Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 20:30:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eug_24412/04_2023/8eug_24412.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eug_24412/04_2023/8eug_24412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eug_24412/04_2023/8eug_24412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eug_24412/04_2023/8eug_24412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eug_24412/04_2023/8eug_24412.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eug_24412/04_2023/8eug_24412.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.015 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 Zn 1 6.06 5 P 3138 5.49 5 S 164 5.16 5 C 65447 2.51 5 N 22852 2.21 5 O 31560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 GLU 5": "OE1" <-> "OE2" Residue "3 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C GLU 354": "OE1" <-> "OE2" Residue "D ASP 192": "OD1" <-> "OD2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "I GLU 58": "OE1" <-> "OE2" Residue "I GLU 66": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L GLU 168": "OE1" <-> "OE2" Residue "L GLU 169": "OE1" <-> "OE2" Residue "M GLU 9": "OE1" <-> "OE2" Residue "M ASP 33": "OD1" <-> "OD2" Residue "M ASP 107": "OD1" <-> "OD2" Residue "N ASP 17": "OD1" <-> "OD2" Residue "P GLU 75": "OE1" <-> "OE2" Residue "P GLU 147": "OE1" <-> "OE2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "Q GLU 149": "OE1" <-> "OE2" Residue "Q GLU 169": "OE1" <-> "OE2" Residue "R TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "R TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "T GLU 21": "OE1" <-> "OE2" Residue "T ASP 41": "OD1" <-> "OD2" Residue "T GLU 86": "OE1" <-> "OE2" Residue "T GLU 147": "OE1" <-> "OE2" Residue "T TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 102": "OE1" <-> "OE2" Residue "V ASP 91": "OD1" <-> "OD2" Residue "V TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 98": "OE1" <-> "OE2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "X ASP 77": "OD1" <-> "OD2" Residue "X ASP 78": "OD1" <-> "OD2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "X ASP 130": "OD1" <-> "OD2" Residue "X ASP 133": "OD1" <-> "OD2" Residue "Y ASP 6": "OD1" <-> "OD2" Residue "Y TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 47": "OE1" <-> "OE2" Residue "Z PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 76": "OD1" <-> "OD2" Residue "a TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 52": "OE1" <-> "OE2" Residue "c TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 16": "OD1" <-> "OD2" Residue "d TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 40": "OE1" <-> "OE2" Residue "e ASP 78": "OD1" <-> "OD2" Residue "h GLU 22": "OE1" <-> "OE2" Residue "m GLU 492": "OE1" <-> "OE2" Residue "m TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 121": "OE1" <-> "OE2" Residue "n TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 44": "OD1" <-> "OD2" Residue "o PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 123162 Number of models: 1 Model: "" Number of chains: 47 Chain: "1" Number of atoms: 61386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2869, 61386 Classifications: {'RNA': 2869} Modifications used: {'rna2p_pur': 312, 'rna2p_pyr': 192, 'rna3p_pur': 1297, 'rna3p_pyr': 1068} Link IDs: {'rna2p': 504, 'rna3p': 2364} Chain breaks: 32 Chain: "2" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3211 Classifications: {'RNA': 151} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 12, 'rna3p_pur': 61, 'rna3p_pyr': 61} Link IDs: {'rna2p': 29, 'rna3p': 121} Chain breaks: 1 Chain: "3" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1006 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "8" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 437 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "9" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2519 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 58, 'rna3p_pyr': 49} Link IDs: {'rna2p': 11, 'rna3p': 106} Chain: "A" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1847 Classifications: {'peptide': 244} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 230} Chain: "B" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3003 Classifications: {'peptide': 377} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 360} Chain: "C" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2795 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 340} Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2305 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "E" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1338 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 158} Chain: "F" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1745 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "G" Number of atoms: 1817 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 230, 1809 Classifications: {'peptide': 230} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217} Conformer: "B" Number of residues, atoms: 230, 1809 Classifications: {'peptide': 230} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217} bond proxies already assigned to first conformer: 1829 Chain: "H" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1415 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 1 Chain: "I" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1372 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain breaks: 1 Chain: "J" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1276 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 4, 'TRANS': 152} Chain breaks: 1 Chain: "K" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 695 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "L" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1612 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain: "M" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1007 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1676 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 190} Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "P" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1357 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain breaks: 1 Chain: "Q" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1486 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1220 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 3, 'TRANS': 144} Chain: "S" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1388 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 2 Chain: "T" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1282 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "U" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 791 Classifications: {'peptide': 98} Link IDs: {'TRANS': 97} Chain: "V" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1026 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "X" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 962 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "Y" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "Z" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "a" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1169 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 138} Chain: "b" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 463 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "c" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 714 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "d" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 849 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "e" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 939 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "f" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 839 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "g" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 861 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "h" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 999 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "i" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 767 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "j" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 657 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 80} Chain: "k" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 560 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "m" Number of atoms: 3127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3127 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 27, 'TRANS': 370} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "n" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2903 Classifications: {'peptide': 354} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 337} Chain breaks: 4 Chain: "o" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 789 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "p" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 1431 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 868 Unresolved non-hydrogen angles: 1130 Unresolved non-hydrogen dihedrals: 738 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 9, 'ASP:plan': 22, 'PHE:plan': 10, 'GLU:plan': 9, 'HIS:plan': 12} Unresolved non-hydrogen planarities: 452 Chain: "u" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 493 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0AAL SG CYS j 19 130.115 146.167 162.886 1.00 0.00 S ATOM A0ABD SG CYS j 22 132.593 146.609 160.019 1.00 0.00 S ATOM A0AE1 SG CYS j 34 130.869 143.342 160.528 1.00 2.06 S ATOM A0AEI SG CYS j 37 133.474 144.431 163.112 1.00 0.81 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP G 227 " occ=0.05 ... (14 atoms not shown) pdb=" OD2BASP G 227 " occ=0.95 Time building chain proxies: 46.18, per 1000 atoms: 0.37 Number of scatterers: 123162 At special positions: 0 Unit cell: (239.56, 214.12, 273.48, 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) Zn 1 29.99 S 164 16.00 P 3138 15.00 O 31560 8.00 N 22852 7.00 C 65447 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: 47.55 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " Number of angles added : 6 13966 Ramachandran restraints generated. 6983 Oldfield, 0 Emsley, 6983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13274 Finding SS restraints... Secondary structure from input PDB file: 242 helices and 84 sheets defined 36.7% alpha, 17.6% beta 955 base pairs and 1780 stacking pairs defined. Time for finding SS restraints: 37.41 Creating SS restraints... Processing helix chain '3' and resid 3 through 12 Processing helix chain '3' and resid 85 through 98 Processing helix chain '3' and resid 103 through 121 removed outlier: 3.849A pdb=" N ARG 3 107 " --> pdb=" O ARG 3 103 " (cutoff:3.500A) Processing helix chain '8' and resid 6 through 20 Processing helix chain '8' and resid 24 through 30 Processing helix chain 'A' and resid 12 through 16 removed outlier: 3.509A pdb=" N GLN A 16 " --> pdb=" O GLY A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 180 through 190 removed outlier: 3.890A pdb=" N VAL A 190 " --> pdb=" O HIS A 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 removed outlier: 4.035A pdb=" N LEU B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 3.818A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 140 through 155 removed outlier: 4.247A pdb=" N ILE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.988A pdb=" N THR B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 116 through 132 Processing helix chain 'C' and resid 133 through 141 Processing helix chain 'C' and resid 155 through 161 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.794A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 removed outlier: 4.094A pdb=" N ASN C 198 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 Processing helix chain 'C' and resid 254 through 265 removed outlier: 4.507A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.874A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 44 Processing helix chain 'D' and resid 81 through 86 Proline residue: D 84 - end of helix No H-bonds generated for 'chain 'D' and resid 81 through 86' Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 176 through 180 removed outlier: 4.127A pdb=" N ARG D 179 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 200 Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.580A pdb=" N ALA D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 223 Processing helix chain 'D' and resid 223 through 229 Processing helix chain 'D' and resid 235 through 250 Processing helix chain 'D' and resid 259 through 271 removed outlier: 3.705A pdb=" N LYS D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 292 Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 150 through 171 Proline residue: E 166 - end of helix Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'F' and resid 38 through 80 Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.647A pdb=" N VAL F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 158 Processing helix chain 'F' and resid 172 through 181 removed outlier: 3.940A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA F 179 " --> pdb=" O ILE F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 198 Processing helix chain 'F' and resid 201 through 209 Processing helix chain 'F' and resid 241 through 250 removed outlier: 3.587A pdb=" N LEU F 245 " --> pdb=" O HIS F 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 69 Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 83 through 97 removed outlier: 