Starting phenix.real_space_refine on Tue Mar 26 01:22:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5t_17452/03_2024/8p5t_17452_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5t_17452/03_2024/8p5t_17452.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5t_17452/03_2024/8p5t_17452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5t_17452/03_2024/8p5t_17452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5t_17452/03_2024/8p5t_17452_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5t_17452/03_2024/8p5t_17452_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= 1.217 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 30 5.49 5 Mg 6 5.21 5 S 228 5.16 5 C 32994 2.51 5 N 9228 2.21 5 O 10104 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 314": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 314": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 314": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 314": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 52590 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' MG': 1, 'ACO': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' MG': 1, 'ACO': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' MG': 1, 'ACO': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' MG': 1, 'ACO': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' MG': 1, 'ACO': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' MG': 1, 'ACO': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 26.34, per 1000 atoms: 0.50 Number of scatterers: 52590 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 228 16.00 P 30 15.00 Mg 6 11.99 O 10104 8.00 N 9228 7.00 C 32994 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: 18.57 Conformation dependent library (CDL) restraints added in 9.4 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 42.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.19 Creating SS restraints... Processing helix chain 'A' and resid 110 through 123 removed outlier: 3.899A pdb=" N LEU A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 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: 4.002A pdb=" N THR A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 368 through 386 removed outlier: 6.638A pdb=" N HIS A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.873A 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: 3.661A pdb=" N ASP A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 3.553A 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: 4.193A 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: 3.517A 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 780 Processing helix chain 'A' and resid 786 through 809 removed outlier: 3.948A pdb=" N VAL A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 4.566A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 873 removed outlier: 4.143A pdb=" N VAL A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 5.156A 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: 3.646A pdb=" N ALA A 978 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN A 979 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 982 " --> pdb=" O ASN A 979 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR A 983 " --> pdb=" O GLY A 980 " (cutoff:3.500A) removed outlier: 3.625A 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: 4.208A pdb=" N ALA A1118 " --> pdb=" O TYR A1115 " (cutoff:3.500A) removed outlier: 3.738A 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: 3.715A 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: 3.896A pdb=" N LEU B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 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: 4.002A pdb=" N THR B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 368 through 386 removed outlier: 6.638A pdb=" N HIS B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.874A 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: 3.661A pdb=" N ASP B 523 " --> pdb=" O PRO B 520 " (cutoff:3.500A) removed outlier: 3.553A 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: 4.193A 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: 3.517A 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 780 Processing helix chain 'B' and resid 786 through 809 removed outlier: 3.948A pdb=" N VAL B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 847 removed outlier: 4.566A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 873 removed outlier: 4.142A pdb=" N VAL B 871 " --> pdb=" O ARG B 867 " (cutoff:3.500A) removed outlier: 5.156A 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: 3.646A pdb=" N ALA B 978 " --> pdb=" O GLY B 975 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN B 979 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 982 " --> pdb=" O ASN B 979 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N THR B 983 " --> pdb=" O GLY B 980 " (cutoff:3.500A) removed outlier: 3.625A 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: 4.206A 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: 3.714A 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: 3.900A pdb=" N LEU C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 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: 3.999A pdb=" N THR C 336 " --> pdb=" O SER C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 368 through 386 removed outlier: 6.638A pdb=" N HIS C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 4.874A 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: 3.661A pdb=" N ASP C 523 " --> pdb=" O PRO C 520 " (cutoff:3.500A) removed outlier: 3.553A 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: 4.194A 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: 3.517A 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 780 Processing helix chain 'C' and resid 786 through 809 removed outlier: 3.947A pdb=" N VAL C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 847 removed outlier: 4.565A pdb=" N PHE C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 873 removed outlier: 4.142A pdb=" N VAL C 871 " --> pdb=" O ARG C 867 " (cutoff:3.500A) removed outlier: 5.155A 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: 3.646A pdb=" N ALA C 978 " --> pdb=" O GLY C 975 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN C 979 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN C 982 " --> pdb=" O ASN C 979 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR C 983 " --> pdb=" O GLY C 980 " (cutoff:3.500A) removed outlier: 3.626A 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: 4.206A pdb=" N ALA C1118 " --> pdb=" O TYR C1115 " (cutoff:3.500A) removed outlier: 3.738A 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: 3.714A 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: 3.894A pdb=" N LEU D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLU D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 151 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: 3.999A pdb=" N THR D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 Processing helix chain 'D' and resid 368 through 386 removed outlier: 6.640A pdb=" N HIS D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.874A 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: 3.661A pdb=" N ASP D 523 " --> pdb=" O PRO D 520 " (cutoff:3.500A) removed outlier: 3.553A 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: 4.193A 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: 3.518A 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 780 Processing helix chain 'D' and resid 786 through 809 removed outlier: 3.948A pdb=" N VAL D 793 " --> pdb=" O ALA D 789 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 847 removed outlier: 4.567A pdb=" N PHE D 847 " --> pdb=" O LEU D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 873 removed outlier: 4.144A pdb=" N VAL D 871 " --> pdb=" O ARG D 867 " (cutoff:3.500A) removed outlier: 5.157A 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: 3.646A pdb=" N ALA D 978 " --> pdb=" O GLY D 975 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN D 979 " --> pdb=" O ASP D 976 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN D 982 " --> pdb=" O ASN D 979 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR D 983 " --> pdb=" O GLY D 980 " (cutoff:3.500A) removed outlier: 3.625A 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: 4.208A pdb=" N ALA D1118 " --> pdb=" O TYR D1115 " (cutoff:3.500A) removed outlier: 3.738A 