed outlier: 3.844A pdb=" N ARG D 144 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 151 through 156 removed outlier: 6.805A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.990A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 642 through 645 removed outlier: 8.235A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE D 645 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR D 517 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 27 through 29 Processing sheet with id= AB, first strand: chain 'E' and resid 38 through 42 removed outlier: 8.192A pdb=" N VAL E 39 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.857A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 151 through 156 removed outlier: 6.792A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 365 through 368 removed outlier: 9.008A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 642 through 645 removed outlier: 8.246A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE E 645 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR E 517 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 27 through 29 Processing sheet with id= AH, first strand: chain 'F' and resid 38 through 42 removed outlier: 8.181A pdb=" N VAL F 39 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE F 70 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU F 41 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU F 72 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 144 through 147 removed outlier: 3.849A pdb=" N ARG F 144 " --> pdb=" O VAL F 176 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 151 through 156 removed outlier: 6.815A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 365 through 368 removed outlier: 8.970A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 642 through 645 removed outlier: 8.248A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE F 645 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR F 517 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL 1086 hydrogen bonds defined for protein. 3060 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: 13.79 Time building geometry restraints manager: 13.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11109 1.34 - 1.46: 5871 1.46 - 1.58: 18636 1.58 - 1.70: 54 1.70 - 1.82: 288 Bond restraints: 35958 Sorted by residual: bond pdb=" O3A ANP D 901 " pdb=" PB ANP D 901 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" O3A ANP A 902 " pdb=" PB ANP A 902 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" O3A ANP E 901 " pdb=" PB ANP E 901 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.41e+01 bond pdb=" O3A ANP C 901 " pdb=" PB ANP C 901 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.31e+01 ... (remaining 35953 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.21: 1118 106.21 - 113.40: 18922 113.40 - 120.60: 15696 120.60 - 127.80: 12568 127.80 - 135.00: 314 Bond angle restraints: 48618 Sorted by residual: angle pdb=" PB ANP F 901 " pdb=" N3B ANP F 901 " pdb=" PG ANP F 901 " ideal model delta sigma weight residual 126.95 110.84 16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" PB ANP C 901 " pdb=" N3B ANP C 901 " pdb=" PG ANP C 901 " ideal model delta sigma weight residual 126.95 110.85 16.10 3.00e+00 1.11e-01 2.88e+01 angle pdb=" PB ANP B 901 " pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 126.95 110.97 15.98 3.00e+00 1.11e-01 2.84e+01 angle pdb=" PB ANP E 901 " pdb=" N3B ANP E 901 " pdb=" PG ANP E 901 " ideal model delta sigma weight residual 126.95 110.97 15.98 3.00e+00 1.11e-01 2.84e+01 angle pdb=" PB ANP A 902 " pdb=" N3B ANP A 902 " pdb=" PG ANP A 902 " ideal model delta sigma weight residual 126.95 111.06 15.89 3.00e+00 1.11e-01 2.80e+01 ... (remaining 48613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 22077 34.81 - 69.62: 328 69.62 - 104.44: 49 104.44 - 139.25: 0 139.25 - 174.06: 4 Dihedral angle restraints: 22458 sinusoidal: 9600 harmonic: 12858 Sorted by residual: dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 114.06 -174.06 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PB ADP D 902 " pdb=" PA ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 113.97 -173.97 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PB ADP B 902 " pdb=" PA ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 113.56 -173.56 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 22455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4579 0.099 - 0.197: 765 0.197 - 0.296: 78 0.296 - 0.394: 11 0.394 - 0.493: 3 Chirality restraints: 5436 Sorted by residual: chirality pdb=" CB VAL E 57 " pdb=" CA VAL E 57 " pdb=" CG1 VAL E 57 " pdb=" CG2 VAL E 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CB VAL B 57 " pdb=" CA VAL B 57 " pdb=" CG1 VAL B 57 " pdb=" CG2 VAL B 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CB THR B 549 " pdb=" CA THR B 549 " pdb=" OG1 THR B 549 " pdb=" CG2 THR B 549 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 5433 not shown) Planarity restraints: 6408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 293 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ALA B 293 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA B 293 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU B 294 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 292 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.33e+00 pdb=" C GLU A 292 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU A 292 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 293 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 293 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C ALA A 293 " -0.053 2.00e-02 2.50e+03 pdb=" O ALA A 293 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU A 294 " 0.018 2.00e-02 2.50e+03 ... (remaining 6405 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1564 2.72 - 3.26: 33071 3.26 - 3.81: 51517 3.81 - 4.35: 65066 4.35 - 4.90: 112513 Nonbonded interactions: 263731 Sorted by model distance: nonbonded pdb=" O ALA B 455 " pdb=" ND2 ASN B 460 " model vdw 2.169 2.520 nonbonded pdb=" O ALA E 455 " pdb=" ND2 ASN E 460 " model vdw 2.172 2.520 nonbonded pdb=" OD2 ASP B 373 " pdb=" OG1 THR B 375 " model vdw 2.299 2.440 nonbonded pdb=" OD2 ASP F 373 " pdb=" OG1 THR F 375 " model vdw 2.300 2.440 nonbonded pdb=" OD2 ASP A 373 " pdb=" OG1 THR A 375 " model vdw 2.300 2.440 ... (remaining 263726 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 18 through 591 or resid 593 through 766)) selection = (chain 'B' and (resid 18 through 591 or resid 593 through 766)) selection = (chain 'C' and (resid 18 through 591 or resid 593 through 766)) selection = (chain 'D' and (resid 18 through 591 or resid 593 through 766)) selection = (chain 'E' and (resid 18 through 591 or resid 593 through 766)) selection = (chain 'F' and (resid 18 through 591 or resid 593 through 766)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.950 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: 0.030 Extract box with map and model: 12.290 Check model and map are aligned: 0.480 Set scattering table: 0.310 Process input model: 113.520 Find NCS groups from input model: 3.390 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.009 0.148 35958 Z= 0.559 Angle : 1.254 16.109 48618 Z= 0.666 Chirality : 0.074 0.493 5436 Planarity : 0.007 0.054 6408 Dihedral : 14.109 174.059 14118 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -3.01 (0.11), residues: 4446 helix: -1.45 (0.11), residues: 1812 sheet: -1.46 (0.18), residues: 624 loop : -2.67 (0.12), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 551 HIS 0.007 0.002 HIS C 384 PHE 0.026 0.003 PHE E 290 TYR 0.017 0.003 TYR E 143 ARG 0.009 0.001 ARG C 766 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 748 time to evaluate : 4.270 Fit side-chains REVERT: A 29 ASP cc_start: 0.8345 (p0) cc_final: 0.8119 (p0) REVERT: A 288 LYS cc_start: 0.8556 (mttp) cc_final: 0.8195 (mtpp) REVERT: A 449 MET cc_start: 0.7937 (tpp) cc_final: 0.7610 (tpp) REVERT: A 460 ASN cc_start: 0.8564 (p0) cc_final: 0.7516 (p0) REVERT: B 113 ARG cc_start: 