3.647A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 118 Processing helix chain 'G' and resid 121 through 126 removed outlier: 4.197A pdb=" N SER G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 190 removed outlier: 4.173A pdb=" N LEU G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'G' and resid 241 through 252 Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 61 through 84 removed outlier: 4.066A pdb=" N CYS H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG H 69 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 removed outlier: 3.631A pdb=" N GLY H 117 " --> pdb=" O ASN H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'I' and resid 62 through 80 Processing helix chain 'I' and resid 144 through 157 removed outlier: 4.231A pdb=" N TYR I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 188 Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'J' and resid 7 through 11 Processing helix chain 'J' and resid 27 through 42 Processing helix chain 'J' and resid 73 through 87 Processing helix chain 'J' and resid 92 through 96 removed outlier: 3.502A pdb=" N PHE J 96 " --> pdb=" O LYS J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 141 Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 155 through 168 Processing helix chain 'K' and resid 8 through 15 removed outlier: 3.510A pdb=" N LYS K 13 " --> pdb=" O VAL K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 35 Processing helix chain 'K' and resid 75 through 92 Processing helix chain 'L' and resid 18 through 20 No H-bonds generated for 'chain 'L' and resid 18 through 20' Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.945A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'L' and resid 148 through 153 Processing helix chain 'L' and resid 167 through 172 Processing helix chain 'L' and resid 174 through 188 Processing helix chain 'L' and resid 188 through 203 Processing helix chain 'M' and resid 70 through 81 Processing helix chain 'M' and resid 90 through 104 Processing helix chain 'M' and resid 106 through 122 Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 16 through 33 Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 75 through 79 Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.652A pdb=" N GLN N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'N' and resid 184 through 194 Processing helix chain 'O' and resid 16 through 30 Processing helix chain 'O' and resid 38 through 41 Processing helix chain 'O' and resid 47 through 61 removed outlier: 3.976A pdb=" N LYS O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 89 Processing helix chain 'O' and resid 93 through 101 Processing helix chain 'O' and resid 121 through 124 Processing helix chain 'O' and resid 125 through 130 Processing helix chain 'O' and resid 139 through 145 Processing helix chain 'O' and resid 150 through 186 removed outlier: 3.568A pdb=" N ARG O 160 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU O 184 " --> pdb=" O ALA O 180 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA O 185 " --> pdb=" O SER O 181 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER O 186 " --> pdb=" O ALA O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 192 Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 77 removed outlier: 3.850A pdb=" N GLY P 73 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS P 74 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'P' and resid 132 through 134 No H-bonds generated for 'chain 'P' and resid 132 through 134' Processing helix chain 'P' and resid 168 through 180 Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 53 Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 108 through 118 Processing helix chain 'Q' and resid 124 through 132 Processing helix chain 'Q' and resid 144 through 153 removed outlier: 3.837A pdb=" N ARG Q 148 " --> pdb=" O LYS Q 145 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU Q 149 " --> pdb=" O HIS Q 146 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA Q 150 " --> pdb=" O ALA Q 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 20 No H-bonds generated for 'chain 'R' and resid 18 through 20' Processing helix chain 'R' and resid 28 through 35 Processing helix chain 'R' and resid 37 through 47 Processing helix chain 'R' and resid 60 through 72 removed outlier: 3.934A pdb=" N LEU R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 113 Processing helix chain 'R' and resid 116 through 129 removed outlier: 3.809A pdb=" N TYR R 124 " --> pdb=" O TYR R 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA R 127 " --> pdb=" O LEU R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 145 Processing helix chain 'S' and resid 32 through 48 removed outlier: 3.587A pdb=" N ILE S 47 " --> pdb=" O PHE S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 114 Processing helix chain 'S' and resid 137 through 143 Processing helix chain 'T' and resid 54 through 58 Processing helix chain 'T' and resid 99 through 123 Processing helix chain 'U' and resid 16 through 22 Processing helix chain 'U' and resid 26 through 38 Processing helix chain 'U' and resid 70 through 85 removed outlier: 3.691A pdb=" N PHE U 81 " --> pdb=" O LEU U 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 122 through 128 Processing helix chain 'V' and resid 128 through 135 Processing helix chain 'X' and resid 57 through 61 Processing helix chain 'X' and resid 68 through 79 removed outlier: 3.764A pdb=" N ASN X 79 " --> pdb=" O ILE X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 103 Processing helix chain 'X' and resid 130 through 139 Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 3.783A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 74 through 77 Processing helix chain 'Y' and resid 99 through 101 No H-bonds generated for 'chain 'Y' and resid 99 through 101' Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'Z' and resid 58 through 67 Processing helix chain 'Z' and resid 89 through 93 Processing helix chain 'Z' and resid 97 through 103 Processing helix chain 'Z' and resid 103 through 125 Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'a' and resid 14 through 19 removed outlier: 3.574A pdb=" N ALA a 17 " --> pdb=" O HIS a 14 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY a 18 " --> pdb=" O VAL a 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 49 Processing helix chain 'a' and resid 65 through 69 Processing helix chain 'a' and resid 76 through 78 No H-bonds generated for 'chain 'a' and resid 76 through 78' Processing helix chain 'a' and resid 83 through 91 Processing helix chain 'a' and resid 103 through 107 Processing helix chain 'a' and resid 130 through 140 Processing helix chain 'b' and resid 11 through 19 removed outlier: 4.250A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 58 