Starting phenix.real_space_refine on Sun Sep 29 20:29:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io9_35612/09_2024/8io9_35612.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io9_35612/09_2024/8io9_35612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io9_35612/09_2024/8io9_35612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io9_35612/09_2024/8io9_35612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io9_35612/09_2024/8io9_35612.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io9_35612/09_2024/8io9_35612.cif" } resolution = 2.36 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= 0.005 sd= 0.050 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: 6 Type Number sf(0) Gaussians P 60 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 47904 2.51 5 N 13572 2.21 5 O 14004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 75744 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "C" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "B" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "C" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "C" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "C" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "D" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "E" Number of atoms: 6254 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "C" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "F" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "G" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "C" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "H" Number of atoms: 6254 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "C" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "I" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "J" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "K" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "L" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ATRP A 703 " occ=0.38 ... (26 atoms not shown) pdb=" CH2CTRP A 703 " occ=0.62 residue: pdb=" N ATRP B 703 " occ=0.38 ... (26 atoms not shown) pdb=" CH2CTRP B 703 " occ=0.62 residue: pdb=" N ATRP C 703 " occ=0.38 ... (26 atoms not shown) pdb=" CH2CTRP C 703 " occ=0.62 residue: pdb=" N ATRP D 703 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP D 703 " occ=0.50 residue: pdb=" N BTRP E 703 " occ=0.38 ... (26 atoms not shown) pdb=" CH2CTRP E 703 " occ=0.62 residue: pdb=" N ATRP F 703 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP F 703 " occ=0.50 residue: pdb=" N ATRP G 703 " occ=0.38 ... (26 atoms not shown) pdb=" CH2CTRP G 703 " occ=0.62 residue: pdb=" N BTRP H 703 " occ=0.38 ... (26 atoms not shown) pdb=" CH2CTRP H 703 " occ=0.62 residue: pdb=" N ATRP I 703 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP I 703 " occ=0.50 residue: pdb=" N ATRP J 703 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP J 703 " occ=0.50 residue: pdb=" N ATRP K 703 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP K 703 " occ=0.50 residue: pdb=" N ATRP L 703 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP L 703 " occ=0.50 Time building chain proxies: 58.08, per 1000 atoms: 0.77 Number of scatterers: 75744 At special positions: 0 Unit cell: (210.74, 217.3, 99.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 60 15.00 Mg 12 11.99 O 14004 8.00 N 13572 7.00 C 47904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.91 Conformation dependent library (CDL) restraints added in 12.9 seconds 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17568 Finding SS restraints... Secondary structure from input PDB file: 480 helices and 60 sheets defined 51.8% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.54 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 63 through 82 removed outlier: 3.669A pdb=" N HIS A 73 " --> pdb=" O PHE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.787A pdb=" N LEU A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 118 through 129 removed outlier: 4.032A pdb=" N PHE A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.631A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 247 through 275 removed outlier: 4.283A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 337 through 342 removed outlier: 5.962A pdb=" N GLU A 340 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.887A pdb=" N ILE A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 402 through 416 Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.656A pdb=" N ASP A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 495 through 498 Processing helix chain 'A' and resid 499 through 516 Processing helix chain 'A' and resid 547 through 557 removed outlier: 4.117A pdb=" N ASP A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 580 Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 636 through 653 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 680 through 688 Processing helix chain 'A' and resid 702 through 709 removed outlier: 3.744A pdb=" N HIS A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 755 through 758 removed outlier: 3.850A pdb=" N ARG A 758 " --> pdb=" O PRO A 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 758' Processing helix chain 'A' and resid 761 through 783 Processing helix chain 'A' and resid 786 through 791 Processing helix chain 'B' and resid 14 through 38 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 63 through 82 removed outlier: 3.672A pdb=" N HIS B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 105 removed outlier: 3.763A pdb=" N LEU B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 118 through 129 removed outlier: 4.016A pdb=" N PHE B 129 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 178 through 182 removed outlier: 3.529A pdb=" N GLU B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 178 through 182' Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.620A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 247 through 275 removed outlier: 4.265A pdb=" N GLY B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 337 through 342 removed outlier: 5.911A pdb=" N GLU B 340 " --> pdb=" O TYR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.863A pdb=" N ILE B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 402 through 416 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.630A pdb=" N ASP B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 495 through 498 Processing helix chain 'B' and resid 499 through 516 Processing helix chain 'B' and resid 547 through 555 removed outlier: 4.145A pdb=" N ASP B 551 " --> pdb=" O PRO B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 580 Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 636 through 653 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 680 through 688 Processing helix chain 'B' and resid 702 through 709 removed outlier: 3.775A pdb=" N HIS B 706 " --> pdb=" O PRO B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 731 through 739 Processing helix chain 'B' and resid 742 through 754 Processing helix chain 'B' and resid 755 through 758 removed outlier: 3.862A pdb=" N ARG B 758 " --> pdb=" O PRO B 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 758' Processing helix chain 'B' and resid 761 through 783 Processing helix chain 'B' and resid 786 through 791 Processing helix chain 'C' and resid 14 through 38 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 63 through 82 removed outlier: 3.672A pdb=" N HIS C 73 " --> pdb=" O PHE C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.790A pdb=" N LEU C 98 " --> pdb=" O GLY C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 118 through 129 removed outlier: 4.011A pdb=" N PHE C 129 " --> pdb=" O PHE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 165 Processing helix chain 'C' and resid 178 through 182 removed outlier: 3.524A pdb=" N GLU C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 178 through 182' Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.612A pdb=" N TRP C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 225 through 236 Processing helix chain 'C' and resid 247 through 275 removed outlier: 4.291A pdb=" N GLY C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 337 through 342 removed outlier: 5.961A pdb=" N GLU C 340 " --> pdb=" O TYR C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.864A pdb=" N ILE C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 371 through 376 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 402 through 416 Processing helix chain 'C' and resid 433 through 439 Processing helix chain 'C' and resid 449 through 454 removed outlier: 3.666A pdb=" N ASP C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 483 removed outlier: 3.513A pdb=" N LEU C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 498 Processing helix chain 'C' and resid 499 through 516 Processing helix chain 'C' and resid 547 through 557 removed outlier: 4.134A pdb=" N ASP C 551 " --> pdb=" O PRO C 547 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER C 557 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 580 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 636 through 653 Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 680 through 688 Processing helix chain 'C' and resid 702 through 709 removed outlier: 3.713A pdb=" N HIS C 706 " --> pdb=" O PRO C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 716 No H-bonds generated for 'chain 'C' and resid 714 through 716' Processing helix chain 'C' and resid 731 through 739 Processing helix chain 'C' and resid 742 through 754 Processing helix chain 'C' and resid 755 through 758 removed outlier: 3.882A pdb=" N ARG C 758 " --> pdb=" O PRO C 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 755 through 758' Processing helix chain 'C' and resid 761 through 783 Processing helix chain 'C' and resid 786 through 791 Processing helix chain 'D' and resid 14 through 38 Processing helix chain 'D' and resid 49 through 53 Processing helix chain 'D' and resid 63 through 82 removed outlier: 3.667A pdb=" N HIS D 73 " --> pdb=" O PHE D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 94 through 105 removed outlier: 3.761A pdb=" N LEU D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 Processing helix chain 'D' and resid 118 through 129 removed outlier: 3.995A pdb=" N PHE D 129 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 Processing helix chain 'D' and resid 178 through 182 removed outlier: 3.536A pdb=" N GLU D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 178 through 182' Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.613A pdb=" N TRP D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 225 through 236 Processing helix chain 'D' and resid 247 through 275 removed outlier: 4.288A pdb=" N GLY D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 313 Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 337 through 342 removed outlier: 5.915A pdb=" N GLU D 340 " --> pdb=" O TYR D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.853A pdb=" N ILE D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 371 through 376 Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 402 through 416 Processing helix chain 'D' and resid 433 through 439 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.626A pdb=" N ASP D 454 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 483 removed outlier: 3.509A pdb=" N LEU D 473 " --> pdb=" O SER D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 498 Processing helix chain 'D' and resid 499 through 516 Processing helix chain 'D' and resid 547 through 557 removed outlier: 4.120A pdb=" N ASP D 551 " --> pdb=" O PRO D 547 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS D 556 " --> pdb=" O LEU D 552 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER D 557 " --> pdb=" O VAL D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 580 Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 636 through 653 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 680 through 688 Processing helix chain 'D' and resid 702 through 709 removed outlier: 3.775A pdb=" N HIS D 706 " --> pdb=" O PRO D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 716 No H-bonds generated for 'chain 'D' and resid 714 through 716' Processing helix chain 'D' and resid 731 through 739 Processing helix chain 'D' and resid 742 through 754 Processing helix chain 'D' and resid 755 through 758 removed outlier: 3.868A pdb=" N ARG D 758 " --> pdb=" O PRO D 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 755 through 758' Processing helix chain 'D' and resid 761 through 783 Processing helix chain 'D' and resid 786 through 791 Processing helix chain 'E' and resid 14 through 38 Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 63 through 82 removed outlier: 3.679A pdb=" N HIS E 73 " --> pdb=" O PHE E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 94 through 105 removed outlier: 3.781A pdb=" N LEU E 98 " --> pdb=" O GLY E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 118 through 129 removed outlier: 4.028A pdb=" N PHE E 129 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 165 Processing helix chain 'E' and resid 178 through 182 removed outlier: 3.509A pdb=" N GLU E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 178 through 182' Processing helix chain 'E' and resid 183 through 190 removed outlier: 3.592A pdb=" N TRP E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 247 through 275 removed outlier: 4.311A pdb=" N GLY E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 313 Processing helix chain 'E' and resid 323 through 336 Processing helix chain 'E' and resid 337 through 342 removed outlier: 5.901A pdb=" N GLU E 340 " --> pdb=" O TYR E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 356 removed outlier: 3.878A pdb=" N ILE E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 371 through 376 Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 402 through 416 Processing helix chain 'E' and resid 433 through 439 Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.663A pdb=" N ASP E 454 " --> pdb=" O GLU E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 483 removed outlier: 3.581A pdb=" N LEU E 473 " --> pdb=" O SER E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 498 Processing helix chain 'E' and resid 499 through 516 Processing helix chain 'E' and resid 547 through 557 removed outlier: 4.095A pdb=" N ASP E 551 " --> pdb=" O PRO E 547 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS E 556 " --> pdb=" O LEU E 552 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER E 557 " --> pdb=" O VAL E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 580 Processing helix chain 'E' and resid 601 through 612 Processing helix chain 'E' and resid 636 through 653 Processing helix chain 'E' and resid 665 through 670 Processing helix chain 'E' and resid 680 through 688 Processing helix chain 'E' and resid 702 through 709 removed outlier: 3.733A pdb=" N HIS E 706 " --> pdb=" O PRO E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 716 No H-bonds generated for 'chain 'E' and resid 714 through 716' Processing helix chain 'E' and resid 731 through 739 Processing helix chain 'E' and resid 742 through 754 Processing helix chain 'E' and resid 755 through 758 removed outlier: 3.874A pdb=" N ARG E 758 " --> pdb=" O PRO E 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 755 through 758' Processing helix chain 'E' and resid 761 through 783 Processing helix chain 'E' and resid 786 through 791 Processing helix chain 'F' and resid 14 through 38 Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 63 through 82 removed outlier: 3.660A pdb=" N HIS F 73 " --> pdb=" O PHE F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 94 through 105 removed outlier: 3.774A pdb=" N LEU F 98 " --> pdb=" O GLY F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 112 Processing helix chain 'F' and resid 118 through 129 removed outlier: 4.014A pdb=" N PHE F 129 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 165 Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.641A pdb=" N TRP F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'F' and resid 219 through 224 Processing helix chain 'F' and resid 225 through 236 Processing helix chain 'F' and resid 247 through 275 removed outlier: 4.315A pdb=" N GLY F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 313 Processing helix chain 'F' and resid 323 through 336 Processing helix chain 'F' and resid 337 through 342 removed outlier: 5.972A pdb=" N GLU F 340 " --> pdb=" O TYR F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 356 removed outlier: 3.884A pdb=" N ILE F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 363 Processing helix chain 'F' and resid 371 through 376 Processing helix chain 'F' and resid 383 through 387 Processing helix chain 'F' and resid 402 through 416 Processing helix chain 'F' and resid 433 through 439 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.635A pdb=" N ASP F 454 " --> pdb=" O GLU F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 483 removed outlier: 3.507A pdb=" N LEU F 473 " --> pdb=" O SER F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 498 Processing helix chain 'F' and resid 499 through 516 Processing helix chain 'F' and resid 547 through 555 removed outlier: 4.082A pdb=" N ASP F 551 " --> pdb=" O PRO F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 580 Processing helix chain 'F' and resid 601 through 612 Processing helix chain 'F' and resid 636 through 653 Processing helix chain 'F' and resid 665 through 670 Processing helix chain 'F' and resid 680 through 688 Processing helix chain 'F' and resid 702 through 709 removed outlier: 3.755A pdb=" N HIS F 706 " --> pdb=" O PRO F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 716 No H-bonds generated for 'chain 'F' and resid 714 through 716' Processing helix chain 'F' and resid 731 through 739 Processing helix chain 'F' and resid 742 through 754 Processing helix chain 'F' and resid 755 through 758 removed outlier: 3.854A pdb=" N ARG F 758 " --> pdb=" O PRO F 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 755 through 758' Processing helix chain 'F' and resid 761 through 783 Processing helix chain 'F' and resid 786 through 791 Processing helix chain 'G' and resid 14 through 38 Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 63 through 82 removed outlier: 3.670A pdb=" N HIS G 73 " --> pdb=" O PHE G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 93 No H-bonds generated for 'chain 'G' and resid 91 through 93' Processing helix chain 'G' and resid 94 through 105 removed outlier: 3.787A pdb=" N LEU G 98 " --> pdb=" O GLY G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 112 Processing helix chain 'G' and resid 118 through 129 removed outlier: 4.033A pdb=" N PHE G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 165 Processing helix chain 'G' and resid 178 through 182 Processing helix chain 'G' and resid 183 through 190 removed outlier: 3.646A pdb=" N TRP G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 Processing helix chain 'G' and resid 219 through 224 Processing helix chain 'G' and resid 225 through 236 Processing helix chain 'G' and resid 247 through 275 removed outlier: 4.289A pdb=" N GLY G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 313 Processing helix chain 'G' and resid 323 through 336 Processing helix chain 'G' and resid 337 through 342 removed outlier: 5.959A pdb=" N GLU G 340 " --> pdb=" O TYR G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 356 removed outlier: 3.886A pdb=" N ILE G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 363 Processing helix chain 'G' and resid 371 through 376 Processing helix chain 'G' and resid 383 through 387 Processing helix chain 'G' and resid 402 through 416 Processing helix chain 'G' and resid 433 through 439 Processing helix chain 'G' and resid 449 through 454 removed outlier: 3.656A pdb=" N ASP G 454 " --> pdb=" O GLU G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 469 through 483 removed outlier: 3.501A pdb=" N LEU G 473 " --> pdb=" O SER G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 495 through 498 Processing helix chain 'G' and resid 499 through 516 Processing helix chain 'G' and resid 547 through 555 removed outlier: 4.079A pdb=" N ASP G 551 " --> pdb=" O PRO G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 568 through 580 Processing helix chain 'G' and resid 601 through 612 Processing helix chain 'G' and resid 636 through 653 Processing helix chain 'G' and resid 665 through 670 Processing helix chain 'G' and resid 680 through 688 Processing helix chain 'G' and resid 702 through 709 removed outlier: 3.753A pdb=" N HIS G 706 " --> pdb=" O PRO G 702 " (cutoff:3.500A) Processing helix chain 'G' and resid 714 through 716 No H-bonds generated for 'chain 'G' and resid 714 through 716' Processing helix chain 'G' and resid 731 through 739 Processing helix chain 'G' and resid 742 through 754 Processing helix chain 'G' and resid 755 through 758 removed outlier: 3.881A pdb=" N ARG G 758 " --> pdb=" O PRO G 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 755 through 758' Processing helix chain 'G' and resid 761 through 783 Processing helix chain 'G' and resid 786 through 791 Processing helix chain 'H' and resid 14 through 38 Processing helix chain 'H' and resid 49 through 53 Processing helix chain 'H' and resid 63 through 82 removed outlier: 3.677A pdb=" N HIS H 73 " --> pdb=" O PHE H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 94 through 105 removed outlier: 3.762A pdb=" N LEU H 98 " --> pdb=" O GLY H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 112 Processing helix chain 'H' and resid 118 through 129 removed outlier: 4.009A pdb=" N PHE H 129 " --> pdb=" O PHE H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 165 Processing helix chain 'H' and resid 178 through 182 removed outlier: 3.531A pdb=" N GLU H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 178 through 182' Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.616A pdb=" N TRP H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 Processing helix chain 'H' and resid 219 through 224 Processing helix chain 'H' and resid 225 through 236 Processing helix chain 'H' and resid 247 through 275 removed outlier: 4.264A pdb=" N GLY H 253 " --> pdb=" O ALA H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 313 Processing helix chain 'H' and resid 323 through 336 Processing helix chain 'H' and resid 337 through 342 removed outlier: 5.970A pdb=" N GLU H 340 " --> pdb=" O TYR H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 356 removed outlier: 3.868A pdb=" N ILE H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 363 Processing helix chain 'H' and resid 371 through 376 Processing helix chain 'H' and resid 383 through 387 Processing helix chain 'H' and resid 402 through 416 Processing helix chain 'H' and resid 433 through 439 Processing helix chain 'H' and resid 449 through 454 removed outlier: 3.631A pdb=" N ASP H 454 " --> pdb=" O GLU H 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 483 removed outlier: 3.503A pdb=" N LEU H 473 " --> pdb=" O SER H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 498 Processing helix chain 'H' and resid 499 through 516 Processing helix chain 'H' and resid 547 through 557 removed outlier: 4.072A pdb=" N ASP H 551 " --> pdb=" O PRO H 547 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN H 555 " --> pdb=" O ASP H 551 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS H 556 " --> pdb=" O LEU H 552 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER H 557 " --> pdb=" O VAL H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 568 through 580 Processing helix chain 'H' and resid 601 through 612 Processing helix chain 'H' and resid 636 through 653 Processing helix chain 'H' and resid 665 through 670 Processing helix chain 'H' and resid 680 through 688 Processing helix chain 'H' and resid 702 through 709 removed outlier: 3.789A pdb=" N HIS H 706 " --> pdb=" O PRO H 702 " (cutoff:3.500A) Processing helix chain 'H' and resid 714 through 716 No H-bonds generated for 'chain 'H' and resid 714 through 716' Processing helix chain 'H' and resid 731 through 739 Processing helix chain 'H' and resid 742 through 754 Processing helix chain 'H' and resid 755 through 758 removed outlier: 3.842A pdb=" N ARG H 758 " --> pdb=" O PRO H 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 755 through 758' Processing helix chain 'H' and resid 761 through 783 Processing helix chain 'H' and resid 786 through 791 Processing helix chain 'I' and resid 14 through 38 Processing helix chain 'I' and resid 49 through 53 Processing helix chain 'I' and resid 63 through 82 removed outlier: 3.672A pdb=" N HIS I 73 " --> pdb=" O PHE I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 93 No H-bonds generated for 'chain 'I' and resid 91 through 93' Processing helix chain 'I' and resid 94 through 105 removed outlier: 3.794A pdb=" N LEU I 98 " --> pdb=" O GLY I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 112 Processing helix chain 'I' and resid 118 through 129 removed outlier: 4.012A pdb=" N PHE I 129 " --> pdb=" O PHE I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 165 Processing helix chain 'I' and resid 178 through 182 removed outlier: 3.501A pdb=" N GLU I 182 " --> pdb=" O ASP I 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 178 through 182' Processing helix chain 'I' and resid 183 through 190 removed outlier: 3.613A pdb=" N TRP I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 196 Processing helix chain 'I' and resid 219 through 224 Processing helix chain 'I' and resid 225 through 236 Processing helix chain 'I' and resid 247 through 275 removed outlier: 4.318A pdb=" N GLY I 253 " --> pdb=" O ALA I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 313 Processing helix chain 'I' and resid 323 through 336 Processing helix chain 'I' and resid 337 through 342 removed outlier: 5.888A pdb=" N GLU I 340 " --> pdb=" O TYR I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 356 removed outlier: 3.859A pdb=" N ILE I 356 " --> pdb=" O GLU I 352 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 363 Processing helix chain 'I' and resid 371 through 376 Processing helix chain 'I' and resid 383 through 387 Processing helix chain 'I' and resid 402 through 416 Processing helix chain 'I' and resid 433 through 439 Processing helix chain 'I' and resid 449 through 454 removed outlier: 3.663A pdb=" N ASP I 454 " --> pdb=" O GLU I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 483 removed outlier: 3.515A pdb=" N LEU I 473 " --> pdb=" O SER I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 498 Processing helix chain 'I' and resid 499 through 516 Processing helix chain 'I' and resid 547 through 555 removed outlier: 4.124A pdb=" N ASP I 551 " --> pdb=" O PRO I 547 " (cutoff:3.500A) Processing helix chain 'I' and resid 568 through 580 Processing helix chain 'I' and resid 601 through 612 Processing helix chain 'I' and resid 636 through 653 Processing helix chain 'I' and resid 665 through 670 Processing helix chain 'I' and resid 680 through 688 Processing helix chain 'I' and resid 702 through 709 removed outlier: 3.736A pdb=" N HIS I 706 " --> pdb=" O PRO I 702 " (cutoff:3.500A) Processing helix chain 'I' and resid 714 through 716 No H-bonds generated for 'chain 'I' and resid 714 through 716' Processing helix chain 'I' and resid 731 through 739 Processing helix chain 'I' and resid 742 through 754 Processing helix chain 'I' and resid 755 through 758 removed outlier: 3.881A pdb=" N ARG I 758 " --> pdb=" O PRO I 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 755 through 758' Processing helix chain 'I' and resid 761 through 783 Processing helix chain 'I' and resid 786 through 791 Processing helix chain 'J' and resid 14 through 38 Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 63 through 82 removed outlier: 3.667A pdb=" N HIS J 73 " --> pdb=" O PHE J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 93 No H-bonds generated for 'chain 'J' and resid 91 through 93' Processing helix chain 'J' and resid 94 through 105 removed outlier: 3.768A pdb=" N LEU J 98 " --> pdb=" O GLY J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 112 Processing helix chain 'J' and resid 118 through 129 removed outlier: 3.995A pdb=" N PHE J 129 " --> pdb=" O PHE J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 165 Processing helix chain 'J' and resid 178 through 182 Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.608A pdb=" N TRP J 190 " --> pdb=" O LEU J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 196 Processing helix chain 'J' and resid 219 through 224 Processing helix chain 'J' and resid 225 through 236 Processing helix chain 'J' and resid 247 through 275 removed outlier: 4.286A pdb=" N GLY J 253 " --> pdb=" O ALA J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 309 through 313 Processing helix chain 'J' and resid 323 through 336 Processing helix chain 'J' and resid 337 through 342 removed outlier: 5.914A pdb=" N GLU J 340 " --> pdb=" O TYR J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 356 removed outlier: 3.857A pdb=" N ILE J 356 " --> pdb=" O GLU J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 363 Processing helix chain 'J' and resid 371 through 376 Processing helix chain 'J' and resid 383 through 387 Processing helix chain 'J' and resid 402 through 416 Processing helix chain 'J' and resid 433 through 439 Processing helix chain 'J' and resid 449 through 454 removed outlier: 3.628A pdb=" N ASP J 454 " --> pdb=" O GLU J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 469 through 483 removed outlier: 3.506A pdb=" N LEU J 473 " --> pdb=" O SER J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 498 Processing helix chain 'J' and resid 499 through 516 Processing helix chain 'J' and resid 547 through 557 removed outlier: 4.174A pdb=" N ASP J 551 " --> pdb=" O PRO J 547 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS J 556 " --> pdb=" O LEU J 552 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER J 557 " --> pdb=" O VAL J 553 " (cutoff:3.500A) Processing helix chain 'J' and resid 568 through 580 Processing helix chain 'J' and resid 601 through 612 Processing helix chain 'J' and resid 636 through 653 Processing helix chain 'J' and resid 665 through 670 Processing helix chain 'J' and resid 680 through 688 Processing helix chain 'J' and resid 702 through 709 removed outlier: 3.762A pdb=" N HIS J 706 " --> pdb=" O PRO J 702 " (cutoff:3.500A) Processing helix chain 'J' and resid 714 through 716 No H-bonds generated for 'chain 'J' and resid 714 through 716' Processing helix chain 'J' and resid 731 through 739 Processing helix chain 'J' and resid 742 through 754 Processing helix chain 'J' and resid 755 through 758 removed outlier: 3.864A pdb=" N ARG J 758 " --> pdb=" O PRO J 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 755 through 758' Processing helix chain 'J' and resid 761 through 783 Processing helix chain 'J' and resid 786 through 791 Processing helix chain 'K' and resid 14 through 38 Processing helix chain 'K' and resid 49 through 53 Processing helix chain 'K' and resid 63 through 82 removed outlier: 3.681A pdb=" N HIS K 73 " --> pdb=" O PHE K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 93 No H-bonds generated for 'chain 'K' and resid 91 through 93' Processing helix chain 'K' and resid 94 through 105 removed outlier: 3.786A pdb=" N LEU K 98 " --> pdb=" O GLY K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 112 Processing helix chain 'K' and resid 118 through 129 removed outlier: 4.029A pdb=" N PHE K 129 " --> pdb=" O PHE K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 165 Processing helix chain 'K' and resid 178 through 182 removed outlier: 3.505A pdb=" N GLU K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 178 through 182' Processing helix chain 'K' and resid 183 through 190 removed outlier: 3.594A pdb=" N TRP K 190 " --> pdb=" O LEU K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 196 Processing helix chain 'K' and resid 219 through 224 Processing helix chain 'K' and resid 225 through 236 Processing helix chain 'K' and resid 247 through 275 removed outlier: 4.282A pdb=" N GLY K 253 " --> pdb=" O ALA K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 313 Processing helix chain 'K' and resid 323 through 336 Processing helix chain 'K' and resid 337 through 342 removed outlier: 5.901A pdb=" N GLU K 340 " --> pdb=" O TYR K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 356 removed outlier: 3.877A pdb=" N ILE K 356 " --> pdb=" O GLU K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 363 Processing helix chain 'K' and resid 371 through 376 Processing helix chain 'K' and resid 383 through 387 Processing helix chain 'K' and resid 402 through 416 Processing helix chain 'K' and resid 433 through 439 Processing helix chain 'K' and resid 449 through 454 removed outlier: 3.665A pdb=" N ASP K 454 " --> pdb=" O GLU K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 469 through 483 removed outlier: 3.581A pdb=" N LEU K 473 " --> pdb=" O SER K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 498 Processing helix chain 'K' and resid 499 through 516 Processing helix chain 'K' and resid 547 through 557 removed outlier: 4.178A pdb=" N ASP K 551 " --> pdb=" O PRO K 547 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS K 556 " --> pdb=" O LEU K 552 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER K 557 " --> pdb=" O VAL K 553 " (cutoff:3.500A) Processing helix chain 'K' and resid 568 through 580 Processing helix chain 'K' and resid 601 through 612 Processing helix chain 'K' and resid 636 through 653 Processing helix chain 'K' and resid 665 through 670 Processing helix chain 'K' and resid 680 through 688 Processing helix chain 'K' and resid 702 through 709 removed outlier: 3.730A pdb=" N HIS K 706 " --> pdb=" O PRO K 702 " (cutoff:3.500A) Processing helix chain 'K' and resid 714 through 716 No H-bonds generated for 'chain 'K' and resid 714 through 716' Processing helix chain 'K' and resid 731 through 739 Processing helix chain 'K' and resid 742 through 754 Processing helix chain 'K' and resid 755 through 758 removed outlier: 3.876A pdb=" N ARG K 758 " --> pdb=" O PRO K 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 755 through 758' Processing helix chain 'K' and resid 761 through 783 Processing helix chain 'K' and resid 786 through 791 Processing helix chain 'L' and resid 14 through 38 Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 63 through 82 removed outlier: 3.659A pdb=" N HIS L 73 " --> pdb=" O PHE L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 93 No H-bonds generated for 'chain 'L' and resid 91 through 93' Processing helix chain 'L' and resid 94 through 105 removed outlier: 3.772A pdb=" N LEU L 98 " --> pdb=" O GLY L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 112 Processing helix chain 'L' and resid 118 through 129 removed outlier: 4.016A pdb=" N PHE L 129 " --> pdb=" O PHE L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 165 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 183 through 190 removed outlier: 3.626A pdb=" N TRP L 190 " --> pdb=" O LEU L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 196 Processing helix chain 'L' and resid 219 through 224 Processing helix chain 'L' and resid 225 through 236 Processing helix chain 'L' and resid 247 through 275 removed outlier: 4.280A pdb=" N GLY L 253 " --> pdb=" O ALA L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 309 through 313 Processing helix chain 'L' and resid 323 through 336 Processing helix chain 'L' and resid 337 through 342 removed outlier: 5.917A pdb=" N GLU L 340 " --> pdb=" O TYR L 337 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 356 removed outlier: 3.883A pdb=" N ILE L 356 " --> pdb=" O GLU L 352 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 363 Processing helix chain 'L' and resid 371 through 376 Processing helix chain 'L' and resid 383 through 387 Processing helix chain 'L' and resid 402 through 416 Processing helix chain 'L' and resid 433 through 439 Processing helix chain 'L' and resid 449 through 454 removed outlier: 3.637A pdb=" N ASP L 454 " --> pdb=" O GLU L 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 469 through 483 Processing helix chain 'L' and resid 495 through 498 Processing helix chain 'L' and resid 499 through 516 Processing helix chain 'L' and resid 547 through 557 removed outlier: 4.142A pdb=" N ASP L 551 " --> pdb=" O PRO L 547 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS L 556 " --> pdb=" O LEU L 552 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER L 557 " --> pdb=" O VAL L 553 " (cutoff:3.500A) Processing helix chain 'L' and resid 568 through 580 Processing helix chain 'L' and resid 601 through 612 Processing helix chain 'L' and resid 636 through 653 Processing helix chain 'L' and resid 665 through 670 Processing helix chain 'L' and resid 680 through 688 Processing helix chain 'L' and resid 702 through 709 removed outlier: 3.736A pdb=" N HIS L 706 " --> pdb=" O PRO L 702 " (cutoff:3.500A) Processing helix chain 'L' and resid 714 through 716 No H-bonds generated for 'chain 'L' and resid 714 through 716' Processing helix chain 'L' and resid 731 through 739 Processing helix chain 'L' and resid 742 through 754 Processing helix chain 'L' and resid 755 through 758 removed outlier: 3.868A pdb=" N ARG L 758 " --> pdb=" O PRO L 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 755 through 758' Processing helix chain 'L' and resid 761 through 783 Processing helix chain 'L' and resid 786 through 791 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 removed outlier: 6.310A pdb=" N ASN A 84 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA A 173 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE A 86 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL A 175 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL A 88 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLY A 177 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 170 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 205 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 172 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE A 207 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS A 174 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N HIS A 209 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE A 176 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA3, first strand: chain 'A' and resid 397 through 400 removed outlier: 4.875A pdb=" N SER A 397 " --> pdb=" O GLN A 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 464 through 466 removed outlier: 6.528A pdb=" N LEU A 422 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE A 423 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR A 492 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE A 489 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER A 531 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR A 491 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU A 526 " --> pdb=" O ASN A 587 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE A 589 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 528 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG A 562 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A 590 " --> pdb=" O ARG A 562 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR A 564 " --> pdb=" O VAL A 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 613 through 616 removed outlier: 4.643A pdb=" N PHE A 660 " --> pdb=" O TRP A 616 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 629 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 661 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE A 631 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL A 663 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER A 633 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL A 630 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN A 697 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA A 632 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE A 694 " --> pdb=" O HIS A 719 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ARG A 721 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE A 696 " --> pdb=" O ARG A 721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.305A pdb=" N ASN B 84 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA B 173 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE B 86 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL B 175 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 88 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLY B 177 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 170 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU B 205 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 172 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE B 207 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS B 174 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N HIS B 209 " --> pdb=" O CYS B 174 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 176 " --> pdb=" O HIS B 209 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 300 through 301 Processing sheet with id=AA8, first strand: chain 'B' and resid 397 through 400 removed outlier: 4.863A pdb=" N SER B 397 " --> pdb=" O GLN B 598 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 464 through 466 removed outlier: 6.520A pdb=" N LEU B 422 " --> pdb=" O MET B 465 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 423 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR B 492 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE B 489 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 531 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR B 491 " --> pdb=" O SER B 531 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU B 526 " --> pdb=" O ASN B 587 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE B 589 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 528 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG B 562 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL B 590 " --> pdb=" O ARG B 562 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR B 564 " --> pdb=" O VAL B 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 613 through 616 removed outlier: 4.652A pdb=" N PHE B 660 " --> pdb=" O TRP B 616 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 629 " --> pdb=" O ARG B 659 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL B 661 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE B 631 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL B 663 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER B 633 " --> pdb=" O VAL B 663 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 630 " --> pdb=" O ILE B 695 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASN B 697 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA B 632 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE B 694 " --> pdb=" O HIS B 719 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ARG B 721 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE B 696 " --> pdb=" O ARG B 721 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 84 through 89 removed outlier: 6.278A pdb=" N ASN C 84 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA C 173 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE C 86 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL C 175 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 88 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY C 177 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU C 170 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU C 205 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C 172 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE C 207 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N CYS C 174 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N HIS C 209 " --> pdb=" O CYS C 174 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE C 176 " --> pdb=" O HIS C 209 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 300 through 301 Processing sheet with id=AB4, first strand: chain 'C' and resid 397 through 400 removed outlier: 4.852A pdb=" N SER C 397 " --> pdb=" O GLN C 598 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 464 through 466 removed outlier: 6.545A pdb=" N LEU C 422 " --> pdb=" O MET C 465 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE C 423 " --> pdb=" O ALA C 490 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N TYR C 492 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 489 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER C 531 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR C 491 " --> pdb=" O SER C 531 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU C 526 " --> pdb=" O ASN C 587 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE C 589 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE C 528 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG C 562 " --> pdb=" O VAL C 588 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL C 590 " --> pdb=" O ARG C 562 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR C 564 " --> pdb=" O VAL C 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 613 through 616 removed outlier: 4.626A pdb=" N PHE C 660 " --> pdb=" O TRP C 616 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 630 " --> pdb=" O ILE C 695 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASN C 697 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA C 632 " --> pdb=" O ASN C 697 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE C 694 " --> pdb=" O HIS C 719 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ARG C 721 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE C 696 " --> pdb=" O ARG C 721 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 84 through 89 removed outlier: 6.285A pdb=" N ASN D 84 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA D 173 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE D 86 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL D 175 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL D 88 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLY D 177 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU D 170 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU D 205 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 172 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE D 207 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS D 174 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N HIS D 209 " --> pdb=" O CYS D 174 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE D 176 " --> pdb=" O HIS D 209 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 300 through 301 Processing sheet with id=AB9, first strand: chain 'D' and resid 397 through 400 removed outlier: 4.861A pdb=" N SER D 397 " --> pdb=" O GLN D 598 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 464 through 466 removed outlier: 6.575A pdb=" N LEU D 422 " --> pdb=" O MET D 465 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE D 423 " --> pdb=" O ALA D 490 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N TYR D 492 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE D 489 " --> pdb=" O LEU D 529 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER D 531 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR D 491 " --> pdb=" O SER D 531 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU D 526 " --> pdb=" O ASN D 587 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE D 589 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE D 528 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG D 562 " --> pdb=" O VAL D 588 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL D 590 " --> pdb=" O ARG D 562 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR D 564 " --> pdb=" O VAL D 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 613 through 616 removed outlier: 4.638A pdb=" N PHE D 660 " --> pdb=" O TRP D 616 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 630 " --> pdb=" O ILE D 695 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN D 697 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA D 632 " --> pdb=" O ASN D 697 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE D 694 " --> pdb=" O HIS D 719 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG D 721 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE D 696 " --> pdb=" O ARG D 721 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 84 through 89 removed outlier: 6.330A pdb=" N ASN E 84 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA E 173 " --> pdb=" O ASN E 84 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE E 86 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL E 175 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL E 88 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY E 177 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 300 through 301 Processing sheet with id=AC5, first strand: chain 'E' and resid 397 through 400 removed outlier: 4.857A pdb=" N SER E 397 " --> pdb=" O GLN E 598 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 464 through 466 removed outlier: 6.518A pdb=" N LEU E 422 " --> pdb=" O MET E 465 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE E 423 " --> pdb=" O ALA E 490 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N TYR E 492 " --> pdb=" O PHE E 423 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE E 489 " --> pdb=" O LEU E 529 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER E 531 " --> pdb=" O PHE E 489 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR E 491 " --> pdb=" O SER E 531 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU E 526 " --> pdb=" O ASN E 587 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE E 589 " --> pdb=" O LEU E 526 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE E 528 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG E 562 " --> pdb=" O VAL E 588 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL E 590 " --> pdb=" O ARG E 562 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR E 564 " --> pdb=" O VAL E 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 613 through 616 removed outlier: 4.651A pdb=" N PHE E 660 " --> pdb=" O TRP E 616 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL E 629 " --> pdb=" O ARG E 659 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL E 661 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE E 631 " --> pdb=" O VAL E 661 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL E 663 " --> pdb=" O ILE E 631 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER E 633 " --> pdb=" O VAL E 663 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL E 630 " --> pdb=" O ILE E 695 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASN E 697 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA E 632 " --> pdb=" O ASN E 697 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE E 694 " --> pdb=" O HIS E 719 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ARG E 721 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE E 696 " --> pdb=" O ARG E 721 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 84 through 89 removed outlier: 6.294A pdb=" N ASN F 84 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA F 173 " --> pdb=" O ASN F 84 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE F 86 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL F 175 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL F 88 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLY F 177 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU F 170 " --> pdb=" O ALA F 203 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU F 205 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL F 172 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE F 207 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS F 174 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N HIS F 209 " --> pdb=" O CYS F 174 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE F 176 " --> pdb=" O HIS F 209 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 300 through 301 Processing sheet with id=AD1, first strand: chain 'F' and resid 397 through 400 removed outlier: 4.876A pdb=" N SER F 397 " --> pdb=" O GLN F 598 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 464 through 466 removed outlier: 6.561A pdb=" N LEU F 422 " --> pdb=" O MET F 465 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE F 423 " --> pdb=" O ALA F 490 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N TYR F 492 " --> pdb=" O PHE F 423 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE F 489 " --> pdb=" O LEU F 529 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER F 531 " --> pdb=" O PHE F 489 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR F 491 " --> pdb=" O SER F 531 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU F 526 " --> pdb=" O ASN F 587 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE F 589 " --> pdb=" O LEU F 526 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE F 528 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG F 562 " --> pdb=" O VAL F 588 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL F 590 " --> pdb=" O ARG F 562 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR F 564 " --> pdb=" O VAL F 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 613 through 616 removed outlier: 4.623A pdb=" N PHE F 660 " --> pdb=" O TRP F 616 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL F 629 " --> pdb=" O ARG F 659 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL F 661 " --> pdb=" O VAL F 629 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE F 631 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL F 663 " --> pdb=" O ILE F 631 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER F 633 " --> pdb=" O VAL F 663 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL F 630 " --> pdb=" O ILE F 695 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN F 697 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA F 632 " --> pdb=" O ASN F 697 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE F 694 " --> pdb=" O HIS F 719 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ARG F 721 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE F 696 " --> pdb=" O ARG F 721 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 84 through 89 removed outlier: 6.276A pdb=" N ASN G 84 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA G 173 " --> pdb=" O ASN G 84 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE G 86 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL G 175 " --> pdb=" O ILE G 86 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL G 88 " --> pdb=" O VAL G 175 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLY G 177 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU G 170 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU G 205 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL G 172 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE G 207 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS G 174 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N HIS G 209 " --> pdb=" O CYS G 174 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE G 176 " --> pdb=" O HIS G 209 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 300 through 301 Processing sheet with id=AD6, first strand: chain 'G' and resid 397 through 400 removed outlier: 4.874A pdb=" N SER G 397 " --> pdb=" O GLN G 598 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 464 through 466 removed outlier: 6.528A pdb=" N LEU G 422 " --> pdb=" O MET G 465 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE G 423 " --> pdb=" O ALA G 490 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR G 492 " --> pdb=" O PHE G 423 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE G 489 " --> pdb=" O LEU G 529 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER G 531 " --> pdb=" O PHE G 489 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR G 491 " --> pdb=" O SER G 531 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG G 562 " --> pdb=" O VAL G 588 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL G 590 " --> pdb=" O ARG G 562 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR G 564 " --> pdb=" O VAL G 590 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 613 through 616 removed outlier: 4.619A pdb=" N PHE G 660 " --> pdb=" O TRP G 616 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL G 629 " --> pdb=" O ARG G 659 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL G 661 " --> pdb=" O VAL G 629 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE G 631 " --> pdb=" O VAL G 661 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL G 663 " --> pdb=" O ILE G 631 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER G 633 " --> pdb=" O VAL G 663 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL G 630 " --> pdb=" O ILE G 695 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN G 697 " --> pdb=" O VAL G 630 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA G 632 " --> pdb=" O ASN G 697 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE G 694 " --> pdb=" O HIS G 719 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG G 721 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE G 696 " --> pdb=" O ARG G 721 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 84 through 89 removed outlier: 6.300A pdb=" N ASN H 84 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA H 173 " --> pdb=" O ASN H 84 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE H 86 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL H 175 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL H 88 " --> pdb=" O VAL H 175 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N GLY H 177 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU H 170 " --> pdb=" O ALA H 203 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU H 205 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL H 172 " --> pdb=" O LEU H 205 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE H 207 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS H 174 " --> pdb=" O ILE H 207 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N HIS H 209 " --> pdb=" O CYS H 174 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE H 176 " --> pdb=" O HIS H 209 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 300 through 301 Processing sheet with id=AE2, first strand: chain 'H' and resid 397 through 400 removed outlier: 4.864A pdb=" N SER H 397 " --> pdb=" O GLN H 598 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 464 through 466 removed outlier: 6.516A pdb=" N LEU H 422 " --> pdb=" O MET H 465 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE H 423 " --> pdb=" O ALA H 490 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR H 492 " --> pdb=" O PHE H 423 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE H 489 " --> pdb=" O LEU H 529 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER H 531 " --> pdb=" O PHE H 489 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR H 491 " --> pdb=" O SER H 531 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU H 526 " --> pdb=" O ASN H 587 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE H 589 " --> pdb=" O LEU H 526 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE H 528 " --> pdb=" O ILE H 589 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG H 562 " --> pdb=" O VAL H 588 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL H 590 " --> pdb=" O ARG H 562 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR H 564 " --> pdb=" O VAL H 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'H' and resid 613 through 616 removed outlier: 4.651A pdb=" N PHE H 660 " --> pdb=" O TRP H 616 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL H 629 " --> pdb=" O ARG H 659 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL H 661 " --> pdb=" O VAL H 629 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE H 631 " --> pdb=" O VAL H 661 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL H 663 " --> pdb=" O ILE H 631 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER H 633 " --> pdb=" O VAL H 663 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL H 630 " --> pdb=" O ILE H 695 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ASN H 697 " --> pdb=" O VAL H 630 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA H 632 " --> pdb=" O ASN H 697 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE H 694 " --> pdb=" O HIS H 719 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG H 721 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE H 696 " --> pdb=" O ARG H 721 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 84 through 89 removed outlier: 6.395A pdb=" N ASN I 84 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA I 173 " --> pdb=" O ASN I 84 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE I 86 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL I 175 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL I 88 " --> pdb=" O VAL I 175 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLY I 177 " --> pdb=" O VAL I 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU I 170 " --> pdb=" O ALA I 203 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU I 205 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL I 172 " --> pdb=" O LEU I 205 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE I 207 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS I 174 " --> pdb=" O ILE I 207 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N HIS I 209 " --> pdb=" O CYS I 174 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE I 176 " --> pdb=" O HIS I 209 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 300 through 301 Processing sheet with id=AE7, first strand: chain 'I' and resid 397 through 400 removed outlier: 4.853A pdb=" N SER I 397 " --> pdb=" O GLN I 598 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 464 through 466 removed outlier: 6.546A pdb=" N LEU I 422 " --> pdb=" O MET I 465 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE I 423 " --> pdb=" O ALA I 490 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N TYR I 492 " --> pdb=" O PHE I 423 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE I 489 " --> pdb=" O LEU I 529 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER I 531 " --> pdb=" O PHE I 489 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR I 491 " --> pdb=" O SER I 531 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU I 526 " --> pdb=" O ASN I 587 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE I 589 " --> pdb=" O LEU I 526 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE I 528 " --> pdb=" O ILE I 589 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG I 562 " --> pdb=" O VAL I 588 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL I 590 " --> pdb=" O ARG I 562 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR I 564 " --> pdb=" O VAL I 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'I' and resid 613 through 616 removed outlier: 4.625A pdb=" N PHE I 660 " --> pdb=" O TRP I 616 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL I 629 " --> pdb=" O ARG I 659 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL I 661 " --> pdb=" O VAL I 629 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE I 631 " --> pdb=" O VAL I 661 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL I 663 " --> pdb=" O ILE I 631 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER I 633 " --> pdb=" O VAL I 663 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL I 630 " --> pdb=" O ILE I 695 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN I 697 " --> pdb=" O VAL I 630 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA I 632 " --> pdb=" O ASN I 697 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE I 694 " --> pdb=" O HIS I 719 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG I 721 " --> pdb=" O ILE I 694 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE I 696 " --> pdb=" O ARG I 721 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 84 through 89 removed outlier: 6.277A pdb=" N ASN J 84 " --> pdb=" O ILE J 171 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA J 173 " --> pdb=" O ASN J 84 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE J 86 " --> pdb=" O ALA J 173 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL J 175 " --> pdb=" O ILE J 86 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL J 88 " --> pdb=" O VAL J 175 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY J 177 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU J 170 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU J 205 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL J 172 " --> pdb=" O LEU J 205 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE J 207 " --> pdb=" O VAL J 172 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS J 174 " --> pdb=" O ILE J 207 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N HIS J 209 " --> pdb=" O CYS J 174 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE J 176 " --> pdb=" O HIS J 209 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 300 through 301 Processing sheet with id=AF3, first strand: chain 'J' and resid 397 through 400 removed outlier: 4.862A pdb=" N SER J 397 " --> pdb=" O GLN J 598 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 464 through 466 removed outlier: 6.490A pdb=" N LEU J 422 " --> pdb=" O MET J 465 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE J 423 " --> pdb=" O ALA J 490 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N TYR J 492 " --> pdb=" O PHE J 423 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE J 489 " --> pdb=" O LEU J 529 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER J 531 " --> pdb=" O PHE J 489 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR J 491 " --> pdb=" O SER J 531 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU J 526 " --> pdb=" O ASN J 587 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE J 589 " --> pdb=" O LEU J 526 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE J 528 " --> pdb=" O ILE J 589 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG J 562 " --> pdb=" O VAL J 588 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL J 590 " --> pdb=" O ARG J 562 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR J 564 " --> pdb=" O VAL J 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'J' and resid 613 through 616 removed outlier: 4.635A pdb=" N PHE J 660 " --> pdb=" O TRP J 616 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL J 630 " --> pdb=" O ILE J 695 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASN J 697 " --> pdb=" O VAL J 630 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA J 632 " --> pdb=" O ASN J 697 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE J 694 " --> pdb=" O HIS J 719 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ARG J 721 " --> pdb=" O ILE J 694 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE J 696 " --> pdb=" O ARG J 721 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 84 through 89 removed outlier: 6.332A pdb=" N ASN K 84 " --> pdb=" O ILE K 171 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA K 173 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE K 86 " --> pdb=" O ALA K 173 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL K 175 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL K 88 " --> pdb=" O VAL K 175 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLY K 177 " --> pdb=" O VAL K 88 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 300 through 301 Processing sheet with id=AF8, first strand: chain 'K' and resid 397 through 400 removed outlier: 4.861A pdb=" N SER K 397 " --> pdb=" O GLN K 598 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 464 through 466 removed outlier: 6.518A pdb=" N LEU K 422 " --> pdb=" O MET K 465 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE K 423 " --> pdb=" O ALA K 490 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N TYR K 492 " --> pdb=" O PHE K 423 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE K 489 " --> pdb=" O LEU K 529 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER K 531 " --> pdb=" O PHE K 489 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR K 491 " --> pdb=" O SER K 531 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU K 526 " --> pdb=" O ASN K 587 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE K 589 " --> pdb=" O LEU K 526 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE K 528 " --> pdb=" O ILE K 589 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG K 562 " --> pdb=" O VAL K 588 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL K 590 " --> pdb=" O ARG K 562 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR K 564 " --> pdb=" O VAL K 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'K' and resid 613 through 616 removed outlier: 4.639A pdb=" N PHE K 660 " --> pdb=" O TRP K 616 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL K 629 " --> pdb=" O ARG K 659 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL K 661 " --> pdb=" O VAL K 629 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE K 631 " --> pdb=" O VAL K 661 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL K 663 " --> pdb=" O ILE K 631 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER K 633 " --> pdb=" O VAL K 663 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL K 630 " --> pdb=" O ILE K 695 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASN K 697 " --> pdb=" O VAL K 630 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA K 632 " --> pdb=" O ASN K 697 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE K 694 " --> pdb=" O HIS K 719 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG K 721 " --> pdb=" O ILE K 694 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE K 696 " --> pdb=" O ARG K 721 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 84 through 89 removed outlier: 6.344A pdb=" N ASN L 84 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ALA L 173 " --> pdb=" O ASN L 84 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE L 86 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL L 175 " --> pdb=" O ILE L 86 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL L 88 " --> pdb=" O VAL L 175 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N GLY L 177 " --> pdb=" O VAL L 88 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU L 170 " --> pdb=" O ALA L 203 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU L 205 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL L 172 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE L 207 " --> pdb=" O VAL L 172 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS L 174 " --> pdb=" O ILE L 207 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N HIS L 209 " --> pdb=" O CYS L 174 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE L 176 " --> pdb=" O HIS L 209 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 300 through 301 Processing sheet with id=AG4, first strand: chain 'L' and resid 397 through 400 removed outlier: 4.875A pdb=" N SER L 397 " --> pdb=" O GLN L 598 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 464 through 466 removed outlier: 6.563A pdb=" N LEU L 422 " --> pdb=" O MET L 465 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE L 423 " --> pdb=" O ALA L 490 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N TYR L 492 " --> pdb=" O PHE L 423 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE L 489 " --> pdb=" O LEU L 529 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER L 531 " --> pdb=" O PHE L 489 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR L 491 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU L 526 " --> pdb=" O ASN L 587 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE L 589 " --> pdb=" O LEU L 526 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE L 528 " --> pdb=" O ILE L 589 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG L 562 " --> pdb=" O VAL L 588 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL L 590 " --> pdb=" O ARG L 562 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR L 564 " --> pdb=" O VAL L 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'L' and resid 613 through 616 removed outlier: 4.639A pdb=" N PHE L 660 " --> pdb=" O TRP L 616 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL L 629 " --> pdb=" O ARG L 659 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL L 661 " --> pdb=" O VAL L 629 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE L 631 " --> pdb=" O VAL L 661 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL L 663 " --> pdb=" O ILE L 631 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER L 633 " --> pdb=" O VAL L 663 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL L 630 " --> pdb=" O ILE L 695 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ASN L 697 " --> pdb=" O VAL L 630 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA L 632 " --> pdb=" O ASN L 697 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE L 694 " --> pdb=" O HIS L 719 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ARG L 721 " --> pdb=" O ILE L 694 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE L 696 " --> pdb=" O ARG L 721 " (cutoff:3.500A) 3232 hydrogen bonds defined for protein. 8718 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: 36.96 Time building geometry restraints manager: 16.80 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: 25528 1.34 - 1.46: 12877 1.46 - 1.57: 39148 1.57 - 1.69: 87 1.69 - 1.81: 276 Bond restraints: 77916 Sorted by residual: bond pdb=" O3A ANP L 901 " pdb=" PB ANP L 901 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" O3A ANP I 901 " pdb=" PB ANP I 901 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" O3A ANP F 901 " pdb=" PB ANP F 901 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" O3A ANP H 901 " pdb=" PB ANP H 901 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" O3A ANP G 901 " pdb=" PB ANP G 901 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.49e+01 ... (remaining 77911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 105901 3.06 - 6.11: 450 6.11 - 9.17: 63 9.17 - 12.23: 14 12.23 - 15.28: 12 Bond angle restraints: 106440 Sorted by residual: angle pdb=" O2B TPP B 902 " pdb=" PB TPP B 902 " pdb=" O3A TPP B 902 " ideal model delta sigma weight residual 104.26 111.30 -7.04 1.33e+00 5.64e-01 2.79e+01 angle pdb=" O2B TPP D 902 " pdb=" PB TPP D 902 " pdb=" O3A TPP D 902 " ideal model delta sigma weight residual 104.26 111.27 -7.01 1.33e+00 5.64e-01 2.77e+01 angle pdb=" O2B TPP H 902 " pdb=" PB TPP H 902 " pdb=" O3A TPP H 902 " ideal model delta sigma weight residual 104.26 111.26 -7.00 1.33e+00 5.64e-01 2.76e+01 angle pdb=" O2B TPP L 902 " pdb=" PB TPP L 902 " pdb=" O3A TPP L 902 " ideal model delta sigma weight residual 104.26 111.17 -6.91 1.33e+00 5.64e-01 2.69e+01 angle pdb=" O2B TPP J 902 " pdb=" PB TPP J 902 " pdb=" O3A TPP J 902 " ideal model delta sigma weight residual 104.26 111.16 -6.90 1.33e+00 5.64e-01 2.68e+01 ... (remaining 106435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 43123 17.87 - 35.73: 2142 35.73 - 53.60: 387 53.60 - 71.47: 183 71.47 - 89.33: 65 Dihedral angle restraints: 45900 sinusoidal: 18600 harmonic: 27300 Sorted by residual: dihedral pdb=" CA GLY L 294 " pdb=" C GLY L 294 " pdb=" N TRP L 295 " pdb=" CA TRP L 295 " ideal model delta harmonic sigma weight residual 180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLY F 294 " pdb=" C GLY F 294 " pdb=" N TRP F 295 " pdb=" CA TRP F 295 " ideal model delta harmonic sigma weight residual 180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA GLY G 294 " pdb=" C GLY G 294 " pdb=" N TRP G 295 " pdb=" CA TRP G 295 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 45897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 10160 0.070 - 0.140: 1175 0.140 - 0.209: 17 0.209 - 0.279: 10 0.279 - 0.349: 2 Chirality restraints: 11364 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.71 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3' ANP D 901 " pdb=" C2' ANP D 901 " pdb=" C4' ANP D 901 " pdb=" O3' ANP D 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.70 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C3' ANP I 901 " pdb=" C2' ANP I 901 " pdb=" C4' ANP I 901 " pdb=" O3' ANP I 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 11361 not shown) Planarity restraints: 13944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 184 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO K 185 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO K 185 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO K 185 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 184 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO E 185 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 185 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 185 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 184 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO B 185 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " 0.028 5.00e-02 4.00e+02 ... (remaining 13941 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 903 2.57 - 3.15: 63966 3.15 - 3.73: 127118 3.73 - 4.32: 188195 4.32 - 4.90: 305428 Nonbonded interactions: 685610 Sorted by model distance: nonbonded pdb=" O2A TPP A 902 " pdb="MG MG A 903 " model vdw 1.987 2.170 nonbonded pdb=" O1A TPP J 902 " pdb="MG MG J 903 " model vdw 1.989 2.170 nonbonded pdb=" O2A TPP G 902 " pdb="MG MG G 903 " model vdw 1.992 2.170 nonbonded pdb=" O1A TPP L 902 " pdb="MG MG L 903 " model vdw 1.992 2.170 nonbonded pdb=" O1A TPP F 902 " pdb="MG MG F 903 " model vdw 1.992 2.170 ... (remaining 685605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'B' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'C' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'D' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'E' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'F' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'G' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'H' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'I' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'J' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'K' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'L' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) } 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=0.38 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 2.220 Check model and map are aligned: 0.440 Set scattering table: 0.540 Process input model: 175.110 Find NCS groups from input model: 3.720 Set up NCS constraints: 0.570 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: 0.020 Load rotamer database and sin/cos tables:10.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.005 0.149 77916 Z= 0.352 Angle : 0.599 15.285 106440 Z= 0.288 Chirality : 0.044 0.349 11364 Planarity : 0.004 0.052 13944 Dihedral : 12.283 89.332 28332 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.48 % Allowed : 3.19 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.09), residues: 9468 helix: 0.89 (0.08), residues: 4242 sheet: 0.22 (0.15), residues: 1128 loop : -0.38 (0.09), residues: 4098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 61 HIS 0.004 0.001 HIS E 596 PHE 0.012 0.002 PHE I 233 TYR 0.009 0.001 TYR A 723 ARG 0.004 0.000 ARG C 520 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 327 time to evaluate : 6.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 217 ASN cc_start: 0.7526 (m-40) cc_final: 0.6954 (m110) REVERT: D 217 ASN cc_start: 0.7424 (m-40) cc_final: 0.6811 (m110) REVERT: E 217 ASN cc_start: 0.7524 (m-40) cc_final: 0.6908 (m110) REVERT: J 217 ASN cc_start: 0.7496 (m-40) cc_final: 0.6894 (m110) REVERT: K 217 ASN cc_start: 0.7536 (m-40) cc_final: 0.6932 (m110) outliers start: 26 outliers final: 7 residues processed: 353 average time/residue: 1.5636 time to fit residues: 743.4758 Evaluate side-chains 189 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 182 time to evaluate : 6.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain K residue 305 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 790 optimal weight: 9.9990 chunk 709 optimal weight: 1.9990 chunk 393 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 478 optimal weight: 8.9990 chunk 379 optimal weight: 0.9990 chunk 733 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 chunk 446 optimal weight: 0.9990 chunk 546 optimal weight: 30.0000 chunk 849 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 77916 Z= 0.239 Angle : 0.560 8.145 106440 Z= 0.288 Chirality : 0.045 0.159 11364 Planarity : 0.005 0.048 13944 Dihedral : 9.333 73.657 10844 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.03 % Allowed : 5.69 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 9468 helix: 1.24 (0.08), residues: 4242 sheet: 0.13 (0.15), residues: 1152 loop : -0.34 (0.10), residues: 4074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 476 HIS 0.004 0.001 HIS C 699 PHE 0.010 0.001 PHE J 233 TYR 0.021 0.001 TYR I 723 ARG 0.003 0.000 ARG F 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 239 time to evaluate : 6.449 Fit side-chains REVERT: A 217 ASN cc_start: 0.7656 (m-40) cc_final: 0.7126 (m110) REVERT: B 217 ASN cc_start: 0.7577 (m-40) cc_final: 0.6920 (m110) REVERT: C 217 ASN cc_start: 0.7525 (m-40) cc_final: 0.7054 (m110) REVERT: D 217 ASN cc_start: 0.7463 (m-40) cc_final: 0.6960 (m110) REVERT: D 283 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6501 (tpt) REVERT: E 217 ASN cc_start: 0.7627 (m-40) cc_final: 0.7081 (m110) REVERT: F 217 ASN cc_start: 0.7636 (m-40) cc_final: 0.7023 (m110) REVERT: F 224 ILE cc_start: 0.7889 (mm) cc_final: 0.7550 (mm) REVERT: G 142 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: G 217 ASN cc_start: 0.7603 (m-40) cc_final: 0.7129 (m110) REVERT: H 217 ASN cc_start: 0.7570 (m-40) cc_final: 0.6907 (m110) REVERT: I 217 ASN cc_start: 0.7539 (m-40) cc_final: 0.7057 (m110) REVERT: J 217 ASN cc_start: 0.7460 (m-40) cc_final: 0.6963 (m110) REVERT: J 283 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6515 (tpt) REVERT: K 217 ASN cc_start: 0.7632 (m-40) cc_final: 0.7094 (m110) REVERT: L 217 ASN cc_start: 0.7642 (m-40) cc_final: 0.7029 (m110) REVERT: L 224 ILE cc_start: 0.7891 (mm) cc_final: 0.7559 (mm) outliers start: 70 outliers final: 11 residues processed: 277 average time/residue: 1.5402 time to fit residues: 577.8916 Evaluate side-chains 179 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 165 time to evaluate : 6.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 283 MET Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain L residue 142 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 472 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 707 optimal weight: 20.0000 chunk 578 optimal weight: 0.8980 chunk 234 optimal weight: 30.0000 chunk 851 optimal weight: 6.9990 chunk 919 optimal weight: 9.9990 chunk 758 optimal weight: 0.9980 chunk 844 optimal weight: 2.9990 chunk 290 optimal weight: 0.8980 chunk 683 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 77916 Z= 0.168 Angle : 0.500 7.881 106440 Z= 0.254 Chirality : 0.043 0.153 11364 Planarity : 0.004 0.045 13944 Dihedral : 8.230 74.221 10841 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.04 % Allowed : 6.30 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 9468 helix: 1.41 (0.08), residues: 4244 sheet: 0.11 (0.15), residues: 1144 loop : -0.28 (0.10), residues: 4080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 476 HIS 0.004 0.001 HIS G 73 PHE 0.010 0.001 PHE B 489 TYR 0.011 0.001 TYR D 701 ARG 0.004 0.000 ARG J 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 229 time to evaluate : 6.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ASN cc_start: 0.7460 (m-40) cc_final: 0.6917 (m110) REVERT: B 217 ASN cc_start: 0.7364 (m-40) cc_final: 0.6760 (m110) REVERT: B 274 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7239 (mtt180) REVERT: C 217 ASN cc_start: 0.7393 (m-40) cc_final: 0.6876 (m110) REVERT: C 283 MET cc_start: 0.6284 (tpt) cc_final: 0.6072 (tpt) REVERT: D 122 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8417 (tt) REVERT: D 217 ASN cc_start: 0.7387 (m-40) cc_final: 0.6728 (m110) REVERT: E 217 ASN cc_start: 0.7441 (m-40) cc_final: 0.6867 (m110) REVERT: F 217 ASN cc_start: 0.7460 (m-40) cc_final: 0.6869 (m110) REVERT: G 142 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: G 217 ASN cc_start: 0.7448 (m-40) cc_final: 0.6917 (m110) REVERT: H 217 ASN cc_start: 0.7373 (m-40) cc_final: 0.6759 (m110) REVERT: I 217 ASN cc_start: 0.7394 (m-40) cc_final: 0.6876 (m110) REVERT: K 217 ASN cc_start: 0.7446 (m-40) cc_final: 0.6868 (m110) REVERT: L 217 ASN cc_start: 0.7462 (m-40) cc_final: 0.6874 (m110) REVERT: L 283 MET cc_start: 0.6009 (tpt) cc_final: 0.5713 (tpt) outliers start: 71 outliers final: 13 residues processed: 273 average time/residue: 1.4657 time to fit residues: 551.7191 Evaluate side-chains 213 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 6.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain L residue 305 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 841 optimal weight: 3.9990 chunk 640 optimal weight: 7.9990 chunk 441 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 406 optimal weight: 7.9990 chunk 571 optimal weight: 10.0000 chunk 854 optimal weight: 3.9990 chunk 904 optimal weight: 0.9980 chunk 446 optimal weight: 0.9980 chunk 809 optimal weight: 7.9990 chunk 243 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN B 45 GLN E 45 GLN F 45 GLN G 45 GLN H 45 GLN L 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 77916 Z= 0.282 Angle : 0.524 10.274 106440 Z= 0.267 Chirality : 0.044 0.152 11364 Planarity : 0.004 0.042 13944 Dihedral : 7.953 76.098 10839 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.13 % Allowed : 6.83 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.09), residues: 9468 helix: 1.37 (0.08), residues: 4232 sheet: 0.07 (0.15), residues: 1144 loop : -0.28 (0.10), residues: 4092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 476 HIS 0.004 0.001 HIS J 699 PHE 0.012 0.001 PHE J 69 TYR 0.015 0.001 TYR J 723 ARG 0.007 0.000 ARG C 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 184 time to evaluate : 6.440 Fit side-chains revert: symmetry clash REVERT: A 217 ASN cc_start: 0.7523 (m-40) cc_final: 0.6955 (m110) REVERT: B 217 ASN cc_start: 0.7520 (m-40) cc_final: 0.6858 (m110) REVERT: B 274 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7297 (mtt180) REVERT: C 217 ASN cc_start: 0.7511 (m-40) cc_final: 0.6963 (m110) REVERT: C 711 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6996 (mtp180) REVERT: D 122 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8405 (tt) REVERT: D 217 ASN cc_start: 0.7441 (m-40) cc_final: 0.6801 (m110) REVERT: D 274 ARG cc_start: 0.7131 (mtt90) cc_final: 0.6871 (mmt90) REVERT: E 217 ASN cc_start: 0.7520 (m-40) cc_final: 0.6901 (m110) REVERT: F 217 ASN cc_start: 0.7517 (m-40) cc_final: 0.6888 (m110) REVERT: G 217 ASN cc_start: 0.7527 (m-40) cc_final: 0.6957 (m110) REVERT: H 217 ASN cc_start: 0.7493 (m-40) cc_final: 0.6822 (m110) REVERT: I 217 ASN cc_start: 0.7468 (m-40) cc_final: 0.6914 (m110) REVERT: J 274 ARG cc_start: 0.7109 (mtt90) cc_final: 0.6832 (mmt90) REVERT: J 465 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7895 (mtm) REVERT: K 217 ASN cc_start: 0.7523 (m-40) cc_final: 0.6907 (m110) REVERT: L 217 ASN cc_start: 0.7523 (m-40) cc_final: 0.6909 (m110) outliers start: 78 outliers final: 25 residues processed: 233 average time/residue: 1.4997 time to fit residues: 484.5349 Evaluate side-chains 202 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 6.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 666 LEU Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 465 MET Chi-restraints excluded: chain J residue 663 VAL Chi-restraints excluded: chain J residue 711 ARG Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 305 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 753 optimal weight: 0.7980 chunk 513 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 673 optimal weight: 0.9990 chunk 373 optimal weight: 2.9990 chunk 772 optimal weight: 8.9990 chunk 625 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 461 optimal weight: 8.9990 chunk 812 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 77916 Z= 0.167 Angle : 0.476 9.763 106440 Z= 0.242 Chirality : 0.042 0.148 11364 Planarity : 0.004 0.044 13944 Dihedral : 7.567 79.291 10839 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.04 % Allowed : 6.93 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.09), residues: 9468 helix: 1.57 (0.08), residues: 4196 sheet: 0.09 (0.15), residues: 1144 loop : -0.18 (0.10), residues: 4128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 476 HIS 0.003 0.001 HIS D 706 PHE 0.012 0.001 PHE B 69 TYR 0.010 0.001 TYR G 585 ARG 0.005 0.000 ARG G 758 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 208 time to evaluate : 6.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: A 217 ASN cc_start: 0.7505 (m-40) cc_final: 0.6931 (m110) REVERT: B 217 ASN cc_start: 0.7399 (m-40) cc_final: 0.6772 (m110) REVERT: B 274 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7332 (mtt180) REVERT: C 217 ASN cc_start: 0.7473 (m-40) cc_final: 0.6916 (m110) REVERT: C 283 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.6437 (tpt) REVERT: D 217 ASN cc_start: 0.7372 (m-40) cc_final: 0.6720 (m110) REVERT: D 283 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6230 (tpt) REVERT: E 217 ASN cc_start: 0.7511 (m-40) cc_final: 0.6875 (m110) REVERT: F 142 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: F 217 ASN cc_start: 0.7482 (m-40) cc_final: 0.6877 (m110) REVERT: G 217 ASN cc_start: 0.7472 (m-40) cc_final: 0.6915 (m110) REVERT: H 217 ASN cc_start: 0.7389 (m-40) cc_final: 0.6744 (m110) REVERT: I 217 ASN cc_start: 0.7464 (m-40) cc_final: 0.6893 (m110) REVERT: J 283 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.6221 (tpt) REVERT: J 711 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6882 (mtp180) REVERT: K 217 ASN cc_start: 0.7516 (m-40) cc_final: 0.6897 (m110) REVERT: L 142 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: L 217 ASN cc_start: 0.7486 (m-40) cc_final: 0.6877 (m110) REVERT: L 283 MET cc_start: 0.5934 (OUTLIER) cc_final: 0.5720 (tpt) outliers start: 72 outliers final: 25 residues processed: 247 average time/residue: 1.3456 time to fit residues: 472.5501 Evaluate side-chains 230 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 6.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 613 ILE Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 502 MET Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 283 MET Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 502 MET Chi-restraints excluded: chain J residue 711 ARG Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 283 MET Chi-restraints excluded: chain L residue 305 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 304 optimal weight: 9.9990 chunk 814 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 531 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 905 optimal weight: 9.9990 chunk 751 optimal weight: 9.9990 chunk 419 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 299 optimal weight: 6.9990 chunk 475 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 77916 Z= 0.378 Angle : 0.559 10.351 106440 Z= 0.286 Chirality : 0.046 0.153 11364 Planarity : 0.005 0.040 13944 Dihedral : 7.903 84.220 10839 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.17 % Allowed : 7.02 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.09), residues: 9468 helix: 1.32 (0.08), residues: 4196 sheet: 0.04 (0.15), residues: 1144 loop : -0.25 (0.10), residues: 4128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 519 HIS 0.005 0.001 HIS K 699 PHE 0.016 0.002 PHE C 233 TYR 0.014 0.001 TYR J 723 ARG 0.007 0.000 ARG J 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 184 time to evaluate : 6.538 Fit side-chains revert: symmetry clash REVERT: A 217 ASN cc_start: 0.7565 (m-40) cc_final: 0.6999 (m110) REVERT: B 274 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7343 (mtt180) REVERT: C 217 ASN cc_start: 0.7523 (m-40) cc_final: 0.6921 (m110) REVERT: C 711 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7114 (mtp180) REVERT: D 217 ASN cc_start: 0.7548 (m-40) cc_final: 0.6879 (m110) REVERT: E 217 ASN cc_start: 0.7545 (m-40) cc_final: 0.6831 (m110) REVERT: F 217 ASN cc_start: 0.7595 (m-40) cc_final: 0.6975 (m110) REVERT: G 217 ASN cc_start: 0.7580 (m-40) cc_final: 0.7010 (m110) REVERT: H 217 ASN cc_start: 0.7503 (m-40) cc_final: 0.6818 (m110) REVERT: I 217 ASN cc_start: 0.7550 (m-40) cc_final: 0.6936 (m110) REVERT: J 217 ASN cc_start: 0.7562 (m-40) cc_final: 0.6883 (m110) REVERT: J 283 MET cc_start: 0.6580 (OUTLIER) cc_final: 0.6373 (tpt) REVERT: J 711 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.7046 (mtp180) REVERT: K 217 ASN cc_start: 0.7555 (m-40) cc_final: 0.6850 (m110) REVERT: L 217 ASN cc_start: 0.7596 (m-40) cc_final: 0.6974 (m110) outliers start: 82 outliers final: 35 residues processed: 233 average time/residue: 1.2522 time to fit residues: 422.8382 Evaluate side-chains 217 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 178 time to evaluate : 6.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 465 MET Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 502 MET Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 283 MET Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 663 VAL Chi-restraints excluded: chain J residue 711 ARG Chi-restraints excluded: chain K residue 255 MET Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 465 MET Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 663 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 873 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 515 optimal weight: 3.9990 chunk 661 optimal weight: 1.9990 chunk 512 optimal weight: 7.9990 chunk 762 optimal weight: 2.9990 chunk 505 optimal weight: 0.8980 chunk 902 optimal weight: 0.4980 chunk 564 optimal weight: 0.7980 chunk 550 optimal weight: 0.9980 chunk 416 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 77916 Z= 0.147 Angle : 0.471 9.859 106440 Z= 0.240 Chirality : 0.042 0.148 11364 Planarity : 0.004 0.044 13944 Dihedral : 7.496 86.566 10839 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.98 % Allowed : 7.42 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.09), residues: 9468 helix: 1.57 (0.08), residues: 4196 sheet: 0.05 (0.15), residues: 1144 loop : -0.22 (0.10), residues: 4128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 476 HIS 0.004 0.001 HIS D 706 PHE 0.013 0.001 PHE E 69 TYR 0.010 0.001 TYR A 585 ARG 0.005 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 222 time to evaluate : 6.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ASN cc_start: 0.7483 (m-40) cc_final: 0.6917 (m110) REVERT: B 217 ASN cc_start: 0.7383 (m-40) cc_final: 0.6726 (m110) REVERT: B 274 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7345 (mtt180) REVERT: C 217 ASN cc_start: 0.7454 (m-40) cc_final: 0.6855 (m110) REVERT: E 217 ASN cc_start: 0.7418 (m-40) cc_final: 0.6772 (m110) REVERT: F 217 ASN cc_start: 0.7495 (m-40) cc_final: 0.6884 (m110) REVERT: G 217 ASN cc_start: 0.7468 (m-40) cc_final: 0.6898 (m110) REVERT: H 217 ASN cc_start: 0.7369 (m-40) cc_final: 0.6705 (m110) REVERT: I 217 ASN cc_start: 0.7412 (m-40) cc_final: 0.6805 (m110) REVERT: I 283 MET cc_start: 0.5968 (tpt) cc_final: 0.5568 (tpt) REVERT: J 711 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6976 (mtp180) REVERT: K 217 ASN cc_start: 0.7474 (m-40) cc_final: 0.6836 (m110) REVERT: L 217 ASN cc_start: 0.7515 (m-40) cc_final: 0.6885 (m110) outliers start: 68 outliers final: 38 residues processed: 259 average time/residue: 1.1960 time to fit residues: 457.1267 Evaluate side-chains 241 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 6.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain H residue 502 MET Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 502 MET Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 502 MET Chi-restraints excluded: chain J residue 663 VAL Chi-restraints excluded: chain J residue 711 ARG Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 663 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 558 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 538 optimal weight: 0.9990 chunk 271 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 573 optimal weight: 2.9990 chunk 614 optimal weight: 0.4980 chunk 446 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 709 optimal weight: 2.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 555 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 77916 Z= 0.165 Angle : 0.470 9.894 106440 Z= 0.238 Chirality : 0.042 0.144 11364 Planarity : 0.004 0.043 13944 Dihedral : 7.466 88.323 10839 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.99 % Allowed : 7.45 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.09), residues: 9468 helix: 1.61 (0.08), residues: 4206 sheet: 0.30 (0.16), residues: 1104 loop : -0.21 (0.10), residues: 4158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 476 HIS 0.003 0.001 HIS I 699 PHE 0.014 0.001 PHE K 69 TYR 0.014 0.001 TYR I 723 ARG 0.009 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 215 time to evaluate : 6.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ASN cc_start: 0.7486 (m-40) cc_final: 0.6894 (m110) REVERT: A 665 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7751 (t0) REVERT: B 217 ASN cc_start: 0.7367 (m-40) cc_final: 0.6699 (m110) REVERT: B 274 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7380 (mtt180) REVERT: C 217 ASN cc_start: 0.7416 (m-40) cc_final: 0.6801 (m110) REVERT: C 465 MET cc_start: 0.7774 (mpt) cc_final: 0.6503 (mpt) REVERT: C 711 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6983 (mtp180) REVERT: E 217 ASN cc_start: 0.7369 (m-40) cc_final: 0.6736 (m110) REVERT: F 217 ASN cc_start: 0.7443 (m-40) cc_final: 0.6816 (m110) REVERT: G 217 ASN cc_start: 0.7480 (m-40) cc_final: 0.6935 (m110) REVERT: H 217 ASN cc_start: 0.7309 (m-40) cc_final: 0.6647 (m110) REVERT: I 217 ASN cc_start: 0.7411 (m-40) cc_final: 0.6790 (m110) REVERT: I 283 MET cc_start: 0.5983 (tpt) cc_final: 0.5781 (tpt) REVERT: J 283 MET cc_start: 0.6085 (tpt) cc_final: 0.5746 (tpt) REVERT: J 465 MET cc_start: 0.7310 (mtt) cc_final: 0.7002 (mpt) REVERT: J 711 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6948 (mtp180) REVERT: K 217 ASN cc_start: 0.7370 (m-40) cc_final: 0.6781 (m110) REVERT: L 217 ASN cc_start: 0.7443 (m-40) cc_final: 0.6813 (m110) outliers start: 69 outliers final: 41 residues processed: 257 average time/residue: 1.1938 time to fit residues: 450.9556 Evaluate side-chains 247 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 202 time to evaluate : 6.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 502 MET Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 502 MET Chi-restraints excluded: chain J residue 663 VAL Chi-restraints excluded: chain J residue 711 ARG Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 663 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 820 optimal weight: 7.9990 chunk 864 optimal weight: 10.0000 chunk 788 optimal weight: 10.0000 chunk 840 optimal weight: 7.9990 chunk 506 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 660 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 759 optimal weight: 2.9990 chunk 795 optimal weight: 5.9990 chunk 837 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 555 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 77916 Z= 0.409 Angle : 0.579 10.317 106440 Z= 0.297 Chirality : 0.047 0.155 11364 Planarity : 0.005 0.041 13944 Dihedral : 7.949 85.590 10839 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.03 % Allowed : 7.53 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.09), residues: 9468 helix: 1.27 (0.08), residues: 4196 sheet: 0.04 (0.16), residues: 1144 loop : -0.28 (0.10), residues: 4128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 519 HIS 0.007 0.001 HIS E 699 PHE 0.019 0.002 PHE B 233 TYR 0.010 0.002 TYR F 480 ARG 0.008 0.001 ARG I 421 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 185 time to evaluate : 6.570 Fit side-chains revert: symmetry clash REVERT: A 217 ASN cc_start: 0.7624 (m-40) cc_final: 0.7020 (m110) REVERT: A 551 ASP cc_start: 0.7461 (m-30) cc_final: 0.7187 (m-30) REVERT: B 217 ASN cc_start: 0.7483 (m-40) cc_final: 0.6716 (m110) REVERT: B 274 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7395 (mtt180) REVERT: C 217 ASN cc_start: 0.7601 (m-40) cc_final: 0.6971 (m110) REVERT: C 465 MET cc_start: 0.7827 (mpt) cc_final: 0.6591 (mpt) REVERT: D 217 ASN cc_start: 0.7630 (m-40) cc_final: 0.6909 (m110) REVERT: E 217 ASN cc_start: 0.7575 (m-40) cc_final: 0.6849 (m110) REVERT: F 217 ASN cc_start: 0.7681 (m-40) cc_final: 0.7052 (m110) REVERT: G 217 ASN cc_start: 0.7645 (m-40) cc_final: 0.7064 (m110) REVERT: H 142 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: H 217 ASN cc_start: 0.7497 (m-40) cc_final: 0.6736 (m110) REVERT: H 551 ASP cc_start: 0.7383 (m-30) cc_final: 0.7076 (m-30) REVERT: I 217 ASN cc_start: 0.7638 (m-40) cc_final: 0.6982 (m110) REVERT: I 465 MET cc_start: 0.7824 (mpt) cc_final: 0.6713 (mpt) REVERT: J 711 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7097 (mtp180) REVERT: K 217 ASN cc_start: 0.7567 (m-40) cc_final: 0.6842 (m110) REVERT: L 217 ASN cc_start: 0.7683 (m-40) cc_final: 0.7054 (m110) outliers start: 73 outliers final: 39 residues processed: 234 average time/residue: 1.2610 time to fit residues: 431.7670 Evaluate side-chains 208 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 6.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 663 VAL Chi-restraints excluded: chain J residue 711 ARG Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 663 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 552 optimal weight: 5.9990 chunk 888 optimal weight: 7.9990 chunk 542 optimal weight: 0.0670 chunk 421 optimal weight: 5.9990 chunk 617 optimal weight: 6.9990 chunk 932 optimal weight: 1.9990 chunk 858 optimal weight: 30.0000 chunk 742 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 573 optimal weight: 0.0370 chunk 455 optimal weight: 0.9980 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 719 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 77916 Z= 0.157 Angle : 0.479 9.729 106440 Z= 0.244 Chirality : 0.042 0.149 11364 Planarity : 0.004 0.043 13944 Dihedral : 7.555 84.982 10839 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.68 % Allowed : 7.92 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.09), residues: 9468 helix: 1.50 (0.08), residues: 4196 sheet: 0.03 (0.15), residues: 1144 loop : -0.24 (0.10), residues: 4128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 476 HIS 0.005 0.001 HIS D 706 PHE 0.012 0.001 PHE E 69 TYR 0.011 0.001 TYR A 585 ARG 0.004 0.000 ARG B 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 206 time to evaluate : 6.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 ASN cc_start: 0.7509 (m-40) cc_final: 0.6923 (m110) REVERT: A 551 ASP cc_start: 0.7271 (m-30) cc_final: 0.7029 (m-30) REVERT: B 217 ASN cc_start: 0.7425 (m-40) cc_final: 0.6721 (m110) REVERT: B 274 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7377 (mtt180) REVERT: C 217 ASN cc_start: 0.7457 (m-40) cc_final: 0.6845 (m110) REVERT: C 465 MET cc_start: 0.7809 (mpt) cc_final: 0.6617 (mpt) REVERT: D 516 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7977 (mm-30) REVERT: E 217 ASN cc_start: 0.7397 (m-40) cc_final: 0.6749 (m110) REVERT: F 217 ASN cc_start: 0.7485 (m-40) cc_final: 0.6859 (m110) REVERT: G 217 ASN cc_start: 0.7516 (m-40) cc_final: 0.6948 (m110) REVERT: H 217 ASN cc_start: 0.7432 (m-40) cc_final: 0.6734 (m110) REVERT: H 551 ASP cc_start: 0.7155 (m-30) cc_final: 0.6852 (m-30) REVERT: I 217 ASN cc_start: 0.7447 (m-40) cc_final: 0.6821 (m110) REVERT: I 465 MET cc_start: 0.7748 (mpt) cc_final: 0.6694 (mpt) REVERT: J 516 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8002 (mm-30) REVERT: J 711 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6970 (mtp180) REVERT: K 217 ASN cc_start: 0.7442 (m-40) cc_final: 0.6800 (m110) REVERT: L 217 ASN cc_start: 0.7488 (m-40) cc_final: 0.6862 (m110) outliers start: 45 outliers final: 36 residues processed: 241 average time/residue: 1.1949 time to fit residues: 425.7400 Evaluate side-chains 240 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 202 time to evaluate : 6.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 663 VAL Chi-restraints excluded: chain J residue 711 ARG Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 663 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 589 optimal weight: 8.9990 chunk 790 optimal weight: 0.6980 chunk 227 optimal weight: 8.9990 chunk 684 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 206 optimal weight: 9.9990 chunk 743 optimal weight: 0.2980 chunk 311 optimal weight: 0.9980 chunk 763 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.111464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.087634 restraints weight = 389655.626| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 4.31 r_work: 0.3391 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 77916 Z= 0.134 Angle : 0.463 9.955 106440 Z= 0.234 Chirality : 0.042 0.199 11364 Planarity : 0.004 0.044 13944 Dihedral : 7.358 82.355 10839 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.72 % Allowed : 7.92 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.09), residues: 9468 helix: 1.66 (0.08), residues: 4206 sheet: 0.32 (0.16), residues: 1070 loop : -0.19 (0.10), residues: 4192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 476 HIS 0.003 0.001 HIS D 706 PHE 0.014 0.001 PHE E 69 TYR 0.017 0.001 TYR I 723 ARG 0.012 0.000 ARG J 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14472.47 seconds wall clock time: 253 minutes 44.59 seconds (15224.59 seconds total)