Starting phenix.real_space_refine on Tue Apr 16 19:12:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k35_36844/04_2024/8k35_36844_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k35_36844/04_2024/8k35_36844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k35_36844/04_2024/8k35_36844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k35_36844/04_2024/8k35_36844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k35_36844/04_2024/8k35_36844_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k35_36844/04_2024/8k35_36844_updated.pdb" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 174 5.16 5 C 25305 2.51 5 N 6996 2.21 5 O 7866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 13": "OE1" <-> "OE2" Residue "I PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 102": "NH1" <-> "NH2" Residue "I PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 341": "OD1" <-> "OD2" Residue "I ASP 380": "OD1" <-> "OD2" Residue "I ASP 381": "OD1" <-> "OD2" Residue "I GLU 411": "OE1" <-> "OE2" Residue "I ASP 434": "OD1" <-> "OD2" Residue "I ASP 463": "OD1" <-> "OD2" Residue "I ASP 484": "OD1" <-> "OD2" Residue "I TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ASP 54": "OD1" <-> "OD2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A ASP 463": "OD1" <-> "OD2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 508": "OD1" <-> "OD2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B ASP 381": "OD1" <-> "OD2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B ASP 483": "OD1" <-> "OD2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "B ASP 525": "OD1" <-> "OD2" Residue "B TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 812": "OE1" <-> "OE2" Residue "B TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 7": "OE1" <-> "OE2" Residue "J GLU 34": "OE1" <-> "OE2" Residue "J PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 128": "OE1" <-> "OE2" Residue "J ASP 180": "OD1" <-> "OD2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J ASP 191": "OD1" <-> "OD2" Residue "G GLU 34": "OE1" <-> "OE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "N GLU 7": "OE1" <-> "OE2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "N GLU 93": "OE1" <-> "OE2" Residue "N ASP 94": "OD1" <-> "OD2" Residue "N TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "O TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O GLU 54": "OE1" <-> "OE2" Residue "O GLU 78": "OE1" <-> "OE2" Residue "E ASP 27": "OD1" <-> "OD2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "F ASP 27": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "x GLU 212": "OE1" <-> "OE2" Residue "K ASP 180": "OD1" <-> "OD2" Residue "K TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 214": "OD1" <-> "OD2" Residue "Q ASP 180": "OD1" <-> "OD2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "L TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 56": "OD1" <-> "OD2" Residue "L PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 118": "OD1" <-> "OD2" Residue "R ASP 25": "OD1" <-> "OD2" Residue "R ASP 44": "OD1" <-> "OD2" Residue "R TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 62": "OD1" <-> "OD2" Residue "T ASP 44": "OD1" <-> "OD2" Residue "T ASP 56": "OD1" <-> "OD2" Residue "T TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 118": "OD1" <-> "OD2" Residue "U ASP 25": "OD1" <-> "OD2" Residue "U TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "U ASP 154": "OD1" <-> "OD2" Residue "V ASP 44": "OD1" <-> "OD2" Residue "V ASP 56": "OD1" <-> "OD2" Residue "V PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 118": "OD1" <-> "OD2" Residue "V PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 135": "OE1" <-> "OE2" Residue "W ASP 25": "OD1" <-> "OD2" Residue "W TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 56": "OD1" <-> "OD2" Residue "W ASP 61": "OD1" <-> "OD2" Residue "W ASP 62": "OD1" <-> "OD2" Residue "W ASP 66": "OD1" <-> "OD2" Residue "P ASP 836": "OD1" <-> "OD2" Residue "M ASP 836": "OD1" <-> "OD2" Residue "S ASP 836": "OD1" <-> "OD2" Residue "S ASP 844": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40353 Number of models: 1 Model: "" Number of chains: 27 Chain: "I" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6633 Classifications: {'peptide': 851} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 40, 'TRANS': 810} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6633 Classifications: {'peptide': 851} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 40, 'TRANS': 810} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6633 Classifications: {'peptide': 851} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 40, 'TRANS': 810} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "G" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "N" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "H" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "D" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "x" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 652 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "K" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 652 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "Q" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 652 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "L" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "R" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "T" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "U" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "V" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "W" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "P" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 