Processing helix chain 'c' and resid 23 through 35 removed outlier: 3.528A pdb=" N LYS c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 51 Processing helix chain 'c' and resid 63 through 77 Processing helix chain 'c' and resid 87 through 96 Processing helix chain 'd' and resid 21 through 26 Processing helix chain 'd' and resid 29 through 31 No H-bonds generated for 'chain 'd' and resid 29 through 31' Processing helix chain 'd' and resid 32 through 50 Processing helix chain 'd' and resid 57 through 65 Processing helix chain 'e' and resid 37 through 42 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 81 Processing helix chain 'e' and resid 98 through 113 Processing helix chain 'f' and resid 38 through 46 removed outlier: 4.274A pdb=" N PHE f 44 " --> pdb=" O GLU f 40 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR f 45 " --> pdb=" O GLU f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 91 through 95 removed outlier: 3.721A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 65 removed outlier: 3.563A pdb=" N ARG g 64 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 71 removed outlier: 3.522A pdb=" N THR g 71 " --> pdb=" O ASN g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 108 removed outlier: 4.016A pdb=" N LEU g 108 " --> pdb=" O LYS g 104 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 10 Processing helix chain 'h' and resid 12 through 37 Processing helix chain 'h' and resid 39 through 72 removed outlier: 3.976A pdb=" N LYS h 47 " --> pdb=" O LEU h 43 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 83 Processing helix chain 'h' and resid 87 through 93 Processing helix chain 'h' and resid 95 through 100 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 23 through 28 Processing helix chain 'i' and resid 32 through 47 Processing helix chain 'i' and resid 49 through 61 Processing helix chain 'i' and resid 63 through 76 Processing helix chain 'i' and resid 77 through 97 Processing helix chain 'j' and resid 7 through 11 removed outlier: 3.688A pdb=" N MET j 10 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.759A pdb=" N ARG j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 76 removed outlier: 3.674A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 Processing helix chain 'k' and resid 50 through 61 Processing helix chain 'm' and resid 228 through 243 Processing helix chain 'm' and resid 328 through 343 removed outlier: 3.880A pdb=" N TYR m 341 " --> pdb=" O CYS m 337 " (cutoff:3.500A) Processing helix chain 'm' and resid 483 through 492 removed outlier: 3.735A pdb=" N ILE m 487 " --> pdb=" O SER m 483 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU m 492 " --> pdb=" O GLU m 488 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 15 Processing helix chain 'n' and resid 19 through 27 Processing helix chain 'n' and resid 29 through 40 Processing helix chain 'n' and resid 49 through 54 Processing helix chain 'n' and resid 66 through 73 Processing helix chain 'n' and resid 75 through 97 removed outlier: 4.108A pdb=" N GLN n 79 " --> pdb=" O GLU n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 99 through 109 Processing helix chain 'n' and resid 115 through 123 Processing helix chain 'n' and resid 125 through 132 Processing helix chain 'n' and resid 133 through 144 Processing helix chain 'n' and resid 153 through 175 Processing helix chain 'n' and resid 215 through 241 removed outlier: 3.562A pdb=" N MET n 219 " --> pdb=" O ASP n 215 " (cutoff:3.500A) Processing helix chain 'n' and resid 365 through 375 removed outlier: 3.895A pdb=" N PHE n 371 " --> pdb=" O PHE n 367 " (cutoff:3.500A) Processing helix chain 'n' and resid 420 through 431 removed outlier: 4.023A pdb=" N VAL n 424 " --> pdb=" O GLN n 420 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR n 425 " --> pdb=" O PRO n 421 " (cutoff:3.500A) Processing helix chain 'n' and resid 435 through 440 removed outlier: 3.792A pdb=" N ALA n 440 " --> pdb=" O ASP n 437 " (cutoff:3.500A) Processing helix chain 'n' and resid 554 through 559 Processing helix chain 'n' and resid 564 through 568 Processing helix chain 'n' and resid 569 through 576 removed outlier: 4.280A pdb=" N TYR n 573 " --> pdb=" O GLN n 569 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 48 Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 Processing helix chain 'u' and resid 52 through 59 Processing sheet with id=AA1, first strand: chain '3' and resid 19 through 22 Processing sheet with id=AA2, first strand: chain '3' and resid 50 through 56 removed outlier: 3.859A pdb=" N TYR 3 50 " --> pdb=" O LYS 3 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS 3 65 " --> pdb=" O TYR 3 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.373A pdb=" N LEU A 57 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE A 47 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS A 59 " --> pdb=" O GLN A 45 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG A 63 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ARG A 41 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.645A pdb=" N ARG A 146 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N HIS A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS A 144 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.048A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 157 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY B 91 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.048A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 157 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY B 91 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.479A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE B 359 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N HIS B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE B 215 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LYS B 281 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE B 321 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AB1, first strand: chain 'C' and resid 7 through 11 removed outlier: 7.321A pdb=" N VAL C 8 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLU C 20 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE C 10 " --> pdb=" O SER C 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.617A pdb=" N GLU C 65 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.418A pdb=" N LEU C 152 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB5, first strand: chain 'D' and resid 72 through 79 removed outlier: 6.790A pdb=" N ILE D 64 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N HIS D 77 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N CYS D 62 " --> pdb=" O HIS D 77 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N HIS D 79 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL D 60 " --> pdb=" O HIS D 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 94 through 97 removed outlier: 6.440A pdb=" N THR E 83 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL E 72 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 82 through 84 Processing sheet with id=AB8, first strand: chain 'F' and resid 212 through 213 removed outlier: 3.801A pdb=" N ASN F 120 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ARG F 238 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N TYR F 143 " --> pdb=" O ARG F 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 160 through 163 Processing sheet with id=AC1, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AC2, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AC3, first strand: chain 'H' and resid 7 through 12 Processing sheet with id=AC4, first strand: chain 'H' and resid 25 through 29 Processing sheet with id=AC5, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.173A pdb=" N ARG H 91 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL H 179 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL H 93 " --> pdb=" O ILE H 177 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE H 177 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.564A pdb=" N VAL H 109 " --> pdb=" O THR H 104 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 35 through 37 removed outlier: 6.273A pdb=" N ILE I 134 " --> pdb=" O SER I 54 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N SER I 54 " --> pdb=" O ILE I 134 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N CYS I 49 " --> pdb=" O SER I 168 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 58 through 61 removed outlier: 4.557A pdb=" N GLY I 124 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL I 97 " --> pdb=" O GLY I 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 190 through 193 Processing sheet with id=AD1, first strand: chain 'J' and resid 46 through 49 removed outlier: 3.645A pdb=" N ALA J 66 " --> pdb=" O SER J 48 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE J 14 " --> pdb=" O ASP J 132 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP J 132 " --> pdb=" O ILE J 14 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE J 102 " --> pdb=" O VAL J 129 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 47 through 51 removed outlier: 5.209A pdb=" N ARG K 49 " --> pdb=" O CYS K 56 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS K 56 " --> pdb=" O ARG K 49 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA K 51 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 22 through 24 removed outlier: 6.311A pdb=" N LYS L 23 " --> pdb=" O LEU N 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AD5, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AD6, first strand: chain 'M' and resid 7 through 9 Processing sheet with id=AD7, first strand: chain 'M' and resid 49 through 52 removed outlier: 7.582A pdb=" N ARG M 36 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE M 31 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL M 13 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.398A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 103 through 105 removed outlier: 8.488A pdb=" N VAL O 119 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL O 9 " --> pdb=" O VAL O 119 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AE2, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.616A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AE4, first strand: chain 'P' and resid 128 through 130 Processing sheet with id=AE5, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.421A pdb=" N ILE Q 61 " --> pdb=" O THR Q 89 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU Q 105 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY Q 86 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N PHE Q 107 " --> pdb=" O GLY Q 86 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL Q 88 " --> pdb=" O PHE Q 107 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.421A pdb=" N ILE Q 61 " --> pdb=" O THR Q 89 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR Q 81 " --> pdb=" O VAL Q 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AE8, first strand: chain 'S' and resid 55 through 63 removed outlier: 5.179A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU S 5 " --> pdb=" O ILE S 63 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 87 through 95 removed outlier: 3.823A pdb=" N HIS S 87 " --> pdb=" O TYR S 80 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL S 73 " --> pdb=" O VAL S 128 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG S 79 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE S 122 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 83 through 92 removed outlier: 3.608A pdb=" N ARG T 83 " --> pdb=" O VAL T 80 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN T 66 " --> pdb=" O GLY T 73 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU T 75 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL T 64 " --> pdb=" O LEU T 75 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N TYR T 77 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N GLY T 62 " --> pdb=" O TYR T 77 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'U' and resid 51 through 53 removed outlier: 6.945A pdb=" N VAL U 100 " --> pdb=" O THR U 96 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AF4, first strand: chain 'V' and resid 24 through 27 removed outlier: 5.445A pdb=" N ILE V 38 " --> pdb=" O THR V 63 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR V 63 " --> pdb=" O ILE V 38 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA V 101 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N GLY V 102 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN V 26 " --> pdb=" O GLY V 102 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE V 104 " --> pdb=" O ASN V 26 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 87 through 88 removed outlier: 6.139A pdb=" N TYR V 94 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL u 22 " --> pdb=" O TYR V 94 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR V 96 " --> pdb=" O VAL u 22 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 119 through 121 removed outlier: 5.150A pdb=" N VAL V 120 " --> pdb=" O VAL V 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'X' and resid 62 through 65 removed outlier: 3.945A pdb=" N LYS X 119 " --> pdb=" O VAL X 85 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AF9, first strand: chain 'Y' and resid 93 through 98 removed outlier: 6.513A pdb=" N VAL Y 84 " --> pdb=" O VAL Y 96 " (cutoff:3.500A) removed outlier: 10.895A pdb=" N ILE Y 98 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 98 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU Y 78 " --> pdb=" O VAL Y 72 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL Y 72 " --> pdb=" O LEU Y 78 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU Y 80 " --> pdb=" O THR Y 70 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS Y 68 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL Y 84 " --> pdb=" O GLU Y 66 " (cutoff:3.500A) removed outlier: 9.881A pdb=" N GLU Y 66 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR Y 56 " --> pdb=" O ILE Y 105 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE Y 105 " --> pdb=" O THR Y 56 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.838A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N HIS Z 40 " --> pdb=" O ALA Z 28 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ALA Z 28 " --> pdb=" O HIS Z 40 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL Z 42 " --> pdb=" O LEU Z 26 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL Z 46 " --> pdb=" O LYS Z 22 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LYS Z 22 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 72 through 74 removed outlier: 6.159A pdb=" N VAL a 73 " --> pdb=" O LEU a 112 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 100 through 102 removed outlier: 6.231A pdb=" N ILE a 101 " --> pdb=" O GLN a 125 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL a 124 " --> pdb=" O GLU a 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'c' and resid 36 through 39 removed outlier: 6.210A pdb=" N LYS c 36 " --> pdb=" O ILE c 107 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE c 56 " --> pdb=" O HIS c 82 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 54 through 56 removed outlier: 4.491A pdb=" N THR d 14 " --> pdb=" O VAL d 111 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'e' and resid 69 through 73 Processing sheet with id=AG7, first strand: chain 'f' and resid 9 through 19 removed outlier: 5.758A pdb=" N HIS f 14 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS f 32 " --> pdb=" O HIS f 14 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER f 16 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR f 28 " --> pdb=" O GLN f 18 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA f 81 " --> pdb=" O HIS f 76 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG f 74 " --> pdb=" O ARG f 83 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG f 85 " --> pdb=" O ILE f 72 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE f 72 " --> pdb=" O ARG f 85 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS f 64 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG f 49 " --> pdb=" O MET f 102 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.230A pdb=" N ARG g 19 " --> pdb=" O ILE g 35 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AH1, first strand: chain 'k' and resid 3 through 4 removed outlier: 6.738A pdb=" N ARG k 3 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL k 47 " --> pdb=" O ARG k 3 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER k 22 " --> pdb=" O ARG k 38 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'm' and resid 375 through 379 removed outlier: 3.821A pdb=" N ASN m 377 " --> pdb=" O MET m 738 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER m 717 " --> pdb=" O ALA m 730 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'm' and resid 388 through 391 Processing sheet with id=AH4, first strand: chain 'm' and resid 452 through 457 removed outlier: 3.929A pdb=" N SER m 454 " --> pdb=" O ALA m 469 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'm' and resid 533 through 536 Processing sheet with id=AH6, first strand: chain 'm' and resid 576 through 581 removed outlier: 4.376A pdb=" N TYR m 595 " --> pdb=" O THR m 592 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN m 600 " --> pdb=" O LEU m 606 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU m 606 " --> pdb=" O ASN m 600 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'm' and resid 617 through 622 Processing sheet with id=AH8, first strand: chain 'm' and resid 660 through 665 removed outlier: 5.418A pdb=" N HIS m 685 " --> pdb=" O PRO m 700 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ARG m 687 " --> pdb=" O ILE m 698 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILE m 698 " --> pdb=" O ARG m 687 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'n' and resid 16 through 18 Processing sheet with id=AI1, first strand: chain 'n' and resid 177 through 182 removed outlier: 6.614A pdb=" N GLN n 190 " --> pdb=" O ARG n 178 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA n 180 " --> pdb=" O TYR n 188 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR n 188 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'n' and resid 357 through 360 removed outlier: 6.303A pdb=" N PHE n 358 " --> pdb=" O GLY n 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'o' and resid 3 through 4 Processing sheet with id=AI4, first strand: chain 'o' and resid 7 through 12 removed outlier: 3.606A pdb=" N LYS o 19 " --> pdb=" O CYS o 12 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL o 68 " --> pdb=" O LEU o 85 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'p' and resid 96 through 102 removed outlier: 6.650A pdb=" N ILE p 430 " --> pdb=" O LEU p 98 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER p 100 " --> pdb=" O LEU p 428 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU p 428 " --> pdb=" O SER p 100 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLN p 427 " --> pdb=" O GLY p 423 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY p 423 " --> pdb=" O GLN p 427 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY p 418 " --> pdb=" O TRP p 413 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP p 413 " --> pdb=" O GLY p 418 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL p 420 " --> pdb=" O VAL p 411 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL p 411 " --> pdb=" O VAL p 420 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY p 422 " --> pdb=" O PHE p 409 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'p' and resid 107 through 112 removed outlier: 5.908A pdb=" N ALA p 126 " --> pdb=" O GLN p 138 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN p 138 " --> pdb=" O ALA p 126 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL p 128 " --> pdb=" O LYS p 136 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'p' and resid 146 through 151 removed outlier: 6.490A pdb=" N ALA p 161 " --> pdb=" O LYS p 147 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA p 149 " --> pdb=" O LEU p 159 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU p 159 " --> pdb=" O ALA p 149 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS p 166 " --> pdb=" O SER p 162 