Starting phenix.real_space_refine on Thu Dec 7 16:16:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5u_17453/12_2023/8p5u_17453_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5u_17453/12_2023/8p5u_17453.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5u_17453/12_2023/8p5u_17453_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5u_17453/12_2023/8p5u_17453_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5u_17453/12_2023/8p5u_17453_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5u_17453/12_2023/8p5u_17453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5u_17453/12_2023/8p5u_17453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5u_17453/12_2023/8p5u_17453_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5u_17453/12_2023/8p5u_17453_updated.pdb" } resolution = 2.17 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= 0.018 sd= 1.215 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 48 5.49 5 Mg 6 5.21 5 S 234 5.16 5 C 33120 2.51 5 N 9270 2.21 5 O 10200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 781": "NH1" <-> "NH2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A GLU 901": "OE1" <-> "OE2" Residue "A GLU 923": "OE1" <-> "OE2" Residue "A GLU 956": "OE1" <-> "OE2" Residue "A GLU 971": "OE1" <-> "OE2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1084": "OE1" <-> "OE2" Residue "A PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A GLU 1164": "OE1" <-> "OE2" Residue "A GLU 1176": "OE1" <-> "OE2" Residue "A ARG 1190": "NH1" <-> "NH2" Residue "A GLU 1220": "OE1" <-> "OE2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B GLU 587": "OE1" <-> "OE2" Residue "B GLU 611": "OE1" <-> "OE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B ARG 781": "NH1" <-> "NH2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B GLU 901": "OE1" <-> "OE2" Residue "B GLU 923": "OE1" <-> "OE2" Residue "B GLU 956": "OE1" <-> "OE2" Residue "B GLU 971": "OE1" <-> "OE2" Residue "B GLU 1023": "OE1" <-> "OE2" Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1084": "OE1" <-> "OE2" Residue "B PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1156": "OE1" <-> "OE2" Residue "B GLU 1164": "OE1" <-> "OE2" Residue "B GLU 1176": "OE1" <-> "OE2" Residue "B ARG 1190": "NH1" <-> "NH2" Residue "B GLU 1220": "OE1" <-> "OE2" Residue "C TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C GLU 454": "OE1" <-> "OE2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C GLU 587": "OE1" <-> "OE2" Residue "C GLU 611": "OE1" <-> "OE2" Residue "C GLU 618": "OE1" <-> "OE2" Residue "C ARG 767": "NH1" <-> "NH2" Residue "C ARG 781": "NH1" <-> "NH2" Residue "C GLU 816": "OE1" <-> "OE2" Residue "C GLU 901": "OE1" <-> "OE2" Residue "C GLU 923": "OE1" <-> "OE2" Residue "C GLU 956": "OE1" <-> "OE2" Residue "C GLU 971": "OE1" <-> "OE2" Residue "C GLU 1023": "OE1" <-> "OE2" Residue "C PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1084": "OE1" <-> "OE2" Residue "C PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1156": "OE1" <-> "OE2" Residue "C GLU 1164": "OE1" <-> "OE2" Residue "C GLU 1176": "OE1" <-> "OE2" Residue "C ARG 1190": "NH1" <-> "NH2" Residue "C GLU 1220": "OE1" <-> "OE2" Residue "D TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 410": "OE1" <-> "OE2" Residue "D ARG 442": "NH1" <-> "NH2" Residue "D GLU 454": "OE1" <-> "OE2" Residue "D GLU 482": "OE1" <-> "OE2" Residue "D GLU 513": "OE1" <-> "OE2" Residue "D GLU 536": "OE1" <-> "OE2" Residue "D GLU 587": "OE1" <-> "OE2" Residue "D GLU 611": "OE1" <-> "OE2" Residue "D GLU 618": "OE1" <-> "OE2" Residue "D ARG 767": "NH1" <-> "NH2" Residue "D ARG 781": "NH1" <-> "NH2" Residue "D GLU 816": "OE1" <-> "OE2" Residue "D GLU 901": "OE1" <-> "OE2" Residue "D GLU 923": "OE1" <-> "OE2" Residue "D GLU 956": "OE1" <-> "OE2" Residue "D GLU 971": "OE1" <-> "OE2" Residue "D GLU 1023": "OE1" <-> "OE2" Residue "D PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1084": "OE1" <-> "OE2" Residue "D PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1156": "OE1" <-> "OE2" Residue "D GLU 1164": "OE1" <-> "OE2" Residue "D GLU 1176": "OE1" <-> "OE2" Residue "D ARG 1190": "NH1" <-> "NH2" Residue "D GLU 1220": "OE1" <-> "OE2" Residue "E TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "E ARG 442": "NH1" <-> "NH2" Residue "E GLU 454": "OE1" <-> "OE2" Residue "E GLU 482": "OE1" <-> "OE2" Residue "E GLU 513": "OE1" <-> "OE2" Residue "E GLU 536": "OE1" <-> "OE2" Residue "E GLU 587": "OE1" <-> "OE2" Residue "E GLU 611": "OE1" <-> "OE2" Residue "E GLU 618": "OE1" <-> "OE2" Residue "E ARG 767": "NH1" <-> "NH2" Residue "E ARG 781": "NH1" <-> "NH2" Residue "E GLU 816": "OE1" <-> "OE2" Residue "E GLU 901": "OE1" <-> "OE2" Residue "E GLU 923": "OE1" <-> "OE2" Residue "E GLU 956": "OE1" <-> "OE2" Residue "E GLU 971": "OE1" <-> "OE2" Residue "E GLU 1023": "OE1" <-> "OE2" Residue "E PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1084": "OE1" <-> "OE2" Residue "E PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1156": "OE1" <-> "OE2" Residue "E GLU 1164": "OE1" <-> "OE2" Residue "E GLU 1176": "OE1" <-> "OE2" Residue "E ARG 1190": "NH1" <-> "NH2" Residue "E GLU 1220": "OE1" <-> "OE2" Residue "F TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 410": "OE1" <-> "OE2" Residue "F ARG 442": "NH1" <-> "NH2" Residue "F GLU 454": "OE1" <-> "OE2" Residue "F GLU 482": "OE1" <-> "OE2" Residue "F GLU 513": "OE1" <-> "OE2" Residue "F GLU 536": "OE1" <-> "OE2" Residue "F GLU 587": "OE1" <-> "OE2" Residue "F GLU 611": "OE1" <-> "OE2" Residue "F GLU 618": "OE1" <-> "OE2" Residue "F ARG 767": "NH1" <-> "NH2" Residue "F ARG 781": "NH1" <-> "NH2" Residue "F GLU 816": "OE1" <-> "OE2" Residue "F GLU 901": "OE1" <-> "OE2" Residue "F GLU 923": "OE1" <-> "OE2" Residue "F GLU 956": "OE1" <-> "OE2" Residue "F GLU 971": "OE1" <-> "OE2" Residue "F GLU 1023": "OE1" <-> "OE2" Residue "F PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1084": "OE1" <-> "OE2" Residue "F PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1156": "OE1" <-> "OE2" Residue "F GLU 1164": "OE1" <-> "OE2" Residue "F GLU 1176": "OE1" <-> "OE2" Residue "F ARG 1190": "NH1" <-> "NH2" Residue "F GLU 1220": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 52878 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {' MG': 1, 'ACO': 1, 'COA': 1, 'TPP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {' MG': 1, 'ACO': 1, 'COA': 1, 'TPP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {' MG': 1, 'ACO': 1, 'COA': 1, 'TPP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {' MG': 1, 'ACO': 1, 'COA': 1, 'TPP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {' MG': 1, 'ACO': 1, 'COA': 1, 'TPP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {' MG': 1, 'ACO': 1, 'COA': 1, 'TPP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 21.00, per 1000 atoms: 0.40 Number of scatterers: 52878 At special positions: 0 Unit cell: (227.9, 209.84, 171.14, 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 234 16.00 P 48 15.00 Mg 6 11.99 O 10200 8.00 N 9270 7.00 C 33120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.68 Conformation dependent library (CDL) restraints added in 7.0 seconds 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 288 helices and 36 sheets defined 42.9% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.86 Creating SS restraints... Processing helix chain 'A' and resid 110 through 123 removed outlier: 3.820A pdb=" N LEU A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.517A pdb=" N GLN A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 173 Processing helix chain 'A' and resid 175 through 178 Processing helix chain 'A' and resid 226 through 242 Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 321 through 336 removed outlier: 3.956A pdb=" N THR A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.528A pdb=" N GLU A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 386 removed outlier: 6.636A pdb=" N HIS A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'A' and resid 480 through 503 Processing helix chain 'A' and resid 516 through 532 Proline residue: A 520 - end of helix removed outlier: 3.643A pdb=" N ASP A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 526 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 558 through 566 Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 614 through 628 Processing helix chain 'A' and resid 645 through 650 Processing helix chain 'A' and resid 653 through 660 removed outlier: 4.199A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 714 through 731 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 760 through 764 removed outlier: 3.526A pdb=" N ILE A 764 " --> pdb=" O MET A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 760 through 764' Processing helix chain 'A' and resid 770 through 781 Processing helix chain 'A' and resid 786 through 809 removed outlier: 3.979A pdb=" N VAL A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 4.533A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 873 removed outlier: 4.106A pdb=" N VAL A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR A 872 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 892 Processing helix chain 'A' and resid 926 through 933 Processing helix chain 'A' and resid 950 through 962 Processing helix chain 'A' and resid 975 through 987 removed outlier: 3.691A pdb=" N ALA A 978 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN A 979 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A 982 " --> pdb=" O ASN A 979 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N THR A 983 " --> pdb=" O GLY A 980 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 987 " --> pdb=" O ILE A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 996 Processing helix chain 'A' and resid 1022 through 1028 Processing helix