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: 3.714A 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: 3.895A pdb=" N LEU E 122 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLU E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 151 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: 4.000A pdb=" N THR E 336 " --> pdb=" O SER E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 348 Processing helix chain 'E' and resid 368 through 386 removed outlier: 6.638A pdb=" N HIS E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU E 385 " --> pdb=" O SER E 381 " (cutoff:3.500A) removed outlier: 4.873A 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: 3.662A pdb=" N ASP E 523 " --> pdb=" O PRO E 520 " (cutoff:3.500A) removed outlier: 3.554A 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: 4.193A 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: 3.517A 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 780 Processing helix chain 'E' and resid 786 through 809 removed outlier: 3.948A pdb=" N VAL E 793 " --> pdb=" O ALA E 789 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE E 796 " --> pdb=" O VAL E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 847 removed outlier: 4.566A pdb=" N PHE E 847 " --> pdb=" O LEU E 843 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 873 removed outlier: 4.143A pdb=" N VAL E 871 " --> pdb=" O ARG E 867 " (cutoff:3.500A) removed outlier: 5.154A 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: 3.646A pdb=" N ALA E 978 " --> pdb=" O GLY E 975 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN E 979 " --> pdb=" O ASP E 976 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN E 982 " --> pdb=" O ASN E 979 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR E 983 " --> pdb=" O GLY E 980 " (cutoff:3.500A) removed outlier: 3.625A 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: 4.208A pdb=" N ALA E1118 " --> pdb=" O TYR E1115 " (cutoff:3.500A) removed outlier: 3.738A 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: 3.714A 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: 3.895A pdb=" N LEU F 122 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLU F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 151 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: 3.998A pdb=" N THR F 336 " --> pdb=" O SER F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 348 Processing helix chain 'F' and resid 368 through 386 removed outlier: 6.640A pdb=" N HIS F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU F 385 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.874A 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: 3.661A pdb=" N ASP F 523 " --> pdb=" O PRO F 520 " (cutoff:3.500A) removed outlier: 3.552A 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: 4.193A 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: 3.517A 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 780 Processing helix chain 'F' and resid 786 through 809 removed outlier: 3.947A pdb=" N VAL F 793 " --> pdb=" O ALA F 789 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE F 796 " --> pdb=" O VAL F 792 " (cutoff:3.500A) Processing helix chain 'F' and resid 837 through 847 removed outlier: 4.565A pdb=" N PHE F 847 " --> pdb=" O LEU F 843 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 873 removed outlier: 4.143A pdb=" N VAL F 871 " --> pdb=" O ARG F 867 " (cutoff:3.500A) removed outlier: 5.155A 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: 3.646A pdb=" N ALA F 978 " --> pdb=" O GLY F 975 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN F 979 " --> pdb=" O ASP F 976 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN F 982 " --> pdb=" O ASN F 979 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR F 983 " --> pdb=" O GLY F 980 " (cutoff:3.500A) removed outlier: 3.626A 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: 4.206A pdb=" N ALA F1118 " --> pdb=" O TYR F1115 " (cutoff:3.500A) removed outlier: 3.738A 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: 3.714A 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: 6.606A pdb=" N SER A 256 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL A 282 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR A 258 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 201 " --> pdb=" O LEU A 257 " (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: 6.826A 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: 6.455A pdb=" N ASP A 738 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ILE A 672 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE A 674 " --> pdb=" O PRO A 639 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 641 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL A 676 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N HIS A 643 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU A 536 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU A 640 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 538 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU A 642 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY A 540 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY A 644 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N VAL A 537 " --> pdb=" O GLU A 598 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS A 600 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE A 539 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 6.791A 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: 3.569A pdb=" N GLY A 900 " --> pdb=" O TYR A 943 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE A 967 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA A 899 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA A 969 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A1003 " --> pdb=" O TRP A 970 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A1061 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU A1006 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A1063 " --> pdb=" O LEU A1006 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR A1035 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE A1064 " --> pdb=" O THR A1035 " (cutoff:3.500A) removed outlier: 7.312A 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: 6.781A pdb=" N LYS A1105 " --> pdb=" O ALA A1130 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A1132 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N MET A1107 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU A1157 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU A1108 " --> pdb=" O GLU A1157 " (cutoff:3.500A) removed outlier: 6.605A 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: 6.607A pdb=" N SER B 256 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL B 282 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 258 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 201 " --> pdb=" O LEU B 257 " (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: 6.825A pdb=" N PHE B 736 " --> pdb=" O PHE B 707 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL B 709 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP B 738 " --> pdb=" O VAL B 709 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ILE B 672 " --> pdb=" O VAL B 637 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE B 674 " --> pdb=" O PRO B 639 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 641 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL B 676 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N HIS B 643 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU B 536 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU B 640 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL B 538 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU B 642 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY B 540 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY B 644 " --> pdb=" O GLY B 540 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N VAL B 537 " --> pdb=" O GLU B 598 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS B 600 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE B 539 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 6.791A 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: 3.568A pdb=" N GLY B 900 " --> pdb=" O TYR B 943 " (cutoff:3.500A) removed outlier: 6.423A 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: 6.416A pdb=" N ALA B 969 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE B1003 " --> pdb=" O