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR p 191 " --> pdb=" O HIS p 169 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL p 171 " --> pdb=" O LEU p 189 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU p 189 " --> pdb=" O VAL p 171 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'p' and resid 200 through 203 removed outlier: 4.099A pdb=" N THR p 220 " --> pdb=" O SER p 216 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'p' and resid 272 through 277 removed outlier: 4.274A pdb=" N GLY p 288 " --> pdb=" O THR p 292 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR p 292 " --> pdb=" O GLY p 288 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP p 305 " --> pdb=" O THR p 295 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP p 297 " --> pdb=" O ASN p 303 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASN p 303 " --> pdb=" O ASP p 297 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'p' and resid 313 through 319 removed outlier: 4.022A pdb=" N CYS p 315 " --> pdb=" O GLY p 328 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS p 333 " --> pdb=" O SER p 329 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'p' and resid 358 through 363 removed outlier: 4.100A pdb=" N THR p 379 " --> pdb=" O SER p 375 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'u' and resid 4 through 5 2285 hydrogen bonds defined for protein. 6414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2311 hydrogen bonds 3666 hydrogen bond angles 0 basepair planarities 955 basepair parallelities 1780 stacking parallelities Total time for adding SS restraints: 176.83 Time building geometry restraints manager: 51.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.52: 95802 1.52 - 1.82: 36399 1.82 - 2.13: 0 2.13 - 2.43: 0 2.43 - 2.74: 1 Bond restraints: 132202 Sorted by residual: bond pdb=" C GLY R 113 " pdb=" N ILE R 115 " ideal model delta sigma weight residual 1.332 2.740 -1.408 1.36e-02 5.41e+03 1.07e+04 bond pdb=" C ARG 3 40 " pdb=" O ARG 3 40 " ideal model delta sigma weight residual 1.236 1.212 0.025 1.15e-02 7.56e+03 4.56e+00 bond pdb=" CA PHE m 371 " pdb=" C PHE m 371 " ideal model delta sigma weight residual 1.524 1.499 0.024 1.26e-02 6.30e+03 3.75e+00 bond pdb=" CB LYS C 347 " pdb=" CG LYS C 347 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.57e+00 bond pdb=" CA TYR 3 32 " pdb=" CB TYR 3 32 " ideal model delta sigma weight residual 1.530 1.563 -0.033 1.84e-02 2.95e+03 3.23e+00 ... (remaining 132197 not shown) Histogram of bond angle deviations from ideal: 84.03 - 98.01: 1 98.01 - 112.00: 86597 112.00 - 125.99: 95958 125.99 - 139.97: 11196 139.97 - 153.96: 1 Bond angle restraints: 193753 Sorted by residual: angle pdb=" O GLY R 113 " pdb=" C GLY R 113 " pdb=" N ILE R 115 " ideal model delta sigma weight residual 122.70 84.03 38.67 1.30e+00 5.92e-01 8.85e+02 angle pdb=" CA GLY R 113 " pdb=" C GLY R 113 " pdb=" N ILE R 115 " ideal model delta sigma weight residual 116.69 153.96 -37.27 2.04e+00 2.40e-01 3.34e+02 angle pdb=" N PRO m 370 " pdb=" CA PRO m 370 " pdb=" C PRO m 370 " ideal model delta sigma weight residual 114.68 101.45 13.23 1.04e+00 9.25e-01 1.62e+02 angle pdb=" O3' G 11388 " pdb=" C3' G 11388 " pdb=" C2' G 11388 " ideal model delta sigma weight residual 113.70 105.18 8.52 1.50e+00 4.44e-01 3.23e+01 angle pdb=" C4' A 12657 " pdb=" C3' A 12657 " pdb=" O3' A 12657 " ideal model delta sigma weight residual 109.40 117.73 -8.33 1.50e+00 4.44e-01 3.08e+01 ... (remaining 193748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 69733 35.71 - 71.42: 2621 71.42 - 107.13: 235 107.13 - 142.84: 12 142.84 - 178.55: 27 Dihedral angle restraints: 72628 sinusoidal: 52061 harmonic: 20567 Sorted by residual: dihedral pdb=" CA GLY R 113 " pdb=" C GLY R 113 " pdb=" N ILE R 115 " pdb=" CA ILE R 115 " ideal model delta harmonic sigma weight residual 180.00 126.26 53.74 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" C4' G 12198 " pdb=" C3' G 12198 " pdb=" C2' G 12198 " pdb=" C1' G 12198 " ideal model delta sinusoidal sigma weight residual -35.00 35.02 -70.02 1 8.00e+00 1.56e-02 9.88e+01 dihedral pdb=" C5' G 12198 " pdb=" C4' G 12198 " pdb=" C3' G 12198 " pdb=" O3' G 12198 " ideal model delta sinusoidal sigma weight residual 147.00 77.00 70.00 1 8.00e+00 1.56e-02 9.87e+01 ... (remaining 72625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 22799 0.069 - 0.138: 1228 0.138 - 0.207: 56 0.207 - 0.276: 6 0.276 - 0.345: 2 Chirality restraints: 24091 Sorted by residual: chirality pdb=" C3' G 12198 " pdb=" C4' G 12198 " pdb=" O3' G 12198 " pdb=" C2' G 12198 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB VAL G 28 " pdb=" CA VAL G 28 " pdb=" CG1 VAL G 28 " pdb=" CG2 VAL G 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C3' U 1 310 " pdb=" C4' U 1 310 " pdb=" O3' U 1 310 " pdb=" C2' U 1 310 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 24088 not shown) Planarity restraints: 12950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY R 113 " 0.034 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C GLY R 113 " -0.069 2.00e-02 2.50e+03 pdb=" O GLY R 113 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE R 115 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER N 183 " -0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO N 184 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO N 184 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 184 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR X 29 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C THR X 29 " -0.038 2.00e-02 2.50e+03 pdb=" O THR X 29 " 0.014 2.00e-02 2.50e+03 pdb=" N THR X 30 " 0.013 2.00e-02 2.50e+03 ... (remaining 12947 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 3818 2.65 - 3.21: 104207 3.21 - 3.78: 242690 3.78 - 4.34: 336603 4.34 - 4.90: 454654 Nonbonded interactions: 1141972 Sorted by model distance: nonbonded pdb=" OG SER i 95 " pdb=" NH1 ARG i 96 " model vdw 2.091 2.520 nonbonded pdb=" O2' A 11012 " pdb=" O5' U 11013 " model vdw 2.145 2.440 nonbonded pdb=" O2' G 1 805 " pdb=" OP1 G 1 806 " model vdw 2.167 2.440 nonbonded pdb=" O2' A 13491 " pdb=" O5' G 13492 " model vdw 2.170 2.440 nonbonded pdb=" O2' C 12779 " pdb=" O5' G 12780 " model vdw 2.179 2.440 ... (remaining 1141967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.05 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: 6.420 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: 0.140 Extract box with map and model: 32.290 Check model and map are aligned: 1.340 Set scattering table: 0.800 Process input model: 410.730 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 465.