chain 'A' and resid 1042 through 1054 Processing helix chain 'A' and resid 1069 through 1071 No H-bonds generated for 'chain 'A' and resid 1069 through 1071' Processing helix chain 'A' and resid 1079 through 1083 Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1112 through 1124 removed outlier: 4.147A pdb=" N ALA A1118 " --> pdb=" O TYR A1115 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A1124 " --> pdb=" O LYS A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1151 Processing helix chain 'A' and resid 1171 through 1181 removed outlier: 3.701A pdb=" N GLU A1176 " --> pdb=" O PRO A1172 " (cutoff:3.500A) Proline residue: A1179 - end of helix Processing helix chain 'A' and resid 1204 through 1218 Processing helix chain 'B' and resid 110 through 123 removed outlier: 3.826A pdb=" N LEU B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLU B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 removed outlier: 3.519A pdb=" N GLN B 148 " --> pdb=" O MET B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 173 Processing helix chain 'B' and resid 175 through 178 Processing helix chain 'B' and resid 226 through 242 Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 321 through 336 removed outlier: 3.955A pdb=" N THR B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.528A pdb=" N GLU B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 386 removed outlier: 6.637A pdb=" N HIS B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 436 through 447 Processing helix chain 'B' and resid 461 through 473 Processing helix chain 'B' and resid 480 through 503 Processing helix chain 'B' and resid 516 through 532 Proline residue: B 520 - end of helix removed outlier: 3.644A pdb=" N ASP B 523 " --> pdb=" O PRO B 520 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 526 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 552 Processing helix chain 'B' and resid 558 through 566 Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 614 through 628 Processing helix chain 'B' and resid 645 through 650 Processing helix chain 'B' and resid 653 through 660 removed outlier: 4.200A pdb=" N LEU B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'B' and resid 714 through 731 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 760 through 764 removed outlier: 3.527A pdb=" N ILE B 764 " --> pdb=" O MET B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 760 through 764' Processing helix chain 'B' and resid 770 through 781 Processing helix chain 'B' and resid 786 through 809 removed outlier: 3.980A pdb=" N VAL B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 847 removed outlier: 4.533A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 873 removed outlier: 4.106A pdb=" N VAL B 871 " --> pdb=" O ARG B 867 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR B 872 " --> pdb=" O VAL B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 892 Processing helix chain 'B' and resid 926 through 933 Processing helix chain 'B' and resid 950 through 962 Processing helix chain 'B' and resid 975 through 987 removed outlier: 3.689A pdb=" N ALA B 978 " --> pdb=" O GLY B 975 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN B 979 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 982 " --> pdb=" O ASN B 979 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N THR B 983 " --> pdb=" O GLY B 980 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 987 " --> pdb=" O ILE B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 996 Processing helix chain 'B' and resid 1022 through 1028 Processing helix chain 'B' and resid 1042 through 1054 Processing helix chain 'B' and resid 1069 through 1071 No H-bonds generated for 'chain 'B' and resid 1069 through 1071' Processing helix chain 'B' and resid 1079 through 1083 Processing helix chain 'B' and resid 1100 through 1102 No H-bonds generated for 'chain 'B' and resid 1100 through 1102' Processing helix chain 'B' and resid 1112 through 1124 removed outlier: 4.147A pdb=" N ALA B1118 " --> pdb=" O TYR B1115 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP B1124 " --> pdb=" O LYS B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1151 Processing helix chain 'B' and resid 1171 through 1181 removed outlier: 3.701A pdb=" N GLU B1176 " --> pdb=" O PRO B1172 " (cutoff:3.500A) Proline residue: B1179 - end of helix Processing helix chain 'B' and resid 1204 through 1218 Processing helix chain 'C' and resid 110 through 123 removed outlier: 3.822A pdb=" N LEU C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.518A pdb=" N GLN C 148 " --> pdb=" O MET C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 173 Processing helix chain 'C' and resid 175 through 178 Processing helix chain 'C' and resid 226 through 242 Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 321 through 336 removed outlier: 3.953A pdb=" N THR C 336 " --> pdb=" O SER C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.530A pdb=" N GLU C 343 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 386 removed outlier: 6.639A pdb=" N HIS C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing helix chain 'C' and resid 436 through 447 Processing helix chain 'C' and resid 461 through 473 Processing helix chain 'C' and resid 480 through 503 Processing helix chain 'C' and resid 516 through 532 Proline residue: C 520 - end of helix removed outlier: 3.643A pdb=" N ASP C 523 " --> pdb=" O PRO C 520 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 526 " --> pdb=" O ASP C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 552 Processing helix chain 'C' and resid 558 through 566 Processing helix chain 'C' and resid 581 through 583 No H-bonds generated for 'chain 'C' and resid 581 through 583' Processing helix chain 'C' and resid 614 through 628 Processing helix chain 'C' and resid 645 through 650 Processing helix chain 'C' and resid 653 through 660 removed outlier: 4.199A pdb=" N LEU C 660 " --> pdb=" O GLU C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 688 No H-bonds generated for 'chain 'C' and resid 686 through 688' Processing helix chain 'C' and resid 697 through 702 Processing helix chain 'C' and resid 714 through 731 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 760 through 764 removed outlier: 3.526A pdb=" N ILE C 764 " --> pdb=" O MET C 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 760 through 764' Processing helix chain 'C' and resid 770 through 781 Processing helix chain 'C' and resid 786 through 809 removed outlier: 3.980A pdb=" N VAL C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 847 removed outlier: 4.533A pdb=" N PHE C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 873 removed outlier: 4.105A pdb=" N VAL C 871 " --> pdb=" O ARG C 867 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR C 872 " --> pdb=" O VAL C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 892 Processing helix chain 'C' and resid 926 through 933 Processing helix chain 'C' and resid 950 through 962 Processing helix chain 'C' and resid 975 through 987 removed outlier: 3.692A pdb=" N ALA C 978 " --> pdb=" O GLY C 975 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN C 979 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C 982 " --> pdb=" O ASN C 979 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N THR C 983 " --> pdb=" O GLY C 980 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C 987 " --> pdb=" O ILE C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 996 Processing helix chain 'C' and resid 1022 through 1028 Processing helix chain 'C' and resid 1042 through 1054 Processing helix chain 'C' and resid 1069 through 1071 No H-bonds generated for 'chain 'C' and resid 1069 through 1071' Processing helix chain 'C' and resid 1079 through 1083 Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1112 through 1124 removed outlier: 4.146A pdb=" N ALA C1118 " --> pdb=" O TYR C1115 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C1124 " --> pdb=" O LYS C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1151 Processing helix chain 'C' and resid 1171 through 1181 removed outlier: 3.702A pdb=" N GLU C1176 " --> pdb=" O PRO C1172 " (cutoff:3.500A) Proline residue: C1179 - end of helix Processing helix chain 'C' and resid 1204 through 1218 Processing helix chain 'D' and resid 110 through 123 removed outlier: 3.822A pdb=" N LEU D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLU D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 151 removed outlier: 3.517A pdb=" N GLN D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 173 Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 226 through 242 Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 296 through 302 Processing helix chain 'D' and resid 321 through 336 removed outlier: 3.953A pdb=" N THR D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 removed outlier: 3.529A pdb=" N GLU D 343 " --> pdb=" O SER D 339 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 386 removed outlier: 6.638A pdb=" N HIS D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE D 386 " --> pdb=" O ARG D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 428 through 430 No H-bonds generated for 'chain 'D' and resid 428 through 430' Processing helix chain 'D' and resid 436 through 447 Processing helix chain 'D' and resid 461 through 473 Processing helix chain 'D' and resid 480 through 503 Processing helix chain 'D' and resid 516 through 532 Proline residue: D 520 - end of helix removed outlier: 3.644A pdb=" N ASP D 523 " --> pdb=" O PRO D 520 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 526 " --> pdb=" O ASP D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 552 Processing helix chain 'D' and resid 558 through 566 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 614 through 628 Processing