TRP B 970 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B1061 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU B1006 " --> pdb=" O LEU B1061 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B1063 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B1035 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE B1064 " --> pdb=" O THR B1035 " (cutoff:3.500A) removed outlier: 7.312A 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: 6.782A pdb=" N LYS B1105 " --> pdb=" O ALA B1130 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL B1132 " --> pdb=" O LYS B1105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET B1107 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU B1157 " --> pdb=" O VAL B1106 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU B1108 " --> pdb=" O GLU B1157 " (cutoff:3.500A) removed outlier: 6.604A 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: 6.606A pdb=" N SER C 256 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL C 282 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR C 258 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C 201 " --> pdb=" O LEU C 257 " (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: 6.824A pdb=" N PHE C 736 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL C 709 " --> pdb=" O PHE C 736 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP C 738 " --> pdb=" O VAL C 709 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N ILE C 672 " --> pdb=" O VAL C 637 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE C 674 " --> pdb=" O PRO C 639 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU C 641 " --> pdb=" O ILE C 674 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL C 676 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N HIS C 643 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU C 536 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU C 640 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 538 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU C 642 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY C 540 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY C 644 " --> pdb=" O GLY C 540 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL C 537 " --> pdb=" O GLU C 598 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS C 600 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE C 539 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 6.790A 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: 3.570A pdb=" N GLY C 900 " --> pdb=" O TYR C 943 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 967 " --> pdb=" O ARG C 897 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA C 899 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 969 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE C1003 " --> pdb=" O TRP C 970 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C1061 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU C1006 " --> pdb=" O LEU C1061 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE C1063 " --> pdb=" O LEU C1006 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR C1035 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE C1064 " --> pdb=" O THR C1035 " (cutoff:3.500A) removed outlier: 7.312A 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: 6.781A pdb=" N LYS C1105 " --> pdb=" O ALA C1130 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL C1132 " --> pdb=" O LYS C1105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET C1107 " --> pdb=" O VAL C1132 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU C1157 " --> pdb=" O VAL C1106 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU C1108 " --> pdb=" O GLU C1157 " (cutoff:3.500A) removed outlier: 6.606A 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: 6.603A pdb=" N SER D 256 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL D 282 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR D 258 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 201 " --> pdb=" O LEU D 257 " (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: 6.825A pdb=" N PHE D 736 " --> pdb=" O PHE D 707 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL D 709 " --> pdb=" O PHE D 736 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP D 738 " --> pdb=" O VAL D 709 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N ILE D 672 " --> pdb=" O VAL D 637 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE D 674 " --> pdb=" O PRO D 639 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 641 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL D 676 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N HIS D 643 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU D 536 " --> pdb=" O VAL D 638 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU D 640 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL D 538 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU D 642 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY D 540 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N GLY D 644 " --> pdb=" O GLY D 540 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL D 537 " --> pdb=" O GLU D 598 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS D 600 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE D 539 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 6.792A 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: 3.569A pdb=" N GLY D 900 " --> pdb=" O TYR D 943 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE D 967 " --> pdb=" O ARG D 897 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA D 899 " --> pdb=" O ILE D 967 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA D 969 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE D1003 " --> pdb=" O TRP D 970 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU D1061 " --> pdb=" O LEU D1004 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU D1006 " --> pdb=" O LEU D1061 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE D1063 " --> pdb=" O LEU D1006 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR D1035 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE D1064 " --> pdb=" O THR D1035 " (cutoff:3.500A) removed outlier: 7.311A 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: 6.781A pdb=" N LYS D1105 " --> pdb=" O ALA D1130 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL D1132 " --> pdb=" O LYS D1105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET D1107 " --> pdb=" O VAL D1132 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU D1157 " --> pdb=" O VAL D1106 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU D1108 " --> pdb=" O GLU D1157 " (cutoff:3.500A) removed outlier: 6.603A 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: 6.605A pdb=" N SER E 256 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL E 282 " --> pdb=" O SER E 256 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR E 258 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA E 201 " --> pdb=" O LEU E 257 " (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: 6.825A pdb=" N PHE E 736 " --> pdb=" O PHE E 707 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL E 709 " --> pdb=" O PHE E 736 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP E 738 " --> pdb=" O VAL E 709 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ILE E 672 " --> pdb=" O VAL E 637 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE E 674 " --> pdb=" O PRO E 639 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU E 641 " --> pdb=" O ILE E 674 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL E 676 " --> pdb=" O LEU E 641 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N HIS E 643 " --> pdb=" O VAL E 676 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU E 536 " --> pdb=" O VAL E 638 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU E 640 " --> pdb=" O GLU E 536 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL E 538 " --> pdb=" O LEU E 640 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU E 642 " --> pdb=" O VAL E 538 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY E 540 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY E 644 " --> pdb=" O GLY E 540 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL E 537 " --> pdb=" O GLU E 598 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS E 600 " --> pdb=" O VAL E 537 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE E 539 " --> pdb=" O LYS E 600 " (cutoff:3.500A) removed