241 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "M" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 241 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "S" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 241 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21326 SG CYS J 182 21.673 62.015 141.149 1.00 15.31 S ATOM 21497 SG CYS J 205 21.822 68.505 141.072 1.00 16.55 S ATOM 21248 SG CYS J 173 27.299 64.828 142.114 1.00 10.73 S ATOM 21542 SG CYS J 212 22.575 65.735 146.364 1.00 13.69 S ATOM 23127 SG CYS G 182 75.808 105.289 141.190 1.00 14.24 S ATOM 23298 SG CYS G 205 81.357 101.813 141.082 1.00 16.22 S ATOM 23049 SG CYS G 173 75.368 99.067 142.141 1.00 10.74 S ATOM 23343 SG CYS G 212 78.543 102.582 146.411 1.00 13.37 S ATOM 24928 SG CYS N 182 86.187 36.682 141.052 1.00 15.07 S ATOM 25099 SG CYS N 205 80.290 33.809 141.043 1.00 17.51 S ATOM 24850 SG CYS N 173 81.010 40.211 142.137 1.00 11.01 S ATOM 25144 SG CYS N 212 82.515 35.637 146.375 1.00 14.24 S Time building chain proxies: 21.11, per 1000 atoms: 0.52 Number of scatterers: 40353 At special positions: 0 Unit cell: (127.84, 129.2, 299.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 174 16.00 O 7866 8.00 N 6996 7.00 C 25305 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: 20.14 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 G 301 " pdb="FE2 SF4 G 301 " - pdb=" SG CYS G 205 " pdb="FE1 SF4 G 301 " - pdb=" SG CYS G 182 " pdb="FE4 SF4 G 301 " - pdb=" SG CYS G 212 " pdb="FE3 SF4 G 301 " - pdb=" SG CYS G 173 " pdb=" SF4 J 301 " pdb="FE2 SF4 J 301 " - pdb=" SG CYS J 205 " pdb="FE1 SF4 J 301 " - pdb=" SG CYS J 182 " pdb="FE4 SF4 J 301 " - pdb=" SG CYS J 212 " pdb="FE3 SF4 J 301 " - pdb=" SG CYS J 173 " pdb=" SF4 N 301 " pdb="FE2 SF4 N 301 " - pdb=" SG CYS N 205 " pdb="FE1 SF4 N 301 " - pdb=" SG CYS N 182 " pdb="FE4 SF4 N 301 " - pdb=" SG CYS N 212 " pdb="FE3 SF4 N 301 " - pdb=" SG CYS N 173 " Number of angles added : 36 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9480 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 79 sheets defined 13.8% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.55 Creating SS restraints... Processing helix chain 'I' and resid 41 through 44 Processing helix chain 'I' and resid 272 through 280 Processing helix chain 'I' and resid 298 through 309 removed outlier: 3.675A pdb=" N VAL I 303 " --> pdb=" O TRP I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 345 removed outlier: 3.532A pdb=" N SER I 344 " --> pdb=" O SER I 340 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA I 345 " --> pdb=" O ASP I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 420 through 426 removed outlier: 3.580A pdb=" N ALA I 424 " --> pdb=" O THR I 420 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG I 425 " --> pdb=" O GLN I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 457 removed outlier: 3.692A pdb=" N LEU I 451 " --> pdb=" O ALA I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 470 through 472 No H-bonds generated for 'chain 'I' and resid 470 through 472' Processing helix chain 'I' and resid 484 through 487 No H-bonds generated for 'chain 'I' and resid 484 through 487' Processing helix chain 'I' and resid 593 through 600 removed outlier: 3.741A pdb=" N GLU I 596 " --> pdb=" O PRO I 593 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA I 597 " --> pdb=" O GLU I 594 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP I 600 " --> pdb=" O ALA I 597 " (cutoff:3.500A) Processing helix chain 'I' and resid 756 through 762 removed outlier: 3.852A pdb=" N GLU I 760 " --> pdb=" O ARG I 757 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER I 762 " --> pdb=" O VAL I 759 " (cutoff:3.500A) Processing helix chain 'I' and resid 811 through 818 removed outlier: 3.960A pdb=" N PHE I 817 " --> pdb=" O GLY I 813 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE I 818 " --> pdb=" O TYR I 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 824 through 826 No H-bonds generated for 'chain 'I' and resid 824 through 826' Processing helix chain 'I' and resid 829 through 850 removed outlier: 4.424A pdb=" N LYS I 834 " --> pdb=" O GLU I 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 272 through 280 Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.910A pdb=" N VAL A 303 " --> pdb=" O TRP A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.531A pdb=" N SER A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.583A pdb=" N ALA A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 457 removed outlier: 3.735A pdb=" N LEU A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.861A pdb=" N GLU A 596 " --> pdb=" O PRO A 593 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 597 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 762 removed outlier: 3.779A pdb=" N GLU A 760 " --> pdb=" O ARG A 757 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A 762 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 818 removed outlier: 4.082A pdb=" N PHE A 817 " --> pdb=" O GLY A 813 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE A 818 " --> pdb=" O TYR A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 826 No H-bonds generated for 'chain 'A' and resid 824 through 826' Processing helix chain 'A' and resid 829 through 850 removed outlier: 4.313A pdb=" N LYS A 834 " --> pdb=" O GLU A 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 272 through 280 Processing helix chain 'B' and resid 298 through 309 removed outlier: 3.863A pdb=" N VAL B 303 " --> pdb=" O TRP