Starting phenix.real_space_refine on Tue Nov 21 23:37:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpa_30149/11_2023/7bpa_30149_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpa_30149/11_2023/7bpa_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_30149/11_2023/7bpa_30149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpa_30149/11_2023/7bpa_30149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpa_30149/11_2023/7bpa_30149_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpa_30149/11_2023/7bpa_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 33.17, 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: 13.85 Conformation dependent library (CDL) restraints added in 12.8 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: 8.91 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: 12.20 Time building geometry restraints manager: 14.91 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: 21945 34.81 - 69.62: 298 69.62 - 104.44: 43 104.44 - 139.25: 0 139.25 - 174.06: 4 Dihedral angle restraints: 22290 sinusoidal: 9432 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 22287 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: 2.510 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: 12.270 Check model and map are aligned: 0.600 Set scattering table: 0.330 Process input model: 115.340 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.190 ------------------------------------------------------------------------------- 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 : 13.687 174.059 13950 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 *********************** 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 : 4.364 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 748 average time/residue: 0.5073 time to fit residues: 597.5370 Evaluate side-chains 573 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 573 time to evaluate : 4.673 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 0.9990 chunk 336 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 348 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 403 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 735 HIS C 91 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 HIS D 91 ASN D 602 ASN D 735 HIS E 91 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS F 91 ASN F 735 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 35958 Z= 0.261 Angle : 0.638 9.219 48618 Z= 0.308 Chirality : 0.047 0.153 5436 Planarity : 0.006 0.121 6408 Dihedral : 8.112 137.223 4950 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.24 % Allowed : 9.25 % Favored : 89.51 % 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: -1.81 (0.12), residues: 4446 helix: -0.36 (0.12), residues: 1830 sheet: -0.91 (0.19), residues: 618 loop : -2.08 (0.13), residues: 1998 *********************** 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 647 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 600 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 34 residues processed: 629 average time/residue: 0.4930 time to fit residues: 499.1198 Evaluate side-chains 584 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 550 time to evaluate : 4.206 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3186 time to fit residues: 26.2753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 335 optimal weight: 7.9990 chunk 274 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 403 optimal weight: 8.9990 chunk 436 optimal weight: 10.0000 chunk 359 optimal weight: 2.9990 chunk 400 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 C 91 ASN D 24 ASN D 91 ASN E 24 ASN E 91 ASN E 443 ASN F 91 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 35958 Z= 0.310 Angle : 0.651 10.170 48618 Z= 0.314 Chirality : 0.047 0.174 5436 Planarity : 0.006 0.139 6408 Dihedral : 8.394 138.322 4950 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.03 % Allowed : 12.01 % Favored : 86.96 % 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: -1.35 (0.12), residues: 4446 helix: 0.02 (0.12), residues: 1836 sheet: -0.70 (0.20), residues: 618 loop : -1.81 (0.13), residues: 1992 *********************** 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 614 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 575 time to evaluate : 4.376 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 598 average time/residue: 0.4790 time to fit residues: 464.3179 Evaluate side-chains 561 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 541 time to evaluate : 4.229 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3634 time to fit residues: 18.9983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 0.9990 chunk 303 optimal weight: 0.7980 chunk 209 optimal weight: 6.9990 chunk 44 optimal weight: 0.0770 chunk 192 optimal weight: 0.0980 chunk 271 optimal weight: 0.0030 chunk 405 optimal weight: 5.9990 chunk 429 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 384 optimal weight: 10.0000 chunk 115 optimal weight: 0.4980 overall best weight: 0.2948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 115 HIS ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN B 91 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN C 24 ASN C 115 HIS D 91 ASN D 115 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN E 91 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN F 24 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 692 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35958 Z= 0.136 Angle : 0.548 8.696 48618 Z= 0.260 Chirality : 0.044 0.157 5436 Planarity : 0.005 0.086 6408 Dihedral : 8.376 171.661 4950 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.71 % Allowed : 13.38 % Favored : 85.91 % 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: -0.67 (0.13), residues: 4446 helix: 0.70 (0.13), residues: 1800 sheet: -0.20 (0.21), residues: 600 loop : -1.58 (0.13), residues: 2046 *********************** REFINEMENT MACRO_CYCLE 4 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 657 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 630 time to evaluate : 4.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 4 residues processed: 641 average time/residue: 0.4533 time to fit residues: 481.1730 Evaluate side-chains 576 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 572 time to evaluate : 4.492 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3127 time to fit residues: 8.4273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 5.9990 chunk 243 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 366 optimal weight: 8.9990 chunk 296 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 385 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 183 HIS B 24 ASN B 91 ASN C 24 ASN C 91 ASN C 692 GLN D 24 ASN D 91 ASN D 183 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN E 91 ASN F 24 ASN F 91 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35958 Z= 0.279 Angle : 0.626 13.199 48618 Z= 0.297 Chirality : 0.046 0.181 5436 Planarity : 0.006 0.121 6408 Dihedral : 8.664 175.723 4950 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.45 % Allowed : 14.35 % Favored : 84.20 % 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: -0.71 (0.13), residues: 4446 helix: 0.55 (0.13), residues: 1836 sheet: -0.32 (0.20), residues: 654 loop : -1.50 (0.14), residues: 1956 *********************** REFINEMENT MACRO_CYCLE 5 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 632 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 577 time to evaluate : 4.468 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 37 residues processed: 613 average time/residue: 0.4592 time to fit residues: 466.1948 Evaluate side-chains 597 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 560 time to evaluate : 4.990 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.3216 time to fit residues: 28.2874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 10.0000 chunk 386 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 251 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 429 optimal weight: 0.0470 chunk 356 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 225 optimal weight: 0.0050 overall best weight: 0.8894 ------------------------------------------------------------------------------- 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 B 24 ASN B 91 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 91 ASN C 183 HIS D 24 ASN D 91 ASN E 24 ASN E 91 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN F 91 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35958 Z= 0.152 Angle : 0.562 12.142 48618 Z= 0.264 Chirality : 0.044 0.156 5436 Planarity : 0.005 0.164 6408 Dihedral : 8.393 178.862 4950 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.42 % Allowed : 15.56 % Favored : 84.02 % 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: -0.41 (0.13), residues: 4446 helix: 0.82 (0.13), residues: 1800 sheet: -0.23 (0.20), residues: 696 loop : -1.31 (0.14), residues: 1950 *********************** REFINEMENT MACRO_CYCLE 6 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 619 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 603 time to evaluate : 4.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 613 average time/residue: 0.4495 time to fit residues: 461.4413 Evaluate side-chains 579 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 572 time to evaluate : 4.407 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3203 time to fit residues: 10.3435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 244 optimal weight: 2.9990 chunk 313 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 361 optimal weight: 9.9990 chunk 239 optimal weight: 0.0870 chunk 427 optimal weight: 20.0000 chunk 267 optimal weight: 8.9990 chunk 260 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 overall best weight: 2.4964 ------------------------------------------------------------------------------- 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 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN B 91 ASN C 24 ASN C 91 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN D 91 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN E 91 ASN F 24 ASN F 91 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35958 Z= 0.270 Angle : 0.632 14.081 48618 Z= 0.298 Chirality : 0.046 0.160 5436 Planarity : 0.005 0.148 6408 Dihedral : 8.476 175.454 4950 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.97 % Allowed : 16.32 % Favored : 82.70 % 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: -0.54 (0.13), residues: 4446 helix: 0.60 (0.13), residues: 1836 sheet: -0.18 (0.20), residues: 660 loop : -1.32 (0.14), residues: 1950 *********************** REFINEMENT MACRO_CYCLE 7 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 603 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 566 time to evaluate : 4.381 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 27 residues processed: 588 average time/residue: 0.4621 time to fit residues: 456.9413 Evaluate side-chains 581 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 554 time to evaluate : 4.376 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3476 time to fit residues: 24.2247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 272 optimal weight: 4.9990 chunk 291 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 336 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 B 24 ASN B 91 ASN C 24 ASN C 91 ASN D 24 ASN E 24 ASN E 91 ASN E 443 ASN F 24 ASN F 91 ASN ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35958 Z= 0.221 Angle : 0.616 15.685 48618 Z= 0.289 Chirality : 0.045 0.164 5436 Planarity : 0.005 0.130 6408 Dihedral : 8.302 176.299 4950 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.66 % Allowed : 16.64 % Favored : 82.70 % 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: -0.48 (0.13), residues: 4446 helix: 0.63 (0.13), residues: 1836 sheet: -0.12 (0.21), residues: 660 loop : -1.28 (0.14), residues: 1950 *********************** REFINEMENT MACRO_CYCLE 8 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 600 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 575 time to evaluate : 4.226 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 590 average time/residue: 0.4675 time to fit residues: 463.5459 Evaluate side-chains 578 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 568 time to evaluate : 4.605 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3584 time to fit residues: 13.3216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 4.9990 chunk 409 optimal weight: 8.9990 chunk 374 optimal weight: 0.9990 chunk 398 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 313 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 360 optimal weight: 1.9990 chunk 377 optimal weight: 0.0030 chunk 397 optimal weight: 4.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 24 ASN B 91 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 91 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 24 ASN E 91 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN F 91 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35958 Z= 0.157 Angle : 0.581 15.384 48618 Z= 0.270 Chirality : 0.044 0.172 5436 Planarity : 0.004 0.075 6408 Dihedral : 7.898 175.725 4950 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.32 % Allowed : 17.03 % Favored : 82.65 % 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: -0.19 (0.13), residues: 4446 helix: 0.91 (0.13), residues: 1794 sheet: -0.05 (0.20), residues: 696 loop : -1.10 (0.15), residues: 1956 *********************** REFINEMENT MACRO_CYCLE 9 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 595 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 583 time to evaluate : 4.788 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 587 average time/residue: 0.4609 time to fit residues: 455.3483 Evaluate side-chains 571 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 568 time to evaluate : 4.671 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3342 time to fit residues: 8.1023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 6.9990 chunk 421 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 200 optimal weight: 0.0570 chunk 293 optimal weight: 9.9990 chunk 442 optimal weight: 10.0000 chunk 407 optimal weight: 9.9990 chunk 352 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 272 optimal weight: 0.0980 chunk 215 optimal weight: 2.9990 overall best weight: 2.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN B 91 ASN C 24 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN E 91 ASN F 24 ASN F 115 HIS F 183 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35958 Z= 0.251 Angle : 0.637 17.506 48618 Z= 0.296 Chirality : 0.046 0.174 5436 Planarity : 0.005 0.080 6408 Dihedral : 8.105 176.760 4950 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.08 % Allowed : 17.74 % Favored : 82.18 % 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: -0.27 (0.13), residues: 4446 helix: 0.79 (0.13), residues: 1800 sheet: -0.10 (0.20), residues: 696 loop : -1.10 (0.15), residues: 1950 ********************** REFINEMENT MACRO_CYCLE 10 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 576 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 573 time to evaluate : 4.893 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 575 average time/residue: 0.4555 time to fit residues: 439.1838 Evaluate side-chains 568 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 566 time to evaluate : 4.297 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3632 time to fit residues: 7.5396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 4.9990 chunk 375 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 324 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 352 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 362 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 24 ASN B 91 ASN C 24 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 24 ASN E 91 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN F 183 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.117999 restraints weight = 124960.622| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.64 r_work: 0.3265 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35958 Z= 0.172 Angle : 0.601 15.882 48618 Z= 0.278 Chirality : 0.044 0.168 5436 Planarity : 0.004 0.065 6408 Dihedral : 7.982 177.157 4950 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.24 % Allowed : 17.82 % Favored : 81.94 % 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: -0.17 (0.13), residues: 4446 helix: 0.87 (0.13), residues: 1800 sheet: 0.00 (0.20), residues: 696 loop : -1.06 (0.15), residues: 1950 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9151.65 seconds wall clock time: 165 minutes 3.84 seconds (9903.84 seconds total)