outlier: 6.792A 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: 3.570A pdb=" N GLY E 900 " --> pdb=" O TYR E 943 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE E 967 " --> pdb=" O ARG E 897 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA E 899 " --> pdb=" O ILE E 967 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA E 969 " --> pdb=" O ALA E 899 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE E1003 " --> pdb=" O TRP E 970 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU E1061 " --> pdb=" O LEU E1004 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU E1006 " --> pdb=" O LEU E1061 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE E1063 " --> pdb=" O LEU E1006 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR E1035 " --> pdb=" O VAL E1062 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE E1064 " --> pdb=" O THR E1035 " (cutoff:3.500A) removed outlier: 7.311A 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: 6.781A pdb=" N LYS E1105 " --> pdb=" O ALA E1130 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL E1132 " --> pdb=" O LYS E1105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET E1107 " --> pdb=" O VAL E1132 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU E1157 " --> pdb=" O VAL E1106 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU E1108 " --> pdb=" O GLU E1157 " (cutoff:3.500A) removed outlier: 6.605A 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: 6.613A pdb=" N SER F 256 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL F 282 " --> pdb=" O SER F 256 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR F 258 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA F 201 " --> pdb=" O LEU F 257 " (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: 6.825A pdb=" N PHE F 736 " --> pdb=" O PHE F 707 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL F 709 " --> pdb=" O PHE F 736 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP F 738 " --> pdb=" O VAL F 709 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N ILE F 672 " --> pdb=" O VAL F 637 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE F 674 " --> pdb=" O PRO F 639 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU F 641 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL F 676 " --> pdb=" O LEU F 641 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N HIS F 643 " --> pdb=" O VAL F 676 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU F 536 " --> pdb=" O VAL F 638 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU F 640 " --> pdb=" O GLU F 536 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL F 538 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU F 642 " --> pdb=" O VAL F 538 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY F 540 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N GLY F 644 " --> pdb=" O GLY F 540 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL F 537 " --> pdb=" O GLU F 598 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS F 600 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE F 539 " --> pdb=" O LYS F 600 " (cutoff:3.500A) removed outlier: 6.791A 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: 3.569A pdb=" N GLY F 900 " --> pdb=" O TYR F 943 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE F 967 " --> pdb=" O ARG F 897 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA F 899 " --> pdb=" O ILE F 967 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA F 969 " --> pdb=" O ALA F 899 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE F1003 " --> pdb=" O TRP F 970 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU F1061 " --> pdb=" O LEU F1004 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU F1006 " --> pdb=" O LEU F1061 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE F1063 " --> pdb=" O LEU F1006 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR F1035 " --> pdb=" O VAL F1062 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE F1064 " --> pdb=" O THR F1035 " (cutoff:3.500A) removed outlier: 7.312A 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: 6.782A pdb=" N LYS F1105 " --> pdb=" O ALA F1130 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL F1132 " --> pdb=" O LYS F1105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET F1107 " --> pdb=" O VAL F1132 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU F1157 " --> pdb=" O VAL F1106 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU F1108 " --> pdb=" O GLU F1157 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU F1159 " --> pdb=" O LEU F1108 " (cutoff:3.500A) 1968 hydrogen bonds defined for protein. 5292 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: 22.24 Time building geometry restraints manager: 20.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11718 1.33 - 1.45: 16360 1.45 - 1.58: 25136 1.58 - 1.71: 60 1.71 - 1.83: 426 Bond restraints: 53700 Sorted by residual: bond pdb=" C5 TPP E1303 " pdb=" S1 TPP E1303 " ideal model delta sigma weight residual 1.727 1.624 0.103 1.00e-02 1.00e+04 1.06e+02 bond pdb=" C5 TPP C1303 " pdb=" S1 TPP C1303 " ideal model delta sigma weight residual 1.727 1.624 0.103 1.00e-02 1.00e+04 1.05e+02 bond pdb=" C5 TPP F1303 " pdb=" S1 TPP F1303 " ideal model delta sigma weight residual 1.727 1.625 0.102 1.00e-02 1.00e+04 1.05e+02 bond pdb=" C5 TPP D1303 " pdb=" S1 TPP D1303 " ideal model delta sigma weight residual 1.727 1.625 0.102 1.00e-02 1.00e+04 1.04e+02 bond pdb=" C5 TPP A1303 " pdb=" S1 TPP A1303 " ideal model delta sigma weight residual 1.727 1.626 0.101 1.00e-02 1.00e+04 1.03e+02 ... (remaining 53695 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.75: 1369 104.75 - 112.44: 25259 112.44 - 120.13: 23926 120.13 - 127.81: 21902 127.81 - 135.50: 360 Bond angle restraints: 72816 Sorted by residual: angle pdb=" C ACO C1302 " pdb=" S1P ACO C1302 " pdb=" C2P ACO C1302 " ideal model delta sigma weight residual 101.25 109.38 -8.13 1.00e+00 1.00e+00 6.60e+01 angle pdb=" C ACO E1302 " pdb=" S1P ACO E1302 " pdb=" C2P ACO E1302 " ideal model delta sigma weight residual 101.25 109.31 -8.06 1.00e+00 1.00e+00 6.50e+01 angle pdb=" C ACO B1302 " pdb=" S1P ACO B1302 " pdb=" C2P ACO B1302 " ideal model delta sigma weight residual 101.25 109.11 -7.86 1.00e+00 1.00e+00 6.18e+01 angle pdb=" C ACO F1302 " pdb=" S1P ACO F1302 " pdb=" C2P ACO F1302 " ideal model delta sigma weight residual 101.25 108.93 -7.68 1.00e+00 1.00e+00 5.89e+01 angle pdb=" C ACO D1302 " pdb=" S1P ACO D1302 " pdb=" C2P ACO D1302 " ideal model delta sigma weight residual 101.25 108.49 -7.24 1.00e+00 1.00e+00 5.24e+01 ... (remaining 72811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 29757 17.82 - 35.64: 1903 35.64 - 53.45: 434 53.45 - 71.27: 218 71.27 - 89.09: 28 Dihedral angle restraints: 32340 sinusoidal: 13188 harmonic: 19152 Sorted by residual: dihedral pdb=" CA LEU A 307 " pdb=" C LEU A 307 " pdb=" N VAL A 308 " pdb=" CA VAL A 308 " ideal model delta harmonic sigma weight residual 180.00 153.63 26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA LEU B 307 " pdb=" C LEU B 307 " pdb=" N VAL B 308 " pdb=" CA VAL B 308 " ideal model delta harmonic sigma weight residual 180.00 153.63 26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA LEU D 307 " pdb=" C LEU D 307 " pdb=" N VAL D 308 " pdb=" CA VAL D 308 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 32337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5341 0.079 - 0.159: 2328 0.159 - 0.238: 234 0.238 - 0.317: 12 0.317 - 0.397: 17 Chirality restraints: 7932 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 0.40 2.00e-01 2.50e+01 3.94e+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 2.33 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA PRO A 714 " pdb=" N PRO A 714 " pdb=" C PRO A 714 " pdb=" CB PRO A 714 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 7929 not shown) Planarity restraints: 9594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO A1302 " -0.071 2.00e-02 2.50e+03 5.86e-02 4.30e+01 pdb=" C5P ACO A1302 " 0.015 2.00e-02 2.50e+03 pdb=" C6P ACO A1302 " -0.052 2.00e-02 2.50e+03 pdb=" N4P ACO A1302 " 0.095 2.00e-02 2.50e+03 pdb=" O5P ACO A1302 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO E1302 " -0.068 2.00e-02 2.50e+03 5.62e-02 3.94e+01 pdb=" C5P ACO E1302 " 0.015 2.00e-02 2.50e+03 pdb=" C6P ACO E1302 " -0.050 2.00e-02 2.50e+03 pdb=" N4P ACO E1302 " 0.091 2.00e-02 2.50e+03 pdb=" O5P ACO E1302 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO F1302 " 0.062 2.00e-02 2.50e+03 5.14e-02 3.30e+01 pdb=" C5P ACO F1302 " -0.014 2.00e-02 2.50e+03 pdb=" C6P ACO F1302 " 0.046 2.00e-02 2.50e+03 pdb=" N4P ACO F1302 " -0.083 2.00e-02 2.50e+03 pdb=" O5P ACO F1302 " -0.011 2.00e-02 2.50e+03 ... (remaining 9591 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 876 2.68 - 3.23: 46711 3.23 - 3.79: 73647 3.79 - 4.34: 110563 4.34 - 4.90: 179278 Nonbonded interactions: 411075 Sorted by model distance: nonbonded pdb="MG MG A1301 " pdb=" O2B TPP A1303 " model vdw 2.125 2.170 nonbonded pdb="MG MG E1301 " pdb=" O2B TPP E1303 " model vdw 2.127 2.170 nonbonded pdb="MG MG F1301 " pdb=" O2B TPP F1303 " model vdw 2.136 2.170 nonbonded pdb="MG MG C1301 " pdb=" O2B TPP C1303 " model vdw 2.137 2.170 nonbonded pdb="MG MG B1301 " pdb=" O2B TPP B1303 " model vdw 2.140 2.170 ... (remaining 411070 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: 5.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 14.680 Check model and map are aligned: 0.770 Set scattering table: 0.520 Process input model: 131.040 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.370 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:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 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 : 0.011 0.103 53700 Z= 0.697 Angle : 1.215 15.071 72816 Z= 0.824 Chirality : 0.078 0.397 7932 Planarity : 0.008 0.104 9594 Dihedral : 13.922 89.090 20088 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.42 % Allowed : 2.58 % Favored : 97.01 % 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: -2.13 (0.08), residues: 6702 helix: -1.46 (0.08), residues: 2694 sheet: 0.12 (0.14), residues: 1098 loop : -1.88 (0.09), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.006 TRP C 466 HIS 0.015 0.004 HIS B 857 PHE 0.032 0.004 PHE E1046 TYR 0.056 0.006 TYR A 761 ARG 0.010 0.002 ARG E1144 *********************** 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 **************************** Evaluate side-chains 1312 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1289 time to evaluate : 6.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8833 (mmp) cc_final: 0.8535 (mmt) REVERT: A 290 GLU cc_start: 0.8715 (pm20) cc_final: 0.8441 (pm20) REVERT: A 296 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8581 (mm-30) REVERT: A 377 GLU cc_start: 0.8368 (tt0) cc_final: 0.8128 (tt0) REVERT: A 434 MET cc_start: 0.9067 (ttm) cc_final: 0.8737 (mtp) REVERT: A 760 MET cc_start: 0.9154 (ttt) cc_final: 0.8851 (ttp) REVERT: A 808 LYS cc_start: 0.8495 (mttt) cc_final: 0.8279 (mttt) REVERT: B 118 MET cc_start: 0.8859 (mmp) cc_final: 0.8551 (mmt) REVERT: B 290 GLU cc_start: 0.8728 (pm20) cc_final: 0.8471 (pm20) REVERT: B 296 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8576 (mm-30) REVERT: B 377 GLU cc_start: 0.8372 (tt0) cc_final: 0.8129 (tt0) REVERT: B 760 MET cc_start: 0.9157 (ttt) cc_final: 0.8861 (ttp) REVERT: B 808 LYS cc_start: 0.8493 (mttt) cc_final: 0.8278 (mttt) REVERT: C 404 HIS cc_start: 0.8845 (p90) cc_final: 0.8624 (p-80) REVERT: C 434 MET cc_start: 0.9060 (ttm) cc_final: 0.8777 (mtt) REVERT: D 118 MET cc_start: 0.8800 (mmp) cc_final: 0.8227 (mmt) REVERT: D 296 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8555 (mm-30) REVERT: D 800 MET cc_start: 0.8824 (mtm) cc_final: 0.8619 (mtp) REVERT: D 1122 GLU cc_start: 0.8775 (tp30) cc_final: 0.8535 (tp30) REVERT: D 1185 MET cc_start: 0.9149 (ttp) cc_final: 0.8801 (ttp) REVERT: E 113 SER cc_start: 0.8906 (m) cc_final: 0.8666 (p) REVERT: E 185 ASP cc_start: 0.8413 (t70) cc_final: 0.8187 (t0) REVERT: E 800 MET cc_start: 0.8825 (mtm) cc_final: 0.8614 (mtp) REVERT: E 1122 GLU cc_start: 0.8774 (tp30) cc_final: 0.8545 (tp30) REVERT: E 1185 MET cc_start: 0.9144 (ttp) cc_final: 0.8792 (ttp) REVERT: F 190 LEU cc_start: 0.9129 (tp) cc_final: 0.8922 (tp) REVERT: F 296 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8556 (mm-30) REVERT: F 404 HIS cc_start: 0.8856 (p90) cc_final: 0.8643 (p-80) REVERT: F 1027 GLN cc_start: 0.8734 (mt0) cc_final: 0.8445 (mt0) outliers start: 23 outliers final: 7 residues processed: 1300 average time/residue: 1.9557 time to fit residues: 3073.7716 Evaluate side-chains 1215 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1208 time to evaluate : 5.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 397 PRO Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain E residue 682 PHE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 397 PRO Chi-restraints excluded: chain F residue 682 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 562 optimal weight: 3.9990 chunk 504 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 340 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 522 optimal weight: 0.6980 chunk 202 optimal weight: 0.9980 chunk 317 optimal weight: 0.9990 chunk 388 optimal weight: 0.7980 chunk 604 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 195 HIS A 404 HIS A 501 GLN A 590 HIS A 773 GLN A 849 ASN B 195 HIS B 501 GLN B 590 HIS B 773 GLN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN B1096 ASN C 292 GLN C 359 GLN C 498 ASN C 501 GLN C 590 HIS C 799 GLN C 849 ASN C1072 ASN D 320 GLN D 404 HIS D 501 GLN D 799 GLN D 849 ASN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 ASN E 292 GLN E 320 GLN E 404 HIS E 501 GLN E 589 GLN E 799 GLN F 292 GLN F 501 GLN F 799 GLN F 849 ASN F1072 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 53700 Z= 0.183 Angle : 0.539 8.072 72816 Z= 0.284 Chirality : 0.043 0.145 7932 Planarity : 0.005 0.047 9594 Dihedral : 7.095 85.419 7648 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.02 % Allowed : 8.36 % Favored : 90.62 % 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: -0.38 (0.09), residues: 6702 helix: 0.63 (0.10), residues: 2694 sheet: 0.54 (0.15), residues: 1146 loop : -1.44 (0.10), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 466 HIS 0.005 0.001 HIS D1045 PHE 0.026 0.001 PHE E1046 TYR 0.014 0.001 TYR C 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 **************************** Evaluate side-chains 1269 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1213 time to evaluate : 5.025 Fit side-chains revert: symmetry clash REVERT: A 225 ASN cc_start: 0.8565 (p0) cc_final: 0.8362 (p0) REVERT: A 290 GLU cc_start: 0.8582 (pm20) cc_final: 0.8307 (pm20) REVERT: A 377 GLU cc_start: 0.8324 (tt0) cc_final: 0.8062 (tt0) REVERT: A 434 MET cc_start: 0.8927 (ttm) cc_final: 0.8642 (mtp) REVERT: A 760 MET cc_start: 0.9105 (ttt) cc_final: 0.8796 (ttt) REVERT: B 118 MET cc_start: 0.8873 (mmp) cc_final: 0.8511 (mmt) REVERT: B 225 ASN cc_start: 0.8722 (p0) cc_final: 0.8509 (p0) REVERT: B 290 GLU cc_start: 0.8592 (pm20) cc_final: 0.8367 (pm20) REVERT: B 377 GLU cc_start: 0.8322 (tt0) cc_final: 0.8087 (tt0) REVERT: B 434 MET cc_start: 0.8923 (ttm) cc_final: 0.8659 (mtp) REVERT: B 760 MET cc_start: 0.9105 (ttt) cc_final: 0.8806 (ttt) REVERT: B 801 GLU cc_start: 0.8915 (tp30) cc_final: 0.8708 (mm-30) REVERT: C 257 LEU cc_start: 0.9059 (tp) cc_final: 0.8755 (tp) REVERT: C 346 ASP cc_start: 0.8531 (t70) cc_final: 0.8324 (t0) REVERT: C 801 GLU cc_start: 0.8944 (tp30) cc_final: 0.8673 (mm-30) REVERT: D 118 MET cc_start: 0.8796 (mmp) cc_final: 0.8200 (mmt) REVERT: D 271 ARG cc_start: 0.8926 (mmm160) cc_final: 0.8706 (mtp180) REVERT: D 1027 GLN cc_start: 0.8481 (mt0) cc_final: 0.8275 (mt0) REVERT: D 1122 GLU cc_start: 0.8618 (tp30) cc_final: 0.8393 (tp30) REVERT: E 108 ARG cc_start: 0.9158 (mtm-85) cc_final: 0.8953 (ptp-110) REVERT: E 185 ASP cc_start: 0.8099 (t70) cc_final: 0.7842 (t0) REVERT: E 1027 GLN cc_start: 0.8539 (mt0) cc_final: 0.8337 (mt0) REVERT: E 1122 GLU cc_start: 0.8620 (tp30) cc_final: 0.8396 (tp30) REVERT: F 190 LEU cc_start: 0.9100 (tp) cc_final: 0.8883 (tp) REVERT: F 541 MET cc_start: 0.9025 (ptm) cc_final: 0.8803 (ptm) outliers start: 56 outliers final: 25 residues processed: 1233 average time/residue: 1.9043 time to fit residues: 2835.0436 Evaluate side-chains 1182 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1157 time to evaluate : 5.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 976 ASP Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 976 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 577 SER Chi-restraints excluded: chain F residue 976 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 336 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 503 optimal weight: 3.9990 chunk 411 optimal weight: 1.9990 chunk 166 optimal weight: 0.0470 chunk 605 optimal weight: 5.9990 chunk 654 optimal weight: 3.9990 chunk 539 optimal weight: 0.0870 chunk 600 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 486 optimal weight: 0.1980 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 359 GLN A 404 HIS A 799 GLN A 818 GLN A1072 ASN A1096 ASN A1213 GLN B 404 HIS B 799 GLN B 805 ASN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN B1096 ASN B1213 GLN C 404 HIS C 944 ASN C1072 ASN C1096 ASN D 225 ASN D 320 GLN D 404 HIS D 501 GLN D 773 GLN D 799 GLN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN E 320 GLN E 404 HIS E 501 GLN E 773 GLN E 799 GLN E1072 ASN F 225 ASN F 404 HIS F 773 GLN F 849 ASN F 944 ASN F1072 ASN F1096 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 53700 Z= 0.201 Angle : 0.505 8.981 72816 Z= 0.264 Chirality : 0.043 0.147 7932 Planarity : 0.005 0.042 9594 Dihedral : 6.653 78.045 7632 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.14 % Allowed : 10.97 % Favored : 87.89 % 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: 0.25 (0.10), residues: 6702 helix: 1.23 (0.10), residues: 2730 sheet: 0.84 (0.15), residues: 1092 loop : -1.15 (0.10), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 466 HIS 0.006 0.001 HIS C1045 PHE 0.026 0.001 PHE B1046 TYR 0.014 0.001 TYR F 761 ARG 0.010 0.000 ARG D 108 *********************** 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 **************************** Evaluate side-chains 1257 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1194 time to evaluate : 5.078 Fit side-chains REVERT: A 290 GLU cc_start: 0.8605 (pm20) cc_final: 0.8339 (pm20) REVERT: A 377 GLU cc_start: 0.8318 (tt0) cc_final: 0.8068 (tt0) REVERT: A 395 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8985 (p) REVERT: A 434 MET cc_start: 0.8884 (ttm) cc_final: 0.8575 (mtp) REVERT: A 760 MET cc_start: 0.9048 (ttt) cc_final: 0.8789 (ttt) REVERT: A 953 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8614 (ttm) REVERT: B 118 MET cc_start: 0.8842 (mmp) cc_final: 0.8606 (mmt) REVERT: B 290 GLU cc_start: 0.8608 (pm20) cc_final: 0.8318 (pm20) REVERT: B 377 GLU cc_start: 0.8321 (tt0) cc_final: 0.8071 (tt0) REVERT: B 395 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8988 (p) REVERT: B 434 MET cc_start: 0.8878 (ttm) cc_final: 0.8595 (mtp) REVERT: B 760 MET cc_start: 0.9054 (ttt) cc_final: 0.8794 (ttt) REVERT: B 953 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8625 (ttm) REVERT: C 346 ASP cc_start: 0.8574 (t70) cc_final: 0.8371 (t0) REVERT: C 801 GLU cc_start: 0.8956 (tp30) cc_final: 0.8694 (mm-30) REVERT: C 1069 MET cc_start: 0.8872 (ttp) cc_final: 0.8627 (ttp) REVERT: D 800 MET cc_start: 0.8599 (mtm) cc_final: 0.8388 (mtp) REVERT: E 1122 GLU cc_start: 0.8610 (tp30) cc_final: 0.8384 (tp30) REVERT: F 190 LEU cc_start: 0.9094 (tp) cc_final: 0.8866 (tp) REVERT: F 1069 MET cc_start: 0.8884 (ttp) cc_final: 0.8667 (ttp) outliers start: 63 outliers final: 23 residues processed: 1213 average time/residue: 1.6756 time to fit residues: 2443.7676 Evaluate side-chains 1203 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1176 time to evaluate : 4.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1072 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1209 LEU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 976 ASP Chi-restraints excluded: chain F residue 1209 LEU 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: 4.9990 chunk 314 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 406 optimal weight: 1.9990 chunk 608 optimal weight: 2.9990 chunk 643 optimal weight: 2.9990 chunk 317 optimal weight: 0.9980 chunk 576 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 799 GLN A1072 ASN A1096 ASN B 573 GLN B 799 GLN B 818 GLN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN B1096 ASN C 359 GLN C 404 HIS C 773 GLN C 944 ASN C1072 ASN C1096 ASN D 195 HIS D 225 ASN D 404 HIS D 799 GLN D 944 ASN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 ASN E 292 GLN E 320 GLN E 404 HIS E 799 GLN E 944 ASN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 944 ASN F1072 ASN F1096 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 53700 Z= 0.244 Angle : 0.516 9.547 72816 Z= 0.269 Chirality : 0.044 0.150 7932 Planarity : 0.005 0.048 9594 Dihedral : 6.536 75.053 7632 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.51 % Allowed : 11.77 % Favored : 86.72 % 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: 0.42 (0.10), residues: 6702 helix: 1.44 (0.10), residues: 2724 sheet: 0.86 (0.16), residues: 1092 loop : -1.11 (0.10), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 466 HIS 0.006 0.001 HIS F1045 PHE 0.027 0.002 PHE E1046 TYR 0.017 0.001 TYR C 761 ARG 0.012 0.000 ARG E 108 *********************** 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 **************************** Evaluate side-chains 1291 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1208 time to evaluate : 4.368 Fit side-chains REVERT: A 290 GLU cc_start: 0.8644 (pm20) cc_final: 0.8363 (pm20) REVERT: A 377 GLU cc_start: 0.8314 (tt0) cc_final: 0.8069 (tt0) REVERT: A 395 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.9001 (p) REVERT: A 434 MET cc_start: 0.8880 (ttm) cc_final: 0.8601 (mtp) REVERT: A 953 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8642 (ttm) REVERT: B 118 MET cc_start: 0.8825 (mmp) cc_final: 0.8587 (mmt) REVERT: B 290 GLU cc_start: 0.8636 (pm20) cc_final: 0.8351 (pm20) REVERT: B 377 GLU cc_start: 0.8324 (tt0) cc_final: 0.8079 (tt0) REVERT: B 434 MET cc_start: 0.8881 (ttm) cc_final: 0.8646 (mtp) REVERT: B 760 MET cc_start: 0.9014 (ttt) cc_final: 0.8807 (ttt) REVERT: B 953 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8643 (ttm) REVERT: B 1208 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: C 801 GLU cc_start: 0.8969 (tp30) cc_final: 0.8704 (mm-30) REVERT: C 1208 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8411 (mt0) REVERT: D 566 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8246 (tp30) REVERT: E 1122 GLU cc_start: 0.8630 (tp30) cc_final: 0.8401 (tp30) REVERT: F 190 LEU cc_start: 0.9106 (tp) cc_final: 0.8878 (tp) REVERT: F 1208 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8422 (mt0) outliers start: 83 outliers final: 37 residues processed: 1239 average time/residue: 1.5415 time to fit residues: 2306.3342 Evaluate side-chains 1238 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1195 time to evaluate : 4.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 880 TRP Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1072 ASN Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 880 TRP Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain B residue 1208 GLN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1197 SER Chi-restraints excluded: chain C residue 1208 GLN Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 806 GLU Chi-restraints excluded: chain D residue 837 ARG Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 976 ASP Chi-restraints excluded: chain F residue 1208 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 536 optimal weight: 3.9990 chunk 365 optimal weight: 0.0170 chunk 9 optimal weight: 5.9990 chunk 479 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 549 optimal weight: 0.0570 chunk 444 optimal weight: 0.0010 chunk 0 optimal weight: 5.9990 chunk 328 optimal weight: 0.1980 chunk 577 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 543 HIS A 799 GLN A1072 ASN A1096 ASN B 543 HIS B 786 ASN B 799 GLN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN B1096 ASN C 404 HIS C 944 ASN C1072 ASN C1096 ASN D 225 ASN D 320 GLN D 404 HIS D 799 GLN E 292 GLN E 320 GLN E 404 HIS E 799 GLN E1072 ASN F 206 GLN F 404 HIS F 799 GLN F 944 ASN F1072 ASN F1096 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 53700 Z= 0.114 Angle : 0.441 8.662 72816 Z= 0.226 Chirality : 0.041 0.152 7932 Planarity : 0.004 0.046 9594 Dihedral : 6.059 71.290 7632 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.98 % Allowed : 12.64 % Favored : 86.38 % 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: 0.81 (0.10), residues: 6702 helix: 1.84 (0.10), residues: 2688 sheet: 1.06 (0.16), residues: 1092 loop : -0.94 (0.10), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 466 HIS 0.003 0.000 HIS B1045 PHE 0.020 0.001 PHE C1046 TYR 0.010 0.001 TYR F 582 ARG 0.012 0.000 ARG E 108 *********************** 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 **************************** Evaluate side-chains 1313 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1259 time to evaluate : 3.942 Fit side-chains REVERT: A 290 GLU cc_start: 0.8563 (pm20) cc_final: 0.8304 (pm20) REVERT: A 377 GLU cc_start: 0.8290 (tt0) cc_final: 0.8028 (tt0) REVERT: B 290 GLU cc_start: 0.8551 (pm20) cc_final: 0.8298 (pm20) REVERT: B 377 GLU cc_start: 0.8288 (tt0) cc_final: 0.8024 (tt0) REVERT: C 801 GLU cc_start: 0.8913 (tp30) cc_final: 0.8682 (mm-30) REVERT: C 1027 GLN cc_start: 0.8096 (mt0) cc_final: 0.7885 (mt0) REVERT: C 1208 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8378 (mt0) REVERT: D 118 MET cc_start: 0.8771 (mmp) cc_final: 0.8197 (mmt) REVERT: F 190 LEU cc_start: 0.9066 (tp) cc_final: 0.8817 (tp) REVERT: F 508 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8879 (ttpp) REVERT: F 1069 MET cc_start: 0.8770 (ttp) cc_final: 0.8546 (ttp) REVERT: F 1208 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8380 (mt0) outliers start: 54 outliers final: 18 residues processed: 1275 average time/residue: 1.3765 time to fit residues: 2121.0403 Evaluate side-chains 1232 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1212 time to evaluate : 3.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1208 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 976 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 1208 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 216 optimal weight: 0.0980 chunk 579 optimal weight: 0.4980 chunk 127 optimal weight: 0.2980 chunk 377 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 644 optimal weight: 4.9990 chunk 534 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 338 optimal weight: 0.4980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS A 424 ASN A 583 HIS A 677 ASN A 799 GLN A1096 ASN B 404 HIS B 424 ASN B 543 HIS B 677 ASN B 799 GLN B1072 ASN B1096 ASN C 404 HIS C 424 ASN C 677 ASN C 818 GLN C 944 ASN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 ASN D 349 ASN D 404 HIS D 488 GLN D 677 ASN D 799 GLN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1096 ASN E 225 ASN E 292 GLN E 349 ASN E 404 HIS E 488 GLN E 799 GLN E 818 GLN E 944 ASN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN F 404 HIS F 424 ASN F 677 ASN F 818 GLN F 944 ASN F1045 HIS F1072 ASN F1096 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 53700 Z= 0.129 Angle : 0.446 9.578 72816 Z= 0.227 Chirality : 0.041 0.136 7932 Planarity : 0.004 0.046 9594 Dihedral : 5.966 71.299 7632 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.16 % Allowed : 12.95 % Favored : 85.89 % 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: 0.97 (0.10), residues: 6702 helix: 2.00 (0.10), residues: 2682 sheet: 1.12 (0.16), residues: 1038 loop : -0.83 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 466 HIS 0.003 0.001 HIS A1045 PHE 0.021 0.001 PHE F1046 TYR 0.012 0.001 TYR B 582 ARG 0.011 0.000 ARG E 108 *********************** 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 **************************** Evaluate side-chains 1273 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1209 time to evaluate : 4.060 Fit side-chains REVERT: A 290 GLU cc_start: 0.8577 (pm20) cc_final: 0.8316 (pm20) REVERT: A 377 GLU cc_start: 0.8286 (tt0) cc_final: 0.8024 (tt0) REVERT: B 290 GLU cc_start: 0.8569 (pm20) cc_final: 0.8318 (pm20) REVERT: B 377 GLU cc_start: 0.8291 (tt0) cc_final: 0.8026 (tt0) REVERT: B 1027 GLN cc_start: 0.8321 (mt0) cc_final: 0.8054 (mt0) REVERT: B 1208 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8395 (mt0) REVERT: C 801 GLU cc_start: 0.8907 (tp30) cc_final: 0.8684 (mm-30) REVERT: D 118 MET cc_start: 0.8781 (mmp) cc_final: 0.8199 (mmt) REVERT: F 190 LEU cc_start: 0.9071 (tp) cc_final: 0.8815 (tp) outliers start: 64 outliers final: 30 residues processed: 1230 average time/residue: 1.3393 time to fit residues: 2010.1935 Evaluate side-chains 1238 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1207 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1208 GLN Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 614 ASN Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 947 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 614 ASN Chi-restraints excluded: chain E residue 617 MET Chi-restraints excluded: chain E residue 947 LEU Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 494 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 621 optimal weight: 0.0270 chunk 72 optimal weight: 0.0010 chunk 367 optimal weight: 0.7980 chunk 470 optimal weight: 0.6980 chunk 364 optimal weight: 0.9980 chunk 542 optimal weight: 3.9990 chunk 359 optimal weight: 0.9990 chunk 641 optimal weight: 0.1980 chunk 401 optimal weight: 0.6980 chunk 391 optimal weight: 0.3980 chunk 296 optimal weight: 0.7980 overall best weight: 0.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS A 424 ASN A 543 HIS A 614 ASN B 404 HIS B 424 ASN B 543 HIS B 583 HIS B 614 ASN B 799 GLN B1072 ASN C 404 HIS C 424 ASN C 677 ASN C 944 ASN C1045 HIS C1072 ASN C1096 ASN D 404 HIS D 799 GLN D 818 GLN D 944 ASN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1096 ASN E 292 GLN E 404 HIS E 799 GLN E 944 ASN E1027 GLN F 404 HIS F 424 ASN F 543 HIS F 677 ASN F 944 ASN F1072 ASN F1096 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 53700 Z= 0.112 Angle : 0.429 9.470 72816 Z= 0.218 Chirality : 0.040 0.159 7932 Planarity : 0.004 0.050 9594 Dihedral : 5.782 71.105 7632 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.83 % Allowed : 13.60 % Favored : 85.56 % 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: 1.13 (0.10), residues: 6702 helix: 2.07 (0.10), residues: 2700 sheet: 1.25 (0.16), residues: 1038 loop : -0.70 (0.10), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 466 HIS 0.003 0.000 HIS C 583 PHE 0.020 0.001 PHE C1046 TYR 0.011 0.001 TYR A 582 ARG 0.012 0.000 ARG E 108 *********************** 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 **************************** Evaluate side-chains 1288 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1242 time to evaluate : 3.859 Fit side-chains REVERT: A 290 GLU cc_start: 0.8540 (pm20) cc_final: 0.8280 (pm20) REVERT: A 377 GLU cc_start: 0.8281 (tt0) cc_final: 0.8009 (tt0) REVERT: B 290 GLU cc_start: 0.8539 (pm20) cc_final: 0.8300 (pm20) REVERT: B 377 GLU cc_start: 0.8281 (tt0) cc_final: 0.8013 (tt0) REVERT: B 1208 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8371 (mt0) REVERT: C 355 MET cc_start: 0.9091 (mmp) cc_final: 0.8831 (mmp) REVERT: C 801 GLU cc_start: 0.8870 (tp30) cc_final: 0.8647 (mm-30) REVERT: D 118 MET cc_start: 0.8770 (mmp) cc_final: 0.8153 (mmt) REVERT: F 190 LEU cc_start: 0.9058 (tp) cc_final: 0.8810 (tp) outliers start: 46 outliers final: 24 residues processed: 1256 average time/residue: 1.3136 time to fit residues: 2001.3315 Evaluate side-chains 1235 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1210 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1208 GLN Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 947 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 947 LEU Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 947 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 397 optimal weight: 0.4980 chunk 256 optimal weight: 3.9990 chunk 383 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 408 optimal weight: 0.6980 chunk 437 optimal weight: 1.9990 chunk 317 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 504 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS A 424 ASN A 583 HIS B 404 HIS B 424 ASN B1096 ASN C 404 HIS C 424 ASN C 677 ASN C 944 ASN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 ASN C1096 ASN D 404 HIS D 488 GLN D 583 HIS D 799 GLN D 944 ASN ** D1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS E 488 GLN E 583 HIS E 677 ASN E 799 GLN E 944 ASN F 404 HIS F 424 ASN F 543 HIS F 677 ASN F 944 ASN F1072 ASN F1096 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 53700 Z= 0.163 Angle : 0.465 10.118 72816 Z= 0.239 Chirality : 0.042 0.157 7932 Planarity : 0.004 0.055 9594 Dihedral : 5.907 73.011 7632 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.03 % Allowed : 13.91 % Favored : 85.06 % 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: 1.09 (0.10), residues: 6702 helix: 2.00 (0.10), residues: 2730 sheet: 1.22 (0.16), residues: 1038 loop : -0.70 (0.11), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 466 HIS 0.004 0.001 HIS C 267 PHE 0.023 0.001 PHE C1046 TYR 0.012 0.001 TYR C 761 ARG 0.014 0.000 ARG E 108 *********************** 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 **************************** Evaluate side-chains 1287 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1230 time to evaluate : 3.758 Fit side-chains REVERT: A 290 GLU cc_start: 0.8606 (pm20) cc_final: 0.8354 (pm20) REVERT: A 377 GLU cc_start: 0.8303 (tt0) cc_final: 0.8037 (tt0) REVERT: B 290 GLU cc_start: 0.8604 (pm20) cc_final: 0.8321 (pm20) REVERT: B 377 GLU cc_start: 0.8300 (tt0) cc_final: 0.8037 (tt0) REVERT: B 1208 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8438 (mt0) REVERT: C 801 GLU cc_start: 0.8900 (tp30) cc_final: 0.8678 (mm-30) REVERT: C 1069 MET cc_start: 0.8746 (ttp) cc_final: 0.8535 (ttp) REVERT: F 190 LEU cc_start: 0.9087 (tp) cc_final: 0.8848 (tp) outliers start: 57 outliers final: 30 residues processed: 1242 average time/residue: 1.3257 time to fit residues: 1997.4171 Evaluate side-chains 1242 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1211 time to evaluate : 3.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1208 GLN Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 947 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 947 LEU Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 947 LEU Chi-restraints excluded: chain F residue 1197 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 583 optimal weight: 1.9990 chunk 614 optimal weight: 0.3980 chunk 561 optimal weight: 0.7980 chunk 598 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 469 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 540 optimal weight: 3.9990 chunk 565 optimal weight: 9.9990 chunk 596 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS A 424 ASN A 543 HIS A 573 GLN A 583 HIS A1027 GLN A1072 ASN B 404 HIS B 424 ASN B 543 HIS B 583 HIS B1072 ASN C 404 HIS C 424 ASN C 614 ASN C 677 ASN C 944 ASN C1072 ASN C1096 ASN D 404 HIS D 583 HIS D 799 GLN D 944 ASN D1072 ASN E 292 GLN E 404 HIS E 488 GLN E 583 HIS E 799 GLN E 944 ASN F 404 HIS F 424 ASN F 543 HIS F 614 ASN F 677 ASN F 944 ASN F1072 ASN F1096 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 53700 Z= 0.193 Angle : 0.484 10.165 72816 Z= 0.249 Chirality : 0.043 0.156 7932 Planarity : 0.004 0.060 9594 Dihedral : 5.975 74.334 7632 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.00 % Allowed : 14.09 % Favored : 84.91 % 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: 1.03 (0.10), residues: 6702 helix: 1.92 (0.10), residues: 2730 sheet: 1.18 (0.16), residues: 1032 loop : -0.71 (0.10), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 466 HIS 0.005 0.001 HIS E 643 PHE 0.024 0.001 PHE B1046 TYR 0.014 0.001 TYR F 761 ARG 0.015 0.000 ARG E 108 *********************** 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 **************************** Evaluate side-chains 1273 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1218 time to evaluate : 3.675 Fit side-chains REVERT: A 290 GLU cc_start: 0.8624 (pm20) cc_final: 0.8363 (pm20) REVERT: A 377 GLU cc_start: 0.8306 (tt0) cc_final: 0.8047 (tt0) REVERT: A 1208 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8471 (mt0) REVERT: B 290 GLU cc_start: 0.8612 (pm20) cc_final: 0.8322 (pm20) REVERT: B 377 GLU cc_start: 0.8304 (tt0) cc_final: 0.8044 (tt0) REVERT: B 1208 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8457 (mt0) REVERT: C 801 GLU cc_start: 0.8918 (tp30) cc_final: 0.8700 (mm-30) REVERT: C 1069 MET cc_start: 0.8792 (ttp) cc_final: 0.8573 (ttp) REVERT: F 190 LEU cc_start: 0.9099 (tp) cc_final: 0.8858 (tp) outliers start: 55 outliers final: 32 residues processed: 1234 average time/residue: 1.3296 time to fit residues: 1987.0110 Evaluate side-chains 1247 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1213 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1208 GLN Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 566 GLU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1197 SER Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 920 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 976 ASP Chi-restraints excluded: chain F residue 1197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 392 optimal weight: 0.6980 chunk 632 optimal weight: 0.9980 chunk 386 optimal weight: 0.7980 chunk 300 optimal weight: 3.9990 chunk 439 optimal weight: 0.9980 chunk 663 optimal weight: 0.0980 chunk 610 optimal weight: 2.9990 chunk 528 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 408 optimal weight: 0.7980 chunk 323 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS A 424 ASN A 543 HIS A 583 HIS ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 424 ASN B 543 HIS B 583 HIS ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN B1096 ASN C 404 HIS C 424 ASN C 543 HIS C 677 ASN C 944 ASN C1072 ASN C1096 ASN D 404 HIS D 799 GLN D 944 ASN E 292 GLN E 404 HIS E 799 GLN E 944 ASN F 404 HIS F 424 ASN F 543 HIS F 677 ASN F 944 ASN F1072 ASN F1096 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 53700 Z= 0.143 Angle : 0.458 10.024 72816 Z= 0.235 Chirality : 0.042 0.156 7932 Planarity : 0.004 0.063 9594 Dihedral : 5.857 73.911 7632 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.62 % Allowed : 14.56 % Favored : 84.82 % 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: 1.11 (0.10), residues: 6702 helix: 1.97 (0.10), residues: 2730 sheet: 1.22 (0.16), residues: 1038 loop : -0.65 (0.11), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 466 HIS 0.005 0.001 HIS E 583 PHE 0.022 0.001 PHE A1046 TYR 0.011 0.001 TYR B 582 ARG 0.015 0.000 ARG E 108 ********************** 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 **************************** Evaluate side-chains 1250 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1216 time to evaluate : 3.663 Fit side-chains REVERT: A 290 GLU cc_start: 0.8598 (pm20) cc_final: 0.8344 (pm20) REVERT: A 377 GLU cc_start: 0.8290 (tt0) cc_final: 0.8029 (tt0) REVERT: B 290 GLU cc_start: 0.8595 (pm20) cc_final: 0.8314 (pm20) REVERT: B 377 GLU cc_start: 0.8285 (tt0) cc_final: 0.8021 (tt0) REVERT: B 448 THR cc_start: 0.8666 (m) cc_final: 0.8283 (m) REVERT: B 1208 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8443 (mt0) REVERT: C 801 GLU cc_start: 0.8900 (tp30) cc_final: 0.8687 (mm-30) REVERT: C 1069 MET cc_start: 0.8752 (ttp) cc_final: 0.8536 (ttp) REVERT: F 190 LEU cc_start: 0.9077 (tp) cc_final: 0.8827 (tp) outliers start: 34 outliers final: 22 residues processed: 1227 average time/residue: 1.3067 time to fit residues: 1938.3748 Evaluate side-chains 1223 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1200 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1208 GLN Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 1197 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 920 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 682 PHE Chi-restraints excluded: chain F residue 1197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 419 optimal weight: 3.9990 chunk 562 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 487 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 529 optimal weight: 0.7980 chunk 221 optimal weight: 0.9990 chunk 543 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 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 195 HIS A 404 HIS A 424 ASN A 543 HIS A 583 HIS A1072 ASN B 404 HIS B 424 ASN B 543 HIS B 583 HIS B1072 ASN C 404 HIS C 424 ASN C 543 HIS C 677 ASN C 944 ASN C1072 ASN D 404 HIS D 799 GLN D 944 ASN E 292 GLN E 404 HIS E 944 ASN F 206 GLN F 404 HIS F 424 ASN F 543 HIS F 677 ASN F 944 ASN F1072 ASN F1096 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.113953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.103789 restraints weight = 69482.694| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.24 r_work: 0.3442 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 53700 Z= 0.168 Angle : 0.475 10.162 72816 Z= 0.243 Chirality : 0.042 0.155 7932 Planarity : 0.004 0.060 9594 Dihedral : 5.895 74.261 7632 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.62 % Allowed : 14.67 % 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: 1.07 (0.10), residues: 6702 helix: 1.94 (0.10), residues: 2730 sheet: 1.18 (0.16), residues: 1038 loop : -0.66 (0.11), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 466 HIS 0.004 0.001 HIS D 643 PHE 0.023 0.001 PHE B1046 TYR 0.012 0.001 TYR F 761 ARG 0.015 0.000 ARG E 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28968.96 seconds wall clock time: 495 minutes 52.67 seconds (29752.67 seconds total)