B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 345 removed outlier: 3.588A pdb=" N SER B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.514A pdb=" N ALA B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 457 removed outlier: 3.730A pdb=" N LEU B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'B' and resid 484 through 487 No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 593 through 600 removed outlier: 3.775A pdb=" N GLU B 596 " --> pdb=" O PRO B 593 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 597 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 600 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 762 removed outlier: 3.848A pdb=" N GLU B 760 " --> pdb=" O ARG B 757 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 762 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 818 removed outlier: 4.203A pdb=" N PHE B 817 " --> pdb=" O GLY B 813 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE B 818 " --> pdb=" O TYR B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 826 No H-bonds generated for 'chain 'B' and resid 824 through 826' Processing helix chain 'B' and resid 829 through 850 removed outlier: 4.431A pdb=" N LYS B 834 " --> pdb=" O GLU B 830 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 13 Processing helix chain 'J' and resid 87 through 94 removed outlier: 3.542A pdb=" N ASP J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 98 No H-bonds generated for 'chain 'J' and resid 96 through 98' Processing helix chain 'J' and resid 110 through 112 No H-bonds generated for 'chain 'J' and resid 110 through 112' Processing helix chain 'J' and resid 209 through 215 removed outlier: 4.026A pdb=" N ARG J 215 " --> pdb=" O GLY J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 220 No H-bonds generated for 'chain 'J' and resid 218 through 220' Processing helix chain 'J' and resid 227 through 231 Processing helix chain 'G' and resid 6 through 13 Processing helix chain 'G' and resid 87 through 94 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 209 through 215 removed outlier: 4.053A pdb=" N ARG G 215 " --> pdb=" O GLY G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 220 No H-bonds generated for 'chain 'G' and resid 218 through 220' Processing helix chain 'G' and resid 227 through 231 Processing helix chain 'N' and resid 6 through 13 Processing helix chain 'N' and resid 87 through 94 removed outlier: 3.552A pdb=" N ASP N 94 " --> pdb=" O GLY N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 98 No H-bonds generated for 'chain 'N' and resid 96 through 98' Processing helix chain 'N' and resid 110 through 112 No H-bonds generated for 'chain 'N' and resid 110 through 112' Processing helix chain 'N' and resid 209 through 215 removed outlier: 4.025A pdb=" N ARG N 215 " --> pdb=" O GLY N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 220 No H-bonds generated for 'chain 'N' and resid 218 through 220' Processing helix chain 'N' and resid 227 through 231 Processing helix chain 'H' and resid 52 through 64 removed outlier: 4.356A pdb=" N THR H 56 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 65 removed outlier: 3.926A pdb=" N THR O 56 " --> pdb=" O GLU O 53 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL O 57 " --> pdb=" O GLU O 54 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU O 64 " --> pdb=" O PHE O 61 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS O 65 " --> pdb=" O LEU O 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 64 removed outlier: 4.334A pdb=" N THR C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 65 removed outlier: 3.774A pdb=" N THR E 56 " --> pdb=" O GLU E 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 57 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU E 64 " --> pdb=" O PHE E 61 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS E 65 " --> pdb=" O LEU E 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 64 removed outlier: 4.216A pdb=" N THR D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 65 removed outlier: 3.813A pdb=" N THR F 56 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL F 57 " --> pdb=" O GLU F 54 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU F 64 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS F 65 " --> pdb=" O LEU F 62 " (cutoff:3.500A) Processing helix chain 'x' and resid 143 through 146 No H-bonds generated for 'chain 'x' and resid 143 through 146' Processing helix chain 'x' and resid 151 through 155 removed outlier: 3.630A pdb=" N LEU x 155 " --> pdb=" O VAL x 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 151 through 155' Processing helix chain 'x' and resid 166 through 168 No H-bonds generated for 'chain 'x' and resid 166 through 168' Processing helix chain 'K' and resid 143 through 148 removed outlier: 3.778A pdb=" N LEU K 148 " --> pdb=" O ALA K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 155 removed outlier: 3.570A pdb=" N LEU K 155 " --> pdb=" O VAL K 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 151 through 155' Processing helix chain 'K' and resid 166 through 168 No H-bonds generated for 'chain 'K' and resid 166 through 168' Processing helix chain 'Q' and resid 143 through 148 removed outlier: 3.559A pdb=" N LEU Q 148 " --> pdb=" O ALA Q 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 151 through 155 removed outlier: 3.800A pdb=" N LEU Q 155 " --> pdb=" O VAL Q 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 151 through 155' Processing helix chain 'Q' and resid 166 through 168 No H-bonds generated for 'chain 'Q' and resid 166 through 168' Processing helix chain 