helix chain 'D' and resid 645 through 650 Processing helix chain 'D' and resid 653 through 660 removed outlier: 4.200A pdb=" N LEU D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 688 No H-bonds generated for 'chain 'D' and resid 686 through 688' Processing helix chain 'D' and resid 697 through 702 Processing helix chain 'D' and resid 714 through 731 Processing helix chain 'D' and resid 753 through 755 No H-bonds generated for 'chain 'D' and resid 753 through 755' Processing helix chain 'D' and resid 760 through 764 removed outlier: 3.527A pdb=" N ILE D 764 " --> pdb=" O MET D 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 760 through 764' Processing helix chain 'D' and resid 770 through 781 Processing helix chain 'D' and resid 786 through 809 removed outlier: 3.979A pdb=" N VAL D 793 " --> pdb=" O ALA D 789 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 847 removed outlier: 4.533A pdb=" N PHE D 847 " --> pdb=" O LEU D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 873 removed outlier: 4.106A pdb=" N VAL D 871 " --> pdb=" O ARG D 867 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR D 872 " --> pdb=" O VAL D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 892 Processing helix chain 'D' and resid 926 through 933 Processing helix chain 'D' and resid 950 through 962 Processing helix chain 'D' and resid 975 through 987 removed outlier: 3.689A pdb=" N ALA D 978 " --> pdb=" O GLY D 975 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN D 979 " --> pdb=" O ASP D 976 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D 982 " --> pdb=" O ASN D 979 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N THR D 983 " --> pdb=" O GLY D 980 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D 987 " --> pdb=" O ILE D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 996 Processing helix chain 'D' and resid 1022 through 1028 Processing helix chain 'D' and resid 1042 through 1054 Processing helix chain 'D' and resid 1069 through 1071 No H-bonds generated for 'chain 'D' and resid 1069 through 1071' Processing helix chain 'D' and resid 1079 through 1083 Processing helix chain 'D' and resid 1100 through 1102 No H-bonds generated for 'chain 'D' and resid 1100 through 1102' Processing helix chain 'D' and resid 1112 through 1124 removed outlier: 4.146A pdb=" N ALA D1118 " --> pdb=" O TYR D1115 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D1124 " --> pdb=" O LYS D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1151 Processing helix chain 'D' and resid 1171 through 1181 removed outlier: 3.700A pdb=" N GLU D1176 " --> pdb=" O PRO D1172 " (cutoff:3.500A) Proline residue: D1179 - end of helix Processing helix chain 'D' and resid 1204 through 1218 Processing helix chain 'E' and resid 110 through 123 removed outlier: 3.820A pdb=" N LEU E 122 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 151 removed outlier: 3.517A pdb=" N GLN E 148 " --> pdb=" O MET E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 173 Processing helix chain 'E' and resid 175 through 178 Processing helix chain 'E' and resid 226 through 242 Processing helix chain 'E' and resid 248 through 250 No H-bonds generated for 'chain 'E' and resid 248 through 250' Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 289 through 291 No H-bonds generated for 'chain 'E' and resid 289 through 291' Processing helix chain 'E' and resid 296 through 302 Processing helix chain 'E' and resid 321 through 336 removed outlier: 3.955A pdb=" N THR E 336 " --> pdb=" O SER E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 348 removed outlier: 3.530A pdb=" N GLU E 343 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 344 " --> pdb=" O PHE E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 386 removed outlier: 6.639A pdb=" N HIS E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU E 385 " --> pdb=" O SER E 381 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE E 386 " --> pdb=" O ARG E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 428 through 430 No H-bonds generated for 'chain 'E' and resid 428 through 430' Processing helix chain 'E' and resid 436 through 447 Processing helix chain 'E' and resid 461 through 473 Processing helix chain 'E' and resid 480 through 503 Processing helix chain 'E' and resid 516 through 532 Proline residue: E 520 - end of helix removed outlier: 3.643A pdb=" N ASP E 523 " --> pdb=" O PRO E 520 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 526 " --> pdb=" O ASP E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 552 Processing helix chain 'E' and resid 558 through 566 Processing helix chain 'E' and resid 581 through 583 No H-bonds generated for 'chain 'E' and resid 581 through 583' Processing helix chain 'E' and resid 614 through 628 Processing helix chain 'E' and resid 645 through 650 Processing helix chain 'E' and resid 653 through 660 removed outlier: 4.198A pdb=" N LEU E 660 " --> pdb=" O GLU E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 688 No H-bonds generated for 'chain 'E' and resid 686 through 688' Processing helix chain 'E' and resid 697 through 702 Processing helix chain 'E' and resid 714 through 731 Processing helix chain 'E' and resid 753 through 755 No H-bonds generated for 'chain 'E' and resid 753 through 755' Processing helix chain 'E' and resid 760 through 764 removed outlier: 3.526A pdb=" N ILE E 764 " --> pdb=" O MET E 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 760 through 764' Processing helix chain 'E' and resid 770 through 781 Processing helix chain 'E' and resid 786 through 809 removed outlier: 3.980A pdb=" N VAL E 793 " --> pdb=" O ALA E 789 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE E 796 " --> pdb=" O VAL E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 847 removed outlier: 4.533A pdb=" N PHE E 847 " --> pdb=" O LEU E 843 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 873 removed outlier: 4.105A pdb=" N VAL E 871 " --> pdb=" O ARG E 867 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR E 872 " --> pdb=" O VAL E 868 " (cutoff:3.500A) Processing helix chain 'E' and resid 878 through 892 Processing helix chain 'E' and resid 926 through 933 Processing helix chain 'E' and resid 950 through 962 Processing helix chain 'E' and resid 975 through 987 removed outlier: 3.691A pdb=" N ALA E 978 " --> pdb=" O GLY E 975 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN E 979 " --> pdb=" O ASP E 976 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN E 982 " --> pdb=" O ASN E 979 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N THR E 983 " --> pdb=" O GLY E 980 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU E 987 " --> pdb=" O ILE E 984 " (cutoff:3.500A) Processing helix chain 'E' and resid 992 through 996 Processing helix chain 'E' and resid 1022 through 1028 Processing helix chain 'E' and resid 1042 through 1054 Processing helix chain 'E' and resid 1069 through 1071 No H-bonds generated for 'chain 'E' and resid 1069 through 1071' Processing helix chain 'E' and resid 1079 through 1083 Processing helix chain 'E' and resid 1100 through 1102 No H-bonds generated for 'chain 'E' and resid 1100 through 1102' Processing helix chain 'E' and resid 1112 through 1124 removed outlier: 4.147A pdb=" N ALA E1118 " --> pdb=" O TYR E1115 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP E1124 " --> pdb=" O LYS E1121 " (cutoff:3.500A) Processing helix chain 'E' and resid 1142 through 1151 Processing helix chain 'E' and resid 1171 through 1181 removed outlier: 3.701A pdb=" N GLU E1176 " --> pdb=" O PRO E1172 " (cutoff:3.500A) Proline residue: E1179 - end of helix Processing helix chain 'E' and resid 1204 through 1218 Processing helix chain 'F' and resid 110 through 123 removed outlier: 3.825A pdb=" N LEU F 122 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLU F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 151 removed outlier: 3.519A pdb=" N GLN F 148 " --> pdb=" O MET F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 173 Processing helix chain 'F' and resid 175 through 178 Processing helix chain 'F' and resid 226 through 242 Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 296 through 302 Processing helix chain 'F' and resid 321 through 336 removed outlier: 3.952A pdb=" N THR F 336 " --> pdb=" O SER F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 348 removed outlier: 3.529A pdb=" N GLU F 343 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE F 344 " --> pdb=" O PHE F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 386 removed outlier: 6.638A pdb=" N HIS F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU F 385 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE F 386 " --> pdb=" O ARG F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 407 No H-bonds generated for 'chain 'F' and resid 405 through 407' Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' Processing helix chain 'F' and resid 428 through 430 No H-bonds generated for 'chain 'F' and resid 428 through 430' Processing helix chain 'F' and resid 436 through 447 Processing helix chain 'F' and resid 461 through 473 Processing helix chain 'F' and resid 480 through 503 Processing helix chain 'F' and resid 516 through 532 Proline residue: F 520 - end of helix removed outlier: 3.643A pdb=" N ASP F 523 " --> pdb=" O PRO F 520 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 526 " --> pdb=" O ASP F 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 552 Processing helix chain 'F' and resid 558 through 566 Processing helix chain 'F' and resid 581 through 583 No H-bonds generated for 'chain 'F' and resid 581 through 583' Processing helix chain 'F' and resid 614 through 628 Processing helix chain 'F' and resid 645 through 650 Processing helix chain 'F' and resid 653 through 660 removed