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 1.408 132202 Z= 0.215 Angle : 0.532 38.672 193753 Z= 0.287 Chirality : 0.033 0.345 24091 Planarity : 0.004 0.080 12950 Dihedral : 15.475 178.551 59354 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.50 % Favored : 96.23 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.01 % 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: -0.23 (0.10), residues: 6983 helix: 0.53 (0.11), residues: 2314 sheet: -0.44 (0.14), residues: 1202 loop : -0.41 (0.10), residues: 3467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13966 Ramachandran restraints generated. 6983 Oldfield, 0 Emsley, 6983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13966 Ramachandran restraints generated. 6983 Oldfield, 0 Emsley, 6983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 700 time to evaluate : 6.596 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 5 residues processed: 716 average time/residue: 1.9784 time to fit residues: 1994.5726 Evaluate side-chains 625 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 620 time to evaluate : 6.488 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.9395 time to fit residues: 9.4330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 846 optimal weight: 0.5980 chunk 759 optimal weight: 8.9990 chunk 421 optimal weight: 4.9990 chunk 259 optimal weight: 5.9990 chunk 512 optimal weight: 5.9990 chunk 405 optimal weight: 0.8980 chunk 785 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 477 optimal weight: 6.9990 chunk 584 optimal weight: 0.3980 chunk 909 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 26 ASN 8 25 GLN 8 33 ASN B 279 ASN B 319 ASN C 272 GLN ** D 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 ASN G 182 ASN K 45 ASN O 97 GLN O 170 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 ASN X 67 ASN X 110 ASN X 136 ASN Y 62 ASN ** Z 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN e 86 ASN g 98 GLN h 15 ASN ** m 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 234 ASN n 567 ASN o 27 GLN o 47 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 132202 Z= 0.168 Angle : 0.568 9.144 193753 Z= 0.294 Chirality : 0.036 0.250 24091 Planarity : 0.004 0.073 12950 Dihedral : 14.714 179.924 45506 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.59 % Favored : 96.19 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.01 % 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: 0.10 (0.10), residues: 6985 helix: 1.06 (0.11), residues: 2311 sheet: -0.42 (0.14), residues: 1210 loop : -0.34 (0.10), residues: 3464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 673 time to evaluate : 6.646 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 28 residues processed: 718 average time/residue: 2.0377 time to fit residues: 2066.1741 Evaluate side-chains 656 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 628 time to evaluate : 6.605 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 17 residues processed: 11 average time/residue: 1.0872 time to fit residues: 28.7486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 505 optimal weight: 0.8980 chunk 282 optimal weight: 20.0000 chunk 757 optimal weight: 4.9990 chunk 619 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 chunk 911 optimal weight: 0.0070 chunk 984 optimal weight: 40.0000 chunk 811 optimal weight: 3.9990 chunk 903 optimal weight: 40.0000 chunk 310 optimal weight: 0.9980 chunk 731 optimal weight: 9.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 GLN 8 33 ASN A 215 HIS C 272 GLN D 270 HIS D 272 GLN E 173 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN K 45 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 127 GLN R 34 ASN R 40 ASN ** T 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 84 HIS X 136 ASN Y 54 GLN Y 62 ASN ** Z 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN e 86 ASN h 15 ASN m 712 ASN n 234 ASN n 567 ASN o 27 GLN o 47 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 132202 Z= 0.214 Angle : 0.563 9.244 193753 Z= 0.292 Chirality : 0.037 0.241 24091 Planarity : 0.005 0.075 12950 Dihedral : 14.628 178.792 45506 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.78 % Favored : 96.03 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.10), residues: 6985 helix: 1.15 (0.11), residues: 2322 sheet: -0.33 (0.14), residues: 1180 loop : -0.35 (0.10), residues: 3483 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 670 time to evaluate : 6.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 46 residues processed: 726 average time/residue: 2.0116 time to fit residues: 2062.4183 Evaluate side-chains 672 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 626 time to evaluate : 6.564 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 31 residues processed: 16 average time/residue: 1.2379 time to fit residues: 41.0349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 900 optimal weight: 7.9990 chunk 685 optimal weight: 6.9990 chunk 473 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 435 optimal weight: 5.9990 chunk 612 optimal weight: 2.9990 chunk 914 optimal weight: 6.9990 chunk 968 optimal weight: 5.9990 chunk 477 optimal weight: 7.9990 chunk 867 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 41 GLN 8 33 ASN C 272 GLN C 323 ASN D 272 GLN E 173 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN K 45 ASN M 119 GLN ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 170 GLN O 176 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 127 GLN Q 137 ASN R 34 ASN R 40 ASN R 58 HIS R 143 GLN ** T 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS V 134 ASN X 84 HIS X 136 ASN Y 54 GLN Y 62 ASN Z 27 GLN ** Z 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN e 86 ASN g 14 ASN g 98 GLN h 13 GLN h 15 ASN h 61 ASN o 27 GLN o 47 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.180 132202 Z= 0.603 Angle : 0.876 12.910 193753 Z= 0.433 Chirality : 0.053 0.439 24091 Planarity : 0.008 0.092 12950 Dihedral : 15.136 178.507 45506 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.33 % Favored : 95.43 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.10), residues: 6985 helix: 0.62 (0.11), residues: 2309 sheet: -0.52 (0.14), residues: 1200 loop : -0.62 (0.10), residues: 3476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 633 time to evaluate : 6.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 178 outliers final: 83 residues processed: 734 average time/residue: 2.0819 time to fit residues: 2151.1624 Evaluate side-chains 713 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 630 time to evaluate : 6.583 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 54 residues processed: 31 average time/residue: 1.2678 time to fit residues: 72.5101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 806 optimal weight: 0.8980 chunk 549 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 721 optimal weight: 0.9990 chunk 399 