'L' and resid 91 through 101 Processing helix chain 'L' and resid 152 through 154 No H-bonds generated for 'chain 'L' and resid 152 through 154' Processing helix chain 'R' and resid 91 through 101 Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'T' and resid 91 through 101 Processing helix chain 'T' and resid 152 through 154 No H-bonds generated for 'chain 'T' and resid 152 through 154' Processing helix chain 'U' and resid 91 through 101 Processing helix chain 'V' and resid 91 through 101 Processing helix chain 'W' and resid 91 through 101 Processing helix chain 'P' and resid 820 through 842 Processing helix chain 'M' and resid 820 through 842 Processing helix chain 'S' and resid 820 through 842 Processing sheet with id= A, first strand: chain 'I' and resid 5 through 9 removed outlier: 7.063A pdb=" N VAL I 218 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ALA I 29 " --> pdb=" O VAL I 218 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL I 220 " --> pdb=" O ILE I 27 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE I 27 " --> pdb=" O VAL I 220 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL I 222 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N SER I 25 " --> pdb=" O VAL I 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 100 through 103 removed outlier: 5.206A pdb=" N ASN I 178 " --> pdb=" O GLN I 142 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER I 133 " --> pdb=" O GLY I 157 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS I 151 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE I 141 " --> pdb=" O THR I 149 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR I 149 " --> pdb=" O ILE I 141 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG I 143 " --> pdb=" O TRP I 147 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TRP I 147 " --> pdb=" O ARG I 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'I' and resid 163 through 168 removed outlier: 6.998A pdb=" N GLY I 117 " --> pdb=" O TRP I 199 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TRP I 199 " --> pdb=" O GLY I 117 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR I 202 " --> pdb=" O THR I 88 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER I 84 " --> pdb=" O ILE I 206 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 243 through 246 Processing sheet with id= E, first strand: chain 'I' and resid 311 through 313 Processing sheet with id= F, first strand: chain 'I' and resid 348 through 352 Processing sheet with id= G, first strand: chain 'I' and resid 386 through 389 removed outlier: 6.484A pdb=" N GLN I 460 " --> pdb=" O GLN I 590 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER I 575 " --> pdb=" O THR I 587 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL I 589 " --> pdb=" O CYS I 573 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS I 573 " --> pdb=" O VAL I 589 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 412 through 418 Processing sheet with id= I, first strand: chain 'I' and resid 492 through 494 removed outlier: 6.857A pdb=" N VAL I 558 " --> pdb=" O VAL I 524 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL I 524 " --> pdb=" O VAL I 558 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 497 through 499 removed outlier: 3.666A pdb=" N ALA I 497 " --> pdb=" O THR I 506 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'I' and resid 625 through 629 Processing sheet with id= L, first strand: chain 'I' and resid 705 through 710 removed outlier: 3.506A pdb=" N PHE I 709 " --> pdb=" O TYR I 688 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN I 687 " --> pdb=" O THR I 659 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR I 659 " --> pdb=" O ASN I 687 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER I 669 " --> pdb=" O LEU I 656 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL I 658 " --> pdb=" O LEU I 667 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU I 667 " --> pdb=" O VAL I 658 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 719 through 724 removed outlier: 3.813A pdb=" N ARG I 719 " --> pdb=" O HIS I 734 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR I 730 " --> pdb=" O THR I 723 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 801 through 805 removed outlier: 3.707A pdb=" N PHE I 744 " --> pdb=" O ALA I 769 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY I 767 " --> pdb=" O PHE I 746 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE I 748 " --> pdb=" O TYR I 765 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR I 765 " --> pdb=" O PHE I 748 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 5 through 9 removed outlier: 3.507A pdb=" N PHE A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A 218 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA A 29 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL A 220 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ILE A 27 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL A 222 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N SER A 25 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.597A pdb=" N SER A 133 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 151 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 141 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR A 149 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 163 through 169 removed outlier: 3.641A pdb=" N LEU A 112 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 201 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY A 117 " --> pdb=" O TRP A 199 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TRP