outlier: 4.201A pdb=" N LEU F 660 " --> pdb=" O GLU F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 688 No H-bonds generated for 'chain 'F' and resid 686 through 688' Processing helix chain 'F' and resid 697 through 702 Processing helix chain 'F' and resid 714 through 731 Processing helix chain 'F' and resid 753 through 755 No H-bonds generated for 'chain 'F' and resid 753 through 755' Processing helix chain 'F' and resid 760 through 764 removed outlier: 3.526A pdb=" N ILE F 764 " --> pdb=" O MET F 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 760 through 764' Processing helix chain 'F' and resid 770 through 781 Processing helix chain 'F' and resid 786 through 809 removed outlier: 3.979A pdb=" N VAL F 793 " --> pdb=" O ALA F 789 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE F 796 " --> pdb=" O VAL F 792 " (cutoff:3.500A) Processing helix chain 'F' and resid 837 through 847 removed outlier: 4.532A pdb=" N PHE F 847 " --> pdb=" O LEU F 843 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 873 removed outlier: 4.106A pdb=" N VAL F 871 " --> pdb=" O ARG F 867 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR F 872 " --> pdb=" O VAL F 868 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 892 Processing helix chain 'F' and resid 926 through 933 Processing helix chain 'F' and resid 950 through 962 Processing helix chain 'F' and resid 975 through 987 removed outlier: 3.689A pdb=" N ALA F 978 " --> pdb=" O GLY F 975 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN F 979 " --> pdb=" O ASP F 976 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN F 982 " --> pdb=" O ASN F 979 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR F 983 " --> pdb=" O GLY F 980 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU F 987 " --> pdb=" O ILE F 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 992 through 996 Processing helix chain 'F' and resid 1022 through 1028 Processing helix chain 'F' and resid 1042 through 1054 Processing helix chain 'F' and resid 1069 through 1071 No H-bonds generated for 'chain 'F' and resid 1069 through 1071' Processing helix chain 'F' and resid 1079 through 1083 Processing helix chain 'F' and resid 1100 through 1102 No H-bonds generated for 'chain 'F' and resid 1100 through 1102' Processing helix chain 'F' and resid 1112 through 1124 removed outlier: 4.145A pdb=" N ALA F1118 " --> pdb=" O TYR F1115 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP F1124 " --> pdb=" O LYS F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1142 through 1151 Processing helix chain 'F' and resid 1171 through 1181 removed outlier: 3.700A pdb=" N GLU F1176 " --> pdb=" O PRO F1172 " (cutoff:3.500A) Proline residue: F1179 - end of helix Processing helix chain 'F' and resid 1204 through 1218 Processing sheet with id= A, first strand: chain 'A' and resid 126 through 134 removed outlier: 6.591A pdb=" N SER A 256 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N VAL A 282 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR A 258 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 180 through 184 Processing sheet with id= C, first strand: chain 'A' and resid 422 through 424 Processing sheet with id= D, first strand: chain 'A' and resid 451 through 454 removed outlier: 6.825A pdb=" N PHE A 736 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL A 709 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP A 738 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N ILE A 672 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE A 674 " --> pdb=" O PRO A 639 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 641 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL A 676 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N HIS A 643 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU A 536 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU A 640 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A 538 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 642 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY A 540 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N GLY A 644 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VAL A 537 " --> pdb=" O GLU A 598 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A 600 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE A 539 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 602 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 939 through 944 removed outlier: 3.596A pdb=" N GLY A 900 " --> pdb=" O TYR A 943 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 967 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ALA A 899 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA A 969 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A1003 " --> pdb=" O TRP A 970 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA A 972 " --> pdb=" O ILE A1003 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU A1005 " --> pdb=" O ALA A 972 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A1061 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU A1006 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A1063 " --> pdb=" O LEU A1006 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR A1035 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE A1064 " --> pdb=" O THR A1035 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA A1037 " --> pdb=" O PHE A1064 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1129 through 1133 removed outlier: 6.771A pdb=" N LYS A1105 " --> pdb=" O ALA A1130 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A1132 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N MET A1107 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU A1157 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU A1108 " --> pdb=" O GLU A1157 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A1159 " --> pdb=" O LEU A1108 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 126 through 134 removed outlier: 6.591A pdb=" N SER B 256 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL B 282 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR B 258 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 180 through 184 Processing sheet with id= I, first strand: chain 'B' and resid 422 through 424 Processing sheet with id= J, first strand: chain 'B' and resid 451 through 454 removed outlier: 6.829A pdb=" N PHE B 736 " --> pdb=" O PHE B 707 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL B 709 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP B 738 " --> pdb=" O VAL B 709 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N ILE B 672 " --> pdb=" O VAL B 637 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE B 674 " --> pdb=" O PRO B 639 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 641 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL B 676 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N HIS B 643 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU B 536 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 640 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL B 538 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU B 642 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 540 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N GLY B 644 " --> pdb=" O GLY B 540 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N VAL B 537 " --> pdb=" O GLU B 598 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS B 600 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE B 539 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER B 602 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 939 through 944 removed outlier: 3.596A pdb=" N GLY B 900 " --> pdb=" O TYR B 943 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 967 " --> pdb=" O ARG B 897 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA B 899 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 969 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE B1003 " --> pdb=" O TRP B 970 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA B 972 " --> pdb=" O ILE B1003 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU B1005 " --> pdb=" O ALA B 972 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B1061 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU B1006 " --> pdb=" O LEU B1061 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B1063 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR B1035 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE B1064 " --> pdb=" O THR B1035 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA B1037 " --> pdb=" O PHE B1064 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1129 through 1133 removed outlier: 6.775A pdb=" N LYS B1105 " --> pdb=" O ALA B1130 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL B1132 " --> pdb=" O LYS B1105 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N MET B1107 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU B1157 " --> pdb=" O VAL B1106 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU B1108 " --> pdb=" O GLU B1157 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B1159 " --> pdb=" O LEU B1108 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 126 through 134 removed outlier: 6.595A pdb=" N SER C 256 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL C 282 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR C 258 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 180 through 184 Processing sheet with id= O, first strand: chain 'C' and resid 422 through 424 Processing sheet with id= P, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.826A pdb=" N PHE C 736 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL C 709 " --> pdb=" O PHE C 736 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP C 738 " --> pdb=" O VAL C 709 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N ILE C 672 " --> pdb=" O VAL C 637 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE C 674 " --> pdb=" O PRO C 639 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 641 " --> pdb=" O ILE C 674 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL C 676 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N HIS C 643 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU C 536 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU C 640 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 538 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU C 642 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY C 540 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N GLY C 644 " --> pdb=" O GLY C 540 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N VAL C 537 " --> pdb=" O GLU C 598 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS C 600 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE C 539 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER C 602 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 939 through 944 removed outlier: 3.599A pdb=" N GLY C 900 " --> pdb=" O TYR C 943 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 967 " --> pdb=" O ARG C 897 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA C 899 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA C 969 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE C1003 " --> pdb=" O TRP C 970 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA C 972 " --> pdb=" O ILE C1003 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU C1005 " --> pdb=" O ALA C 972 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU C1061 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU C1006 " --> pdb=" O LEU C1061 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C1063 " --> pdb=" O LEU C1006 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR C1035 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N PHE C1064 " --> pdb=" O THR C1035 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA C1037 " --> pdb=" O PHE C1064 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1129 through 1133 removed outlier: 6.771A pdb=" N LYS C1105 " --> pdb=" O ALA C1130 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL C1132 " --> pdb=" O LYS C1105 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N MET C1107 " --> pdb=" O VAL C1132 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU C1157 " --> pdb=" O VAL C1106 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LEU C1108 " --> pdb=" O GLU C1157 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C1159 " --> pdb=" O LEU C1108 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 126 through 134 removed outlier: 6.587A pdb=" N SER D 256 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N VAL D 282 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR D 258 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 180 through 184 Processing sheet with id= U, first strand: chain 'D' and resid 422 through 424 Processing sheet with id= V, first strand: chain 'D' and resid 451 through 454 removed outlier: 6.828A pdb=" N PHE D 736 " --> pdb=" O PHE D 707 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL D 709 " --> pdb=" O PHE D 736 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP D 738 " --> pdb=" O VAL D 709 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N ILE D 672 " --> pdb=" O VAL D 637 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE D 674 " --> pdb=" O PRO D 639 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU D 641 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL D 676 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N HIS D 643 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU D 536 " --> pdb=" O VAL D 638 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU D 640 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL D 538 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU D 642 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY D 540 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N GLY D 644 " --> pdb=" O GLY D 540 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VAL D 537 " --> pdb=" O GLU D 598 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS D 600 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE D 539 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER D 602 " --> pdb=" O ILE D 539 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 939 through 944 removed outlier: 3.597A pdb=" N GLY D 900 " --> pdb=" O TYR D 943 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE D 967 " --> pdb=" O ARG D 897 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA D 899 " --> pdb=" O ILE D 967 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA D 969 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE D1003 " --> pdb=" O TRP D 970 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA D 972 " --> pdb=" O ILE D1003 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU D1005 " --> pdb=" O ALA D 972 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU D1061 " --> pdb=" O LEU D1004 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU D1006 " --> pdb=" O LEU D1061 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE D1063 " --> pdb=" O LEU D1006 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR D1035 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N PHE D1064 " --> pdb=" O THR D1035 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA D1037 " --> pdb=" O PHE D1064 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 1129 through 1133 removed outlier: 6.776A pdb=" N LYS D1105 " --> pdb=" O ALA D1130 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL D1132 " --> pdb=" O LYS D1105 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N MET D1107 " --> pdb=" O VAL D1132 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU D1157 " --> pdb=" O VAL D1106 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU D1108 " --> pdb=" O GLU D1157 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU D1159 " --> pdb=" O LEU D1108 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 126 through 134 removed outlier: 6.591A pdb=" N SER E 256 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL E 282 " --> pdb=" O SER E 256 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR E 258 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 180 through 184 Processing sheet with id= AA, first strand: chain 'E' and resid 422 through 424 Processing sheet with id= AB, first strand: chain 'E' and resid 451 through 454 removed outlier: 6.824A pdb=" N PHE E 736 " --> pdb=" O PHE E 707 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL E 709 " --> pdb=" O PHE E 736 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP E 738 " --> pdb=" O VAL E 709 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N ILE E 672 " --> pdb=" O VAL E 637 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE E 674 " --> pdb=" O PRO E 639 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU E 641 " --> pdb=" O ILE E 674 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL E 676 " --> pdb=" O LEU E 641 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N HIS E 643 " --> pdb=" O VAL E 676 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU E 536 " --> pdb=" O VAL E 638 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU E 640 " --> pdb=" O GLU E 536 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL E 538 " --> pdb=" O LEU E 640 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU E 642 " --> pdb=" O VAL E 538 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY E 540 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N GLY E 644 " --> pdb=" O GLY E 540 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N VAL E 537 " --> pdb=" O GLU E 598 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS E 600 " --> pdb=" O VAL E 537 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE E 539 " --> pdb=" O LYS E 600 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER E 602 " --> pdb=" O ILE E 539 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 939 through 944 removed outlier: 3.597A pdb=" N GLY E 900 " --> pdb=" O TYR E 943 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE E 967 " --> pdb=" O ARG E 897 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA E 899 " --> pdb=" O ILE E 967 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA E 969 " --> pdb=" O ALA E 899 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE E1003 " --> pdb=" O TRP E 970 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA E 972 " --> pdb=" O ILE E1003 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU E1005 " --> pdb=" O ALA E 972 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU E1061 " --> pdb=" O LEU E1004 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU E1006 " --> pdb=" O LEU E1061 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE E1063 " --> pdb=" O LEU E1006 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR E1035 " --> pdb=" O VAL E1062 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE E1064 " --> pdb=" O THR E1035 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA E1037 " --> pdb=" O PHE E1064 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 1129 through 1133 removed outlier: 6.770A pdb=" N LYS E1105 " --> pdb=" O ALA E1130 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL E1132 " --> pdb=" O LYS E1105 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N MET E1107 " --> pdb=" O VAL E1132 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU E1157 " --> pdb=" O VAL E1106 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LEU E1108 " --> pdb=" O GLU E1157 