0.7260 (ttt90) cc_final: 0.7039 (mtm180) REVERT: B 354 ASP cc_start: 0.8569 (t0) cc_final: 0.8197 (t0) REVERT: B 427 MET cc_start: 0.7400 (tpp) cc_final: 0.7150 (mmm) REVERT: B 460 ASN cc_start: 0.8255 (p0) cc_final: 0.7778 (p0) REVERT: B 534 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7147 (tm-30) REVERT: B 701 GLU cc_start: 0.7825 (tp30) cc_final: 0.7408 (tm-30) REVERT: B 744 ARG cc_start: 0.6663 (ttp80) cc_final: 0.6104 (mpt180) REVERT: B 757 MET cc_start: 0.7607 (mmm) cc_final: 0.6917 (mmm) REVERT: C 288 LYS cc_start: 0.8476 (mttp) cc_final: 0.8115 (mtpp) REVERT: C 324 ILE cc_start: 0.9129 (mt) cc_final: 0.8851 (tt) REVERT: C 371 ILE cc_start: 0.9308 (mt) cc_final: 0.9087 (mt) REVERT: C 427 MET cc_start: 0.7625 (tpp) cc_final: 0.7392 (mmm) REVERT: C 460 ASN cc_start: 0.8630 (p0) cc_final: 0.8136 (p0) REVERT: C 464 LEU cc_start: 0.7729 (mm) cc_final: 0.7414 (mm) REVERT: C 491 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7671 (mm-30) REVERT: C 495 TYR cc_start: 0.8626 (m-10) cc_final: 0.8391 (m-10) REVERT: C 744 ARG cc_start: 0.6651 (ttp80) cc_final: 0.6128 (mpt180) REVERT: D 29 ASP cc_start: 0.8331 (p0) cc_final: 0.8111 (p0) REVERT: D 79 ASP cc_start: 0.7248 (p0) cc_final: 0.6776 (p0) REVERT: D 80 GLU cc_start: 0.7249 (pm20) cc_final: 0.7008 (pm20) REVERT: D 288 LYS cc_start: 0.8514 (mttp) cc_final: 0.8136 (mtpp) REVERT: D 449 MET cc_start: 0.7934 (tpp) cc_final: 0.7625 (tpp) REVERT: D 460 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7365 (p0) REVERT: E 113 ARG cc_start: 0.7263 (ttt90) cc_final: 0.7043 (mtm180) REVERT: E 288 LYS cc_start: 0.8468 (mttp) cc_final: 0.8019 (mtpp) REVERT: E 354 ASP cc_start: 0.8583 (t0) cc_final: 0.8213 (t0) REVERT: E 427 MET cc_start: 0.7363 (tpp) cc_final: 0.7145 (mmm) REVERT: E 460 ASN cc_start: 0.8241 (p0) cc_final: 0.7767 (p0) REVERT: E 534 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7100 (tm-30) REVERT: E 701 GLU cc_start: 0.7810 (tp30) cc_final: 0.7387 (tm-30) REVERT: E 744 ARG cc_start: 0.7098 (ttp80) cc_final: 0.6207 (mpt180) REVERT: E 757 MET cc_start: 0.7563 (mmm) cc_final: 0.6811 (mmm) REVERT: F 205 ASP cc_start: 0.7970 (m-30) cc_final: 0.7768 (m-30) REVERT: F 324 ILE cc_start: 0.9124 (mt) cc_final: 0.8848 (tt) REVERT: F 371 ILE cc_start: 0.9322 (mt) cc_final: 0.9115 (mt) REVERT: F 427 MET cc_start: 0.7648 (tpp) cc_final: 0.7424 (mmm) REVERT: F 460 ASN cc_start: 0.8639 (p0) cc_final: 0.7514 (p0) REVERT: F 464 LEU cc_start: 0.7707 (mm) cc_final: 0.7375 (mm) REVERT: F 491 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7630 (mm-30) REVERT: F 495 TYR cc_start: 0.8609 (m-10) cc_final: 0.8366 (m-10) REVERT: F 744 ARG cc_start: 0.6633 (ttp80) cc_final: 0.6120 (mpt180) outliers start: 1 outliers final: 0 residues processed: 748 average time/residue: 0.4913 time to fit residues: 577.2770 Evaluate side-chains 583 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 582 time to evaluate : 4.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 460 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 1.9990 chunk 336 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 348 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 403 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 735 HIS B 91 ASN B 443 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 HIS D 91 ASN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS F 91 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 735 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 35958 Z= 0.181 Angle : 0.580 9.169 48618 Z= 0.278 Chirality : 0.045 0.134 5436 Planarity : 0.005 0.095 6408 Dihedral : 8.959 139.978 5120 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.13 % Allowed : 8.83 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -1.56 (0.12), residues: 4446 helix: -0.06 (0.12), residues: 1794 sheet: -0.76 (0.19), residues: 606 loop : -2.02 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 551 HIS 0.003 0.001 HIS C 384 PHE 0.010 0.001 PHE E 290 TYR 0.011 0.001 TYR C 517 ARG 0.011 0.000 ARG C 635 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 629 time to evaluate : 4.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.6976 (mtm180) cc_final: 0.6626 (ttm-80) REVERT: A 210 ARG cc_start: 0.7515 (tpp80) cc_final: 0.7308 (tpp-160) REVERT: A 449 MET cc_start: 0.7941 (tpp) cc_final: 0.7545 (tpp) REVERT: A 460 ASN cc_start: 0.8449 (p0) cc_final: 0.8018 (p0) REVERT: B 354 ASP cc_start: 0.8503 (t0) cc_final: 0.8296 (t0) REVERT: B 427 MET cc_start: 0.7338 (tpp) cc_final: 0.7061 (mmm) REVERT: B 460 ASN cc_start: 0.8093 (p0) cc_final: 0.7489 (p0) REVERT: B 478 ASP cc_start: 0.8109 (m-30) cc_final: 0.7902 (m-30) REVERT: B 534 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7255 (tm-30) REVERT: B 744 ARG cc_start: 0.6866 (ttp80) cc_final: 0.6114 (mmt180) REVERT: C 113 ARG cc_start: 0.6932 (mtm180) cc_final: 0.6429 (ttm-80) REVERT: C 288 LYS cc_start: 0.8359 (mttp) cc_final: 0.8121 (mtpp) REVERT: C 324 ILE cc_start: 0.9126 (mt) cc_final: 0.8880 (tt) REVERT: C 427 MET cc_start: 0.7670 (tpp) cc_final: 0.7412 (mmm) REVERT: C 460 ASN cc_start: 0.8317 (p0) cc_final: 0.7561 (p0) REVERT: C 701 GLU cc_start: 0.7952 (tp30) cc_final: 0.7559 (tm-30) REVERT: C 744 ARG cc_start: 0.6873 (ttp80) cc_final: 0.6255 (mpt180) REVERT: D 113 ARG cc_start: 0.6974 (mtm180) cc_final: 0.6590 (ttt90) REVERT: D 449 MET cc_start: 0.7970 (tpp) cc_final: 0.7661 (tpp) REVERT: E 80 GLU cc_start: 0.7281 (pm20) cc_final: 0.7058 (pm20) REVERT: E 288 LYS cc_start: 0.8291 (mttp) cc_final: 0.7999 (mtpp) REVERT: E 354 ASP cc_start: 0.8518 (t0) cc_final: 0.8312 (t0) REVERT: E 427 MET cc_start: 0.7321 (tpp) cc_final: 0.7044 (mmm) REVERT: E 460 ASN cc_start: 0.8076 (p0) cc_final: 0.7480 (p0) REVERT: E 534 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7258 (tm-30) REVERT: E 744 ARG cc_start: 0.7617 (ttp80) cc_final: 0.6511 (mmt180) REVERT: F 113 ARG cc_start: 0.6932 (mtm180) cc_final: 0.6426 (ttm-80) REVERT: F 205 ASP cc_start: 0.7954 (m-30) cc_final: 0.7742 (m-30) REVERT: F 324 ILE cc_start: 0.9125 (mt) cc_final: 0.8880 (tt) REVERT: F 427 MET cc_start: 0.7666 (tpp) cc_final: 0.7409 (mmm) REVERT: F 442 MET cc_start: 0.7812 (tpp) cc_final: 0.7557 (tpp) REVERT: F 460 ASN cc_start: 0.8324 (p0) cc_final: 0.7592 (p0) REVERT: F 701 GLU cc_start: 0.7954 (tp30) cc_final: 0.7563 (tm-30) REVERT: F 744 ARG cc_start: 0.6863 (ttp80) cc_final: 0.6241 (mpt180) outliers start: 43 outliers final: 31 residues processed: 655 average time/residue: 0.5027 time to fit residues: 529.0772 Evaluate side-chains 593 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 562 time to evaluate : 3.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 335 optimal weight: 7.9990 chunk 274 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 403 optimal weight: 1.9990 chunk 436 optimal weight: 9.9990 chunk 359 optimal weight: 4.9990 chunk 400 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 324 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 91 ASN A 602 ASN B 24 ASN B 91 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 HIS C 91 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN D 91 ASN D 602 ASN D 735 HIS E 24 ASN E 91 ASN E 443 ASN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 35958 Z= 0.273 Angle : 0.619 10.465 48618 Z= 0.297 Chirality : 0.046 0.141 5436 Planarity : 0.006 0.132 6408 Dihedral : 9.070 166.982 5118 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.74 % Allowed : 11.20 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -1.18 (0.12), residues: 4446 helix: 0.21 (0.12), residues: 1836 sheet: -0.59 (0.20), residues: 618 loop : -1.80 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 551 HIS 0.005 0.001 HIS B 384 PHE 0.012 0.002 PHE A 152 TYR 0.011 0.002 TYR A 143 ARG 0.017 0.001 ARG D 635 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 571 time to evaluate : 4.337 Fit side-chains revert: symmetry clash REVERT: A 79 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7020 (p0) REVERT: A 210 ARG cc_start: 0.7640 (tpp80) cc_final: 0.7396 (tpp-160) REVERT: A 460 ASN cc_start: 0.8452 (p0) cc_final: 0.7631 (p0) REVERT: A 744 ARG cc_start: 0.7167 (ttp80) cc_final: 0.6562 (mpt180) REVERT: B 80 GLU cc_start: 0.7399 (pm20) cc_final: 0.7186 (pm20) REVERT: B 324 ILE cc_start: 0.9176 (mt) cc_final: 0.8947 (tt) REVERT: B 427 MET cc_start: 0.7471 (tpp) cc_final: 0.7172 (mmm) REVERT: B 460 ASN cc_start: 0.8193 (p0) cc_final: 0.7557 (p0) REVERT: B 534 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7342 (tm-30) REVERT: B 744 ARG cc_start: 0.7555 (ttp80) cc_final: 0.6615 (mpt180) REVERT: C 113 ARG cc_start: 0.6899 (mtm180) cc_final: 0.6627 (ttm170) REVERT: C 288 LYS cc_start: 0.8347 (mttp) cc_final: 0.8140 (mtpp) REVERT: C 324 ILE cc_start: 0.9172 (mt) cc_final: 0.8956 (tt) REVERT: C 427 MET cc_start: 0.7556 (tpp) cc_final: 0.7313 (mmm) REVERT: C 460 ASN cc_start: 0.8268 (p0) cc_final: 0.7551 (p0) REVERT: C 701 GLU cc_start: 0.7989 (tp30) cc_final: 0.7586 (tm-30) REVERT: D 744 ARG cc_start: 0.7158 (ttp80) cc_final: 0.6575 (mpt180) REVERT: E 80 GLU cc_start: 0.7399 (pm20) cc_final: 0.7171 (pm20) REVERT: E 288 LYS cc_start: 0.8340 (mttp) cc_final: 0.8035 (mtpp) REVERT: E 324 ILE cc_start: 0.9174 (mt) cc_final: 0.8942 (tt) REVERT: E 427 MET cc_start: 0.7430 (tpp) cc_final: 0.7124 (mmm) REVERT: E 460 ASN cc_start: 0.8179 (p0) cc_final: 0.7552 (p0) REVERT: E 534 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7342 (tm-30) REVERT: E 744 ARG cc_start: 0.7789 (ttp80) cc_final: 0.6815 (mmt180) REVERT: F 80 GLU cc_start: 0.7363 (pm20) cc_final: 0.7020 (pm20) REVERT: F 113 ARG cc_start: 0.6895 (mtm180) cc_final: 0.6383 (mtm180) REVERT: F 324 ILE cc_start: 0.9170 (mt) cc_final: 0.8955 (tt) REVERT: F 427 MET cc_start: 0.7586 (tpp) cc_final: 0.7336 (mmm) REVERT: F 460 ASN cc_start: 0.8273 (p0) cc_final: 0.7565 (p0) REVERT: F 701 GLU cc_start: 0.7988 (tp30) cc_final: 0.7588 (tm-30) REVERT: F 744 ARG cc_start: 0.6891 (ttp80) cc_final: 0.6238 (mpt180) outliers start: 66 outliers final: 45 residues processed: 613 average time/residue: 0.4543 time to fit residues: 454.7724 Evaluate side-chains 589 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 543 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 751 ASP Chi-restraints excluded: chain F residue 756 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1036 > 50: distance: 42 - 46: 29.302 distance: 46 - 47: 44.227 distance: 47 - 48: 17.538 distance: 48 - 49: 36.515 distance: 48 - 50: 25.584 distance: 51 - 52: 32.240 distance: 52 - 53: 41.803 distance: 52 - 58: 41.502 distance: 54 - 55: 43.027 distance: 55 - 56: 55.511 distance: 56 - 57: 24.285 distance: 58 - 59: 43.066 distance: 59 - 60: 18.606 distance: 59 - 62: 31.527 distance: 60 - 61: 43.154 distance: 60 - 65: 49.968 distance: 62 - 63: 9.964 distance: 62 - 64: 25.672 distance: 65 - 66: 53.608 distance: 65 - 71: 45.166 distance: 66 - 67: 33.317 distance: 66 - 69: 22.076 distance: 67 - 68: 8.519 distance: 67 - 72: 55.332 distance: 70 - 71: 20.147 distance: 72 - 73: 19.851 distance: 73 - 74: 38.573 distance: 73 - 76: 3.282 distance: 74 - 75: 25.177 distance: 74 - 78: 18.542 distance: 78 - 79: 43.889 distance: 79 - 80: 45.264 distance: 80 - 81: 27.455 distance: 80 - 87: 27.753 distance: 83 - 84: 10.590 distance: 84 - 85: 49.876 distance: 85 - 86: 42.222 distance: 87 - 88: 48.303 distance: 88 - 89: 43.700 distance: 89 - 90: 19.930 distance: 89 - 91: 42.724 distance: 91 - 92: 12.767 distance: 92 - 93: 31.025 distance: 92 - 95: 39.052 distance: 93 - 94: 9.742 distance: 93 - 98: 17.976 distance: 95 - 96: 36.058 distance: 95 - 97: 20.968 distance: 98 - 99: 19.724 distance: 99 - 100: 16.769 distance: 99 - 102: 27.927 distance: 100 - 101: 10.899 distance: 100 - 106: 5.886 distance: 102 - 103: 41.669 distance: 103 - 105: 9.093 distance: 106 - 107: 25.945 distance: 107 - 108: 9.444 distance: 107 - 110: 10.247 distance: 108 - 109: 4.670 distance: 108 - 117: 10.347 distance: 110 - 111: 26.728 distance: 111 - 112: 12.024 distance: 111 - 113: 42.109 distance: 112 - 114: 26.597 distance: 114 - 116: 39.492 distance: 115 - 116: 20.141