A 199 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 202 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 84 " --> pdb=" O ILE A 206 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= S, first strand: chain 'A' and resid 311 through 313 Processing sheet with id= T, first strand: chain 'A' and resid 348 through 352 Processing sheet with id= U, first strand: chain 'A' and resid 386 through 389 removed outlier: 6.567A pdb=" N GLN A 460 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 575 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL A 589 " --> pdb=" O CYS A 573 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N CYS A 573 " --> pdb=" O VAL A 589 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 412 through 418 Processing sheet with id= W, first strand: chain 'A' and resid 492 through 494 removed outlier: 7.086A pdb=" N VAL A 558 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 524 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 497 through 499 removed outlier: 3.590A pdb=" N ALA A 497 " --> pdb=" O THR A 506 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 625 through 629 Processing sheet with id= Z, first strand: chain 'A' and resid 705 through 707 removed outlier: 3.649A pdb=" N SER A 669 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL A 658 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU A 667 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 719 through 724 removed outlier: 3.746A pdb=" N ARG A 719 " --> pdb=" O HIS A 734 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 721 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 730 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 801 through 805 removed outlier: 3.545A pdb=" N PHE A 744 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY A 767 " --> pdb=" O PHE A 746 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N PHE A 748 " --> pdb=" O TYR A 765 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR A 765 " --> pdb=" O PHE A 748 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 5 through 9 removed outlier: 6.954A pdb=" N VAL B 218 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ALA B 29 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B 220 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE B 27 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL B 222 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N SER B 25 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 45 through 47 Processing sheet with id= AE, first strand: chain 'B' and resid 100 through 103 removed outlier: 3.575A pdb=" N SER B 133 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 139 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 151 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE B 141 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR B 149 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.956A pdb=" N GLY B 117 " --> pdb=" O TRP B 199 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP B 199 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 202 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 84 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= AH, first strand: chain 'B' and resid 311 through 313 Processing sheet with id= AI, first strand: chain 'B' and resid 348 through 352 Processing sheet with id= AJ, first strand: chain 'B' and resid 386 through 389 removed outlier: 6.524A pdb=" N GLN B 460 " --> pdb=" O GLN B 590 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 575 " --> pdb=" O THR B 587 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL B 589 " --> pdb=" O CYS B 573 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS B 573 " --> pdb=" O VAL B 589 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'B' and resid 412 through 418 Processing sheet with id= AL, first strand: chain 'B' and resid 492 through 494 removed outlier: 7.055A pdb=" N VAL B 558 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 524 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 497 through 499 removed outlier: 3.718A pdb=" N ALA B 497 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 625 through 629 Processing sheet with id= AO, first strand: chain 'B' and resid 705 through 710 removed outlier: 3.519A pdb=" N PHE B 709 " --> pdb=" O TYR B 688 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN B 687 " --> pdb=" O THR B 659 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 659 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B 669 " --> pdb=" O LEU B 656 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL B 658 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU B 667 " --> pdb=" O VAL B 658 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'B' and resid 719 through 724 removed outlier: 3.752A pdb=" N ARG B 719 " --> pdb=" O HIS B 734 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 730 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 729 " --> pdb=" O ALA B 774 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'B' and resid 801 through 805 removed outlier: 3.502A pdb=" N PHE B 744 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 767 " --> pdb=" O PHE B 746 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE B 748 " --> pdb=" O TYR B 765 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TYR B 765 " --> pdb=" O PHE B 748 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'J' and resid 36 through 39 removed outlier: 6.748A pdb=" N VAL J 151 " --> pdb=" O GLU J 138 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N CYS J 140 " --> pdb=" O SER J 