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU E1159 " --> pdb=" O LEU E1108 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 126 through 134 removed outlier: 6.592A pdb=" N SER F 256 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL F 282 " --> pdb=" O SER F 256 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR F 258 " --> pdb=" O VAL F 282 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 180 through 184 Processing sheet with id= AG, first strand: chain 'F' and resid 422 through 424 Processing sheet with id= AH, first strand: chain 'F' and resid 451 through 454 removed outlier: 6.829A pdb=" N PHE F 736 " --> pdb=" O PHE F 707 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL F 709 " --> pdb=" O PHE F 736 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP F 738 " --> pdb=" O VAL F 709 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N ILE F 672 " --> pdb=" O VAL F 637 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE F 674 " --> pdb=" O PRO F 639 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU F 641 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL F 676 " --> pdb=" O LEU F 641 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N HIS F 643 " --> pdb=" O VAL F 676 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU F 536 " --> pdb=" O VAL F 638 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU F 640 " --> pdb=" O GLU F 536 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL F 538 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU F 642 " --> pdb=" O VAL F 538 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY F 540 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N GLY F 644 " --> pdb=" O GLY F 540 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VAL F 537 " --> pdb=" O GLU F 598 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS F 600 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE F 539 " --> pdb=" O LYS F 600 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER F 602 " --> pdb=" O ILE F 539 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 939 through 944 removed outlier: 3.597A pdb=" N GLY F 900 " --> pdb=" O TYR F 943 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE F 967 " --> pdb=" O ARG F 897 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA F 899 " --> pdb=" O ILE F 967 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA F 969 " --> pdb=" O ALA F 899 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE F1003 " --> pdb=" O TRP F 970 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA F 972 " --> pdb=" O ILE F1003 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU F1005 " --> pdb=" O ALA F 972 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU F1061 " --> pdb=" O LEU F1004 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU F1006 " --> pdb=" O LEU F1061 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE F1063 " --> pdb=" O LEU F1006 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR F1035 " --> pdb=" O VAL F1062 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N PHE F1064 " --> pdb=" O THR F1035 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA F1037 " --> pdb=" O PHE F1064 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 1129 through 1133 removed outlier: 6.776A pdb=" N LYS F1105 " --> pdb=" O ALA F1130 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL F1132 " --> pdb=" O LYS F1105 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N MET F1107 " --> pdb=" O VAL F1132 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU F1157 " --> pdb=" O VAL F1106 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N LEU F1108 " --> pdb=" O GLU F1157 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU F1159 " --> pdb=" O LEU F1108 " (cutoff:3.500A) 1962 hydrogen bonds defined for protein. 5274 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: 18.05 Time building geometry restraints manager: 16.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.70: 53556 1.70 - 2.21: 432 2.21 - 2.71: 0 2.71 - 3.22: 0 3.22 - 3.72: 12 Bond restraints: 54000 Sorted by residual: bond pdb=" AO6 COA E1302 " pdb=" AP2 COA E1302 " ideal model delta sigma weight residual 1.610 3.724 -2.114 2.00e-02 2.50e+03 1.12e+04 bond pdb=" AO6 COA D1302 " pdb=" AP2 COA D1302 " ideal model delta sigma weight residual 1.610 3.715 -2.105 2.00e-02 2.50e+03 1.11e+04 bond pdb=" AO6 COA A1302 " pdb=" AP2 COA A1302 " ideal model delta sigma weight residual 1.610 3.708 -2.098 2.00e-02 2.50e+03 1.10e+04 bond pdb=" AO6 COA B1302 " pdb=" AP2 COA B1302 " ideal model delta sigma weight residual 1.610 3.708 -2.098 2.00e-02 2.50e+03 1.10e+04 bond pdb=" AO6 COA F1302 " pdb=" AP2 COA F1302 " ideal model delta sigma weight residual 1.610 3.708 -2.098 2.00e-02 2.50e+03 1.10e+04 ... (remaining 53995 not shown) Histogram of bond angle deviations from ideal: 30.99 - 51.97: 12 51.97 - 72.94: 0 72.94 - 93.92: 18 93.92 - 114.89: 32778 114.89 - 135.87: 40458 Bond angle restraints: 73266 Sorted by residual: angle pdb=" AO3 COA E1302 " pdb=" AP2 COA E1302 " pdb=" AO6 COA E1302 " ideal model delta sigma weight residual 102.60 30.99 71.61 3.00e+00 1.11e-01 5.70e+02 angle pdb=" AO3 COA D1302 " pdb=" AP2 COA D1302 " pdb=" AO6 COA D1302 " ideal model delta sigma weight residual 102.60 31.33 71.27 3.00e+00 1.11e-01 5.64e+02 angle pdb=" AO3 COA F1302 " pdb=" AP2 COA F1302 " pdb=" AO6 COA F1302 " ideal model delta sigma weight residual 102.60 31.67 70.93 3.00e+00 1.11e-01 5.59e+02 angle pdb=" AO3 COA B1302 " pdb=" AP2 COA B1302 " pdb=" AO6 COA B1302 " ideal model delta sigma weight residual 102.60 31.68 70.92 3.00e+00 1.11e-01 5.59e+02 angle pdb=" AO3 COA A1302 " pdb=" AP2 COA A1302 " pdb=" AO6 COA A1302 " ideal model delta sigma weight residual 102.60 31.69 70.91 3.00e+00 1.11e-01 5.59e+02 ... (remaining 73261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 31729 35.49 - 70.98: 747 70.98 - 106.47: 50 106.47 - 141.96: 6 141.96 - 177.46: 12 Dihedral angle restraints: 32544 sinusoidal: 13392 harmonic: 19152 Sorted by residual: dihedral pdb=" AO7 COA F1302 " pdb="AO3* COA F1302 " pdb="AP3* COA F1302 " pdb="AC3* COA F1302 " ideal model delta sinusoidal sigma weight residual -163.46 13.99 -177.46 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" AO7 COA C1302 " pdb="AO3* COA C1302 " pdb="AP3* COA C1302 " pdb="AC3* COA C1302 " ideal model delta sinusoidal sigma weight residual -163.46 13.75 -177.21 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" AO7 COA A1302 " pdb="AO3* COA A1302 " pdb="AP3* COA A1302 " pdb="AC3* COA A1302 " ideal model delta sinusoidal sigma weight residual -163.46 12.58 -176.04 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 32541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5338 0.079 - 0.158: 2352 0.158 - 0.236: 231 0.236 - 0.315: 18 0.315 - 0.394: 17 Chirality restraints: 7956 Sorted by residual: chirality pdb=" CA PRO C 714 " pdb=" N PRO C 714 " pdb=" C PRO C 714 " pdb=" CB PRO C 714 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA PRO E 714 " pdb=" N PRO E 714 " pdb=" C PRO E 714 " pdb=" CB PRO E 714 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA PRO D 714 " pdb=" N PRO D 714 " pdb=" C PRO D 714 " pdb=" CB PRO D 714 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 7953 not shown) Planarity restraints: 9612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO F1303 " 0.112 2.00e-02 2.50e+03 9.32e-02 1.09e+02 pdb=" C5P ACO F1303 " -0.023 2.00e-02 2.50e+03 pdb=" C6P ACO F1303 " 0.082 2.00e-02 2.50e+03 pdb=" N4P ACO F1303 " -0.153 2.00e-02 2.50e+03 pdb=" O5P ACO F1303 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO E1303 " -0.110 2.00e-02 2.50e+03 9.11e-02 1.04e+02 pdb=" C5P ACO E1303 " 0.021 2.00e-02 2.50e+03 pdb=" C6P ACO E1303 " -0.080 2.00e-02 2.50e+03 pdb=" N4P ACO E1303 " 0.149 2.00e-02 2.50e+03 pdb=" O5P ACO E1303 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO D1303 " 0.108 2.00e-02 2.50e+03 9.00e-02 1.01e+02 pdb=" C5P ACO D1303 " -0.021 2.00e-02 2.50e+03 pdb=" C6P ACO D1303 " 0.079 2.00e-02 2.50e+03 pdb=" N4P ACO D1303 " -0.148 2.00e-02 2.50e+03 pdb=" O5P ACO D1303 " -0.018 2.00e-02 2.50e+03 ... (remaining 9609 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 18 2.26 - 2.92: 19736 2.92 - 3.58: 69103 3.58 - 4.24: 118565 4.24 - 4.90: 205355 Nonbonded interactions: 412777 Sorted by model distance: nonbonded pdb=" AP2 COA F1302 " pdb="AO5* COA F1302 " model vdw 1.601 2.720 nonbonded pdb=" AP2 COA C1302 " pdb="AO5* COA C1302 " model vdw 1.601 2.720 nonbonded pdb=" AP2 COA B1302 " pdb="AO5* COA B1302 " model vdw 1.602 2.720 nonbonded pdb=" AP2 COA A1302 " pdb="AO5* COA A1302 " model vdw 1.602 2.720 nonbonded pdb=" AO6 COA D1302 " pdb=" AP1 COA D1302 " model vdw 1.602 2.720 ... (remaining 412772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 12.620 Check model and map are aligned: 0.580 Set scattering table: 0.360 Process input model: 104.850 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 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 : 0.032 2.114 54000 Z= 2.159 Angle : 1.596 71.611 73266 Z= 0.881 Chirality : 0.079 0.394 7956 Planarity : 0.008 0.093 9612 Dihedral : 15.325 177.456 20292 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.97 % Favored : 97.02 % Rotamer: Outliers : 0.31 % Allowed : 2.70 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -1.97 (0.08), residues: 6702 helix: -1.30 (0.08), residues: 2694 sheet: 0.29 (0.14), residues: 1080 loop : -1.86 (0.09), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.006 TRP B 357 HIS 0.015 0.004 HIS C 857 PHE 0.032 0.004 PHE A1046 TYR 0.054 0.006 TYR A 761 ARG 0.013 0.002 ARG F 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 1296 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1279 time to evaluate : 4.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 1290 average time/residue: 1.6170 time to fit residues: 2532.7985 Evaluate side-chains 1185 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1173 time to evaluate : 4.550 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 6 average time/residue: 0.5067 time to fit residues: 11.2139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 562 optimal weight: 4.9990 chunk 504 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 340 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 chunk 522 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 317 optimal weight: 0.7980 chunk 388 optimal weight: 0.7980 chunk 604 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 568 GLN A 589 GLN A 590 HIS A 786 ASN A 799 GLN A 805 ASN A 849 ASN A1184 ASN B 568 GLN B 799 GLN B 849 ASN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1184 ASN B1213 GLN C 292 GLN C 320 GLN C 424 ASN C 589 GLN C 799 GLN C 805 ASN C 849 ASN D 117 ASN D 349 ASN D 488 GLN D 773 GLN D 849 ASN D1184 ASN E 117 ASN E 349 ASN E 488 GLN E 501 GLN E 773 GLN E 849 ASN F 292 GLN F 320 GLN F 501 GLN F 799 GLN F 805 ASN F 849 ASN F1096 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 54000 Z= 0.242 Angle : 0.585 8.354 73266 Z= 0.299 Chirality : 0.045 0.154 7956 Planarity : 0.005 0.039 9612 Dihedral : 12.231 153.790 7836 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.43 % Allowed : 9.43 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.45 (0.09), residues: 6702 helix: 0.51 (0.10), residues: 2742 sheet: 0.59 (0.15), residues: 1098 loop : -1.44 (0.10), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 466 HIS 0.006 0.001 HIS F 267 PHE 0.028 0.001 PHE F1046 TYR 0.016 0.001 TYR F 761 ARG 0.008 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 1315 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1236 time to evaluate : 4.559 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 30 residues processed: 1256 average time/residue: 1.6515 time to fit residues: 2514.5209 Evaluate side-chains 1194 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1164 time to evaluate : 4.528 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 15 residues processed: 17 average time/residue: 0.9095 time to fit residues: 27.3818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 336 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 503 optimal weight: 0.9990 chunk 411 optimal weight: 3.9990 chunk 166 optimal weight: 0.4980 chunk 605 optimal weight: 5.9990 chunk 654 optimal weight: 5.9990 chunk 539 optimal weight: 1.9990 chunk 600 optimal weight: 0.1980 chunk 206 optimal weight: 0.0980 chunk 486 optimal weight: 1.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 589 GLN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 GLN A 805 ASN A 849 ASN A1184 ASN B 251 GLN B 424 ASN B 799 GLN B 805 ASN B 849 ASN B1027 GLN B1096 ASN B1184 ASN C 117 ASN C 292 GLN C 424 ASN C 748 ASN C 799 GLN C 805 ASN C 849 ASN C 944 ASN C1096 ASN D 117 ASN D 349 ASN D 568 GLN D 573 GLN D 799 GLN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1096 ASN D1184 ASN E 117 ASN E 349 ASN E 568 GLN E 799 GLN F 117 ASN F 292 GLN F 320 GLN F 501 GLN F 748 ASN F 773 GLN F 799 GLN F 805 ASN F 849 ASN F 944 ASN F1096 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 54000 Z= 0.132 Angle : 0.485 8.529 73266 Z= 0.244 Chirality : 0.042 0.143 7956 Planarity : 0.004 0.040 9612 Dihedral : 11.232 163.568 7836 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.61 % Allowed : 10.65 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 (0.10), residues: 6702 helix: 1.19 (0.10), residues: 2748 sheet: 1.06 (0.15), residues: 1044 loop : -1.04 (0.10), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 466 HIS 0.004 0.001 HIS A1045 PHE 0.023 0.001 PHE F1046 TYR 0.012 0.001 TYR B 582 ARG 0.010 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 1303 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1214 time to evaluate : 4.582 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 37 residues processed: 1242 average time/residue: 1.6448 time to fit residues: 2484.7599 Evaluate side-chains 1213 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1176 time to evaluate : 4.532 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 20 residues processed: 20 average time/residue: 0.7533 time to fit residues: 28.2925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 598 optimal weight: 3.9990 chunk 455 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 406 optimal weight: 0.8980 chunk 608 optimal weight: 0.7980 chunk 643 optimal weight: 0.7980 chunk 317 optimal weight: 0.9990 chunk 576 optimal weight: 5.9990 chunk 173 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 HIS A 424 ASN A 589 GLN A 799 GLN A 818 GLN A1184 ASN B 251 GLN B 404 HIS B 424 ASN B 773 GLN B1096 ASN B1184 ASN C 292 GLN C 773 GLN C 799 GLN C1096 ASN D 488 GLN D 677 ASN D 773 GLN D 799 GLN E 117 ASN E 424 ASN E 501 GLN E 773 GLN E 799 GLN E 944 ASN F 292 GLN F 359 GLN F 424 ASN F 501 GLN F 583 HIS F 677 ASN F 799 GLN F 805 ASN F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1096 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 54000 Z= 0.167 Angle : 0.494 8.898 73266 Z= 0.249 Chirality : 0.042 0.148 7956 Planarity : 0.004 0.043 9612 Dihedral : 10.963 165.824 7836 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.60 % Allowed : 12.11 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 (0.10), residues: 6702 helix: 1.48 (0.10), residues: 2736 sheet: 1.07 (0.15), residues: 1068 loop : -0.92 (0.10), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 466 HIS 0.005 0.001 HIS F1045 PHE 0.025 0.001 PHE F1046 TYR 0.016 0.001 TYR A 582 ARG 0.007 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 1287 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1199 time to evaluate : 4.651 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 44 residues processed: 1230 average time/residue: 1.6533 time to fit residues: 2470.1257 Evaluate side-chains 1237 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1193 time to evaluate : 4.512 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 18 residues processed: 26 average time/residue: 0.7893 time to fit residues: 35.8615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 536 optimal weight: 0.8980 chunk 365 optimal weight: 0.1980 chunk 9 optimal weight: 6.9990 chunk 479 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 549 optimal weight: 0.9980 chunk 444 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 328 optimal weight: 2.9990 chunk 577 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 799 GLN A 805 ASN A 818 GLN A1184 ASN A1213 GLN B 251 GLN B 404 HIS B 424 ASN B 799 GLN C 292 GLN C 359 GLN C 799 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1096 ASN D 359 GLN D 488 GLN D 799 GLN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN E 501 GLN E 799 GLN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN F 424 ASN F 501 GLN F 589 GLN F 805 ASN F 944 ASN F1096 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 54000 Z= 0.154 Angle : 0.482 9.363 73266 Z= 0.242 Chirality : 0.042 0.146 7956 Planarity : 0.004 0.046 9612 Dihedral : 10.736 170.762 7836 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.56 % Allowed : 12.59 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.78 (0.10), residues: 6702 helix: 1.62 (0.10), residues: 2742 sheet: 1.15 (0.15), residues: 1068 loop : -0.82 (0.10), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 466 HIS 0.005 0.001 HIS C1045 PHE 0.024 0.001 PHE F1046 TYR 0.012 0.001 TYR C 761 ARG 0.010 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 1306 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1220 time to evaluate : 4.818 Fit side-chains revert: symmetry clash outliers start: 86 outliers final: 45 residues processed: 1254 average time/residue: 1.6488 time to fit residues: 2515.5085 Evaluate side-chains 1248 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1203 time to evaluate : 4.508 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 25 residues processed: 22 average time/residue: 0.7434 time to fit residues: 30.1708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 216 optimal weight: 2.9990 chunk 579 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 377 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 644 optimal weight: 0.0670 chunk 534 optimal weight: 0.0770 chunk 298 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 338 optimal weight: 2.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 614 ASN A 799 GLN B 316 HIS B 404 HIS B 424 ASN B 614 ASN B 799 GLN B1096 ASN C 292 GLN C 583 HIS C 614 ASN C 799 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1096 ASN C1184 ASN D 359 GLN D 488 GLN D 677 ASN D 799 GLN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN E 799 GLN E 944 ASN E1027 GLN F 292 GLN F 424 ASN F 501 GLN F 944 ASN F1096 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 54000 Z= 0.188 Angle : 0.501 9.766 73266 Z= 0.252 Chirality : 0.043 0.151 7956 Planarity : 0.004 0.042 9612 Dihedral : 10.681 175.296 7836 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.58 % Allowed : 13.31 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.83 (0.10), residues: 6702 helix: 1.68 (0.10), residues: 2730 sheet: 1.30 (0.16), residues: 1032 loop : -0.83 (0.10), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 466 HIS 0.006 0.001 HIS B 316 PHE 0.025 0.001 PHE F1046 TYR 0.014 0.001 TYR C 761 ARG 0.008 0.000 ARG F 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 1312 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1225 time to evaluate : 4.490 Fit side-chains outliers start: 87 outliers final: 49 residues processed: 1258 average time/residue: 1.6532 time to fit residues: 2534.8297 Evaluate side-chains 1262 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1213 time to evaluate : 4.525 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 30 residues processed: 22 average time/residue: 0.7503 time to fit residues: 30.5825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 621 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 367 optimal weight: 0.8980 chunk 470 optimal weight: 0.7980 chunk 364 optimal weight: 4.9990 chunk 542 optimal weight: 0.0570 chunk 359 optimal weight: 0.6980 chunk 641 optimal weight: 3.9990 chunk 401 optimal weight: 7.9990 chunk 391 optimal weight: 0.0040 chunk 296 optimal weight: 3.9990 overall best weight: 0.4910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 805 ASN B 404 HIS B 424 ASN B 773 GLN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 799 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1096 ASN C1184 ASN D 359 GLN D 488 GLN D 799 GLN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 GLN E 799 GLN E 944 ASN F 292 GLN F 424 ASN F 501 GLN F 614 ASN F 677 ASN F 805 ASN F 944 ASN F1045 HIS F1096 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 54000 Z= 0.129 Angle : 0.469 9.534 73266 Z= 0.235 Chirality : 0.041 0.143 7956 Planarity : 0.004 0.041 9612 Dihedral : 10.465 179.980 7836 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.03 % Allowed : 14.16 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.99 (0.10), residues: 6702 helix: 1.79 (0.10), residues: 2736 sheet: 1.39 (0.15), residues: 1044 loop : -0.73 (0.11), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 466 HIS 0.003 0.001 HIS F1045 PHE 0.023 0.001 PHE F1046 TYR 0.010 0.001 TYR C 761 ARG 0.006 0.000 ARG F 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 1296 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1239 time to evaluate : 4.591 Fit side-chains outliers start: 57 outliers final: 39 residues processed: 1263 average time/residue: 1.6159 time to fit residues: 2495.2320 Evaluate side-chains 1260 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1221 time to evaluate : 4.540 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 25 residues processed: 15 average time/residue: 0.8812 time to fit residues: 24.8044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 397 optimal weight: 0.9980 chunk 256 optimal weight: 2.9990 chunk 383 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 408 optimal weight: 0.7980 chunk 437 optimal weight: 0.7980 chunk 317 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 504 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 424 ASN A 799 GLN B 404 HIS B 424 ASN B 799 GLN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1096 ASN C 292 GLN C 359 GLN C 583 HIS C 677 ASN C 799 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1045 HIS C1096 ASN C1184 ASN D 359 GLN D 488 GLN D 677 ASN D 799 GLN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 GLN E 799 GLN E 944 ASN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1184 ASN F 292 GLN F 424 ASN F 501 GLN F 677 ASN F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1096 ASN F1184 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 54000 Z= 0.178 Angle : 0.495 10.174 73266 Z= 0.249 Chirality : 0.043 0.180 7956 Planarity : 0.004 0.041 9612 Dihedral : 10.415 179.818 7836 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.09 % Allowed : 14.20 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 (0.10), residues: 6702 helix: 1.77 (0.10), residues: 2736 sheet: 1.27 (0.15), residues: 1068 loop : -0.72 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 466 HIS 0.005 0.001 HIS C1045 PHE 0.025 0.001 PHE C1046 TYR 0.013 0.001 TYR C 761 ARG 0.009 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 1285 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1225 time to evaluate : 4.555 Fit side-chains outliers start: 60 outliers final: 41 residues processed: 1255 average time/residue: 1.6580 time to fit residues: 2537.1694 Evaluate side-chains 1256 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1215 time to evaluate : 4.488 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 27 residues processed: 15 average time/residue: 0.9112 time to fit residues: 25.3538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 583 optimal weight: 5.9990 chunk 614 optimal weight: 0.6980 chunk 561 optimal weight: 0.9980 chunk 598 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 260 optimal weight: 0.7980 chunk 469 optimal weight: 2.9990 chunk 183 optimal weight: 0.2980 chunk 540 optimal weight: 0.6980 chunk 565 optimal weight: 5.9990 chunk 596 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 HIS A 404 HIS A 424 ASN A 805 ASN A1045 HIS B 404 HIS B 424 ASN B 799 GLN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 583 HIS C 799 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1045 HIS C1096 ASN D 359 GLN D 488 GLN D 799 GLN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 GLN E 799 GLN E1184 ASN F 292 GLN F 424 ASN F 501 GLN F 805 ASN F 944 ASN F1096 ASN F1184 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 54000 Z= 0.134 Angle : 0.473 10.020 73266 Z= 0.237 Chirality : 0.042 0.178 7956 Planarity : 0.004 0.040 9612 Dihedral : 10.173 178.337 7836 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.76 % Allowed : 14.82 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.08 (0.10), residues: 6702 helix: 1.89 (0.10), residues: 2700 sheet: 1.46 (0.16), residues: 1044 loop : -0.69 (0.11), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 466 HIS 0.005 0.001 HIS A 404 PHE 0.023 0.001 PHE F1046 TYR 0.010 0.001 TYR C 761 ARG 0.008 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 1283 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1241 time to evaluate : 4.619 Fit side-chains outliers start: 42 outliers final: 28 residues processed: 1268 average time/residue: 1.6369 time to fit residues: 2538.5221 Evaluate side-chains 1255 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1227 time to evaluate : 4.565 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 5 average time/residue: 1.0402 time to fit residues: 13.1493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 392 optimal weight: 2.9990 chunk 632 optimal weight: 0.1980 chunk 386 optimal weight: 3.9990 chunk 300 optimal weight: 3.9990 chunk 439 optimal weight: 0.4980 chunk 663 optimal weight: 5.9990 chunk 610 optimal weight: 0.9990 chunk 528 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 408 optimal weight: 0.9990 chunk 323 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 HIS A 404 HIS A 424 ASN A 583 HIS A 677 ASN B 404 HIS B 424 ASN B 799 GLN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1096 ASN C 292 GLN C 799 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1045 HIS C1096 ASN D 359 GLN D 488 GLN D 677 ASN D 799 GLN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 GLN E 501 GLN E 573 GLN E 799 GLN E 944 ASN E1184 ASN F 424 ASN F 501 GLN F 677 ASN F 944 ASN F1096 ASN F1184 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 54000 Z= 0.182 Angle : 0.500 10.329 73266 Z= 0.251 Chirality : 0.043 0.203 7956 Planarity : 0.004 0.041 9612 Dihedral : 10.208 178.954 7836 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.58 % Allowed : 15.25 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.98 (0.10), residues: 6702 helix: 1.80 (0.10), residues: 2730 sheet: 1.17 (0.15), residues: 1128 loop : -0.71 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 466 HIS 0.005 0.001 HIS A 404 PHE 0.025 0.001 PHE F1046 TYR 0.014 0.001 TYR C 761 ARG 0.008 0.000 ARG F 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 1259 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1227 time to evaluate : 4.638 Fit side-chains outliers start: 32 outliers final: 30 residues processed: 1250 average time/residue: 1.6512 time to fit residues: 2524.4450 Evaluate side-chains 1245 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1215 time to evaluate : 4.644 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 7 average time/residue: 0.6862 time to fit residues: 14.0721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 419 optimal weight: 6.9990 chunk 562 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 487 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 529 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 543 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 424 ASN A 583 HIS A 799 GLN A 845 GLN ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 424 ASN B 590 HIS B 799 GLN B 845 GLN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 359 GLN C 845 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1045 HIS C1096 ASN C1184 ASN D 359 GLN D 488 GLN D 799 GLN D 845 GLN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN E 488 GLN E 501 GLN E 799 GLN E 845 GLN E 944 ASN E1184 ASN F 424 ASN F 501 GLN F 944 ASN F1096 ASN F1184 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.109829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.100341 restraints weight = 69454.739| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.21 r_work: 0.3392 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 54000 Z= 0.433 Angle : 0.621 11.368 73266 Z= 0.315 Chirality : 0.050 0.257 7956 Planarity : 0.005 0.044 9612 Dihedral : 10.560 179.209 7836 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.83 % Allowed : 15.13 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 (0.10), residues: 6702 helix: 1.52 (0.10), residues: 2724 sheet: 0.95 (0.15), residues: 1122 loop : -0.91 (0.10), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 417 HIS 0.010 0.002 HIS C 267 PHE 0.030 0.002 PHE F1046 TYR 0.024 0.002 TYR C 761 ARG 0.007 0.001 ARG E 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31742.47 seconds wall clock time: 544 minutes 24.96 seconds (32664.96 seconds total)