149 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER J 149 " --> pdb=" O CYS J 140 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'G' and resid 36 through 39 removed outlier: 6.797A pdb=" N VAL G 151 " --> pdb=" O GLU G 138 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS G 140 " --> pdb=" O SER G 149 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER G 149 " --> pdb=" O CYS G 140 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'N' and resid 36 through 39 removed outlier: 6.733A pdb=" N VAL N 151 " --> pdb=" O GLU N 138 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N CYS N 140 " --> pdb=" O SER N 149 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER N 149 " --> pdb=" O CYS N 140 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.651A pdb=" N ALA H 15 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 20 through 24 Processing sheet with id= AW, first strand: chain 'H' and resid 89 through 93 Processing sheet with id= AX, first strand: chain 'O' and resid 13 through 15 removed outlier: 3.507A pdb=" N ALA O 102 " --> pdb=" O VAL O 46 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'O' and resid 20 through 23 Processing sheet with id= AZ, first strand: chain 'O' and resid 89 through 93 Processing sheet with id= BA, first strand: chain 'C' and resid 13 through 15 removed outlier: 3.546A pdb=" N ALA C 15 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'C' and resid 20 through 24 Processing sheet with id= BC, first strand: chain 'C' and resid 89 through 93 Processing sheet with id= BD, first strand: chain 'E' and resid 13 through 15 Processing sheet with id= BE, first strand: chain 'E' and resid 20 through 23 Processing sheet with id= BF, first strand: chain 'E' and resid 89 through 93 Processing sheet with id= BG, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.678A pdb=" N ALA D 15 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'D' and resid 20 through 24 Processing sheet with id= BI, first strand: chain 'D' and resid 89 through 93 Processing sheet with id= BJ, first strand: chain 'F' and resid 13 through 15 Processing sheet with id= BK, first strand: chain 'F' and resid 20 through 23 Processing sheet with id= BL, first strand: chain 'F' and resid 89 through 93 Processing sheet with id= BM, first strand: chain 'L' and resid 36 through 39 removed outlier: 4.570A pdb=" N LEU L 17 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALA L 107 " --> pdb=" O TYR L 20 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS L 142 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE L 127 " --> pdb=" O THR L 140 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR L 140 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS L 129 " --> pdb=" O THR L 138 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR L 138 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA L 85 " --> pdb=" O VAL L 42 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL L 42 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'L' and resid 50 through 52 Processing sheet with id= BO, first strand: chain 'L' and resid 54 through 56 Processing sheet with id= BP, first strand: chain 'R' and resid 36 through 39 removed outlier: 4.592A pdb=" N LEU R 17 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'R' and resid 54 through 56 Processing sheet with id= BR, first strand: chain 'R' and resid 42 through 46 removed outlier: 6.505A pdb=" N THR R 83 " --> pdb=" O LYS R 43 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU R 45 " --> pdb=" O SER R 81 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER R 81 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N THR R 144 " --> pdb=" O VAL R 124 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL R 124 " --> pdb=" O THR R 144 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'T' and resid 36 through 39 removed outlier: 4.548A pdb=" N LEU T 17 " --> pdb=" O LEU T 39 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ALA T 107 " --> pdb=" O TYR T 20 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS T 142 " --> pdb=" O SER T 125 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE T 127 " --> pdb=" O THR T 140 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR T 140 " --> pdb=" O ILE T 127 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS T 129 " --> pdb=" O THR T 138 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR T 138 " --> pdb=" O LYS T 129 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA T 85 " --> pdb=" O VAL T 42 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL T 42 " --> pdb=" O ALA T 85 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'T' and resid 54 through 56 Processing sheet with id= BU, first strand: chain 'U' and resid 36 through 39 removed outlier: 4.663A pdb=" N LEU U 17 " --> pdb=" O LEU U 39 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA U 107 " --> pdb=" O TYR U 20 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR U 108 " --> pdb=" O PHE U 120 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS U 142 " --> pdb=" O SER U 125 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE U 127 " --> pdb=" O THR U 140 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR U 140 " --> pdb=" O ILE U 127 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS U 129 " --> pdb=" O THR U 138 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR U 138 " --> pdb=" O LYS U 129 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA U 85 " --> pdb=" O VAL U 42 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL U 42 " --> pdb=" O ALA U 85 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'U' and resid 54 through 56 Processing sheet with id= BW, first strand: chain 'V' and resid 36 through 39 removed outlier: 4.597A pdb=" N LEU V 17 " --> pdb=" O LEU V 39 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA V 107 " --> pdb=" O TYR V 20 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS V 142 " --> pdb=" O SER V 125 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE V 127 " --> pdb=" O THR V 140 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR V 140 " --> pdb=" O ILE V 127 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS V 129 " --> pdb=" O THR V 138 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR V 138 " --> pdb=" O LYS V 129 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA V 85 " --> pdb=" O VAL V 42 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL V 42 " --> pdb=" O ALA V 85 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'V' and resid 50 through 52 Processing sheet with id= BY, first strand: chain 'V' and resid 54 through 56 Processing sheet with id= BZ, first strand: chain 'W' and resid 36 through 39 removed outlier: 4.680A pdb=" N LEU W 17 " --> pdb=" O LEU W 39 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ALA W 107 " --> pdb=" O TYR W 20 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS W 142 " --> pdb=" O SER W 125 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE W 127 " --> pdb=" O THR W 140 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR W 140 " --> pdb=" O ILE W 127 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS W 129 " --> pdb=" O THR W 138 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR W 138 " --> pdb=" O LYS W 129 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA W 85 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL W 42 " --> pdb=" O ALA W 85 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'W' and resid 54 through 56 1171 hydrogen bonds defined for protein. 3138 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: 19.51 Time building geometry restraints manager: 21.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 17045 1.41 - 1.63: 23896 1.63 - 1.84: 267 1.84 - 2.06: 0 2.06 - 2.28: 36 Bond restraints: 41244 Sorted by residual: bond pdb=" CA TYR A 486 " pdb=" C TYR A 486 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.26e-02 6.30e+03 1.77e+01 bond pdb=" C LEU A 172 " pdb=" N PRO A 173 " ideal model delta sigma weight residual 1.329 1.374 -0.044 1.18e-02 7.18e+03 1.42e+01 bond pdb=" C LEU B 172 " pdb=" N PRO B 173 " ideal model delta sigma weight residual 1.329 1.373 -0.044 1.18e-02 7.18e+03 1.39e+01 bond pdb=" C MET G 91 " pdb=" O MET G 91 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.26e-02 6.30e+03 1.19e+01 bond pdb=" CA GLY T 73 " pdb=" C GLY T 73 " ideal model delta sigma weight residual 1.513 1.477 0.036 1.06e-02 8.90e+03 1.17e+01 ... (remaining 41239 not shown) Histogram of bond angle deviations from ideal: 73.66 - 85.76: 36 85.76 - 97.85: 0 97.85 - 109.95: 6567 109.95 - 122.05: 40335 122.05 - 134.14: 9117 Bond angle restraints: 56055 Sorted by residual: angle pdb=" N ALA G 92 " pdb=" CA ALA G 92 " pdb=" C ALA G 92 " ideal model delta sigma weight residual 111.36 117.87 -6.51 1.09e+00 8.42e-01 3.56e+01 angle pdb=" N LEU B 172 " pdb=" CA LEU B 172 " pdb=" C LEU B 172 " ideal model delta sigma weight residual 109.57 116.65 -7.08 1.23e+00 6.61e-01 3.31e+01 angle pdb=" N TYR T 55 " pdb=" CA TYR T 55 " pdb=" C TYR T 55 " ideal model delta sigma weight residual 110.14 102.87 7.27 1.55e+00 4.16e-01 2.20e+01 angle pdb=" N LEU A 172 " pdb=" CA LEU A 172 " pdb=" C LEU A 172 " ideal model delta sigma weight residual 109.57 115.28 -5.71 1.23e+00 6.61e-01 2.16e+01 angle pdb=" N ASP J 94 " pdb=" CA ASP J 94 " pdb=" C ASP J 94 " ideal model delta sigma weight residual 111.40 116.54 -5.14 1.22e+00 6.72e-01 1.78e+01 ... (remaining 56050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 22605 18.04 - 36.08: 1585 36.08 - 54.12: 248 54.12 - 72.16: 29 72.16 - 90.20: 31 Dihedral angle restraints: 24498 sinusoidal: 9687 harmonic: 14811 Sorted by residual: dihedral pdb=" CA PRO G 164 " pdb=" C PRO G 164 " pdb=" N GLY G 165 " pdb=" CA GLY G 165 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA LEU A 47 " pdb=" C LEU A 47 " pdb=" N ASN A 48 " pdb=" CA ASN A 48 " ideal model delta harmonic sigma weight residual -180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA LEU U 39 " pdb=" C LEU U 39 " pdb=" N ALA U 40 " pdb=" CA ALA U 40 " ideal model delta harmonic sigma weight residual 180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 24495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 5620 0.081 - 0.161: 556 0.161 - 0.242: 10 0.242 - 0.323: 0 0.323 - 0.404: 3 Chirality restraints: 6189 Sorted by residual: chirality pdb=" CA ALA G 92 " pdb=" N ALA G 92 " pdb=" C ALA G 92 " pdb=" CB ALA G 92 " both_signs ideal model delta sigma weight residual False 2.48 2.08 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ALA J 92 " pdb=" N ALA J 92 " pdb=" C ALA J 92 " pdb=" CB ALA J 92 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA ALA N 92 " pdb=" N ALA N 92 " pdb=" C ALA N 92 " pdb=" CB ALA N 92 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 6186 not shown) Planarity restraints: 7290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 172 " -0.032 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO B 173 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 282 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO I 283 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO I 283 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 283 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA T 52 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C ALA T 52 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA T 52 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU T 53 " 0.010 2.00e-02 2.50e+03 ... (remaining 7287 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 300 2.64 - 3.21: 34297 3.21 - 3.77: 55150 3.77 - 4.34: 80228 4.34 - 4.90: 138954 Nonbonded interactions: 308929 Sorted by model distance: nonbonded pdb=" OD1 ASP I 54 " pdb=" N THR I 55 " model vdw 2.079 2.520 nonbonded pdb=" OH TYR V 108 " pdb=" OD1 ASN V 145 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR W 108 " pdb=" OD1 ASN W 145 " model vdw 2.230 2.440 nonbonded pdb=" OH TYR L 108 " pdb=" OD1 ASN L 145 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR U 108 " pdb=" OD1 ASN U 145 " model vdw 2.236 2.440 ... (remaining 308924 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 'I' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'Q' selection = chain 'x' } ncs_group { reference = chain 'L' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 4.580 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 120.830 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 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 : 0.004 0.053 41244 Z= 0.267 Angle : 0.604 8.568 56055 Z= 0.350 Chirality : 0.044 0.404 6189 Planarity : 0.004 0.051 7290 Dihedral : 12.729 90.200 15018 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.11), residues: 5136 helix: 0.36 (0.21), residues: 636 sheet: -0.07 (0.12), residues: 1836 loop : -1.38 (0.10), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 175 HIS 0.005 0.001 HIS A 282 PHE 0.019 0.001 PHE B 116 TYR 0.023 0.001 TYR I 249 ARG 0.007 0.000 ARG V 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 5.120 Fit side-chains REVERT: I 685 LEU cc_start: 0.8572 (tp) cc_final: 0.8278 (tt) REVERT: A 202 TYR cc_start: 0.9070 (p90) cc_final: 0.8809 (p90) REVERT: B 259 ILE cc_start: 0.8826 (mm) cc_final: 0.8602 (mm) REVERT: G 180 ASP cc_start: 0.8055 (t70) cc_final: 0.7728 (t0) REVERT: O 22 LYS cc_start: 0.8771 (ptmt) cc_final: 0.8447 (pttt) REVERT: D 95 MET cc_start: 0.8467 (mmm) cc_final: 0.8152 (mmt) REVERT: F 22 LYS cc_start: 0.8776 (ptmt) cc_final: 0.8465 (pttt) REVERT: x 153 GLN cc_start: 0.7455 (mt0) cc_final: 0.7132 (pt0) REVERT: x 178 SER cc_start: 0.8884 (t) cc_final: 0.8683 (t) REVERT: T 87 MET cc_start: 0.8851 (mtm) cc_final: 0.8647 (mtp) REVERT: W 38 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8662 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.5737 time to fit residues: 468.2533 Evaluate side-chains 444 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 428 optimal weight: 7.9990 chunk 384 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 205 optimal weight: 0.0870 chunk 397 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 241 optimal weight: 4.9990 chunk 295 optimal weight: 5.9990 chunk 460 optimal weight: 5.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 734 HIS B 499 ASN B 734 HIS C 109 ASN Q 165 GLN R 29 ASN T 29 ASN V 101 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41244 Z= 0.280 Angle : 0.534 7.885 56055 Z= 0.283 Chirality : 0.044 0.167 6189 Planarity : 0.004 0.050 7290 Dihedral : 4.587 19.969 5640 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.87 % Allowed : 5.44 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.11), residues: 5136 helix: 0.22 (0.21), residues: 642 sheet: -0.05 (0.12), residues: 1872 loop : -1.31 (0.11), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 73 HIS 0.004 0.001 HIS A 282 PHE 0.018 0.002 PHE A 748 TYR 0.023 0.001 TYR I 249 ARG 0.008 0.000 ARG U 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 464 time to evaluate : 4.572 Fit side-chains REVERT: I 685 LEU cc_start: 0.8674 (tp) cc_final: 0.8366 (tt) REVERT: A 202 TYR cc_start: 0.8944 (p90) cc_final: 0.8701 (p90) REVERT: B 97 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: B 259 ILE cc_start: 0.8893 (mm) cc_final: 0.8663 (mm) REVERT: G 180 ASP cc_start: 0.8094 (t70) cc_final: 0.7768 (t0) REVERT: H 95 MET cc_start: 0.8777 (mmm) cc_final: 0.8351 (mmp) REVERT: O 22 LYS cc_start: 0.8786 (ptmt) cc_final: 0.8490 (pttt) REVERT: F 22 LYS cc_start: 0.8823 (ptmt) cc_final: 0.8502 (pttt) REVERT: x 153 GLN cc_start: 0.7574 (mt0) cc_final: 0.7264 (pt0) REVERT: x 178 SER cc_start: 0.8938 (t) cc_final: 0.8725 (t) REVERT: T 87 MET cc_start: 0.8911 (mtm) cc_final: 0.8708 (mtp) REVERT: V 155 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8419 (mtm-85) REVERT: W 38 ARG cc_start: 0.8788 (ttp80) cc_final: 0.8565 (ttt-90) outliers start: 38 outliers final: 33 residues processed: 483 average time/residue: 0.5368 time to fit residues: 413.8129 Evaluate side-chains 474 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 440 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain x residue 161 THR Chi-restraints excluded: chain x residue 208 SER Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 209 THR Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 79 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 255 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 383 optimal weight: 0.5980 chunk 313 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 461 optimal weight: 9.9990 chunk 498 optimal weight: 0.0670 chunk 410 optimal weight: 9.9990 chunk 457 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 370 optimal weight: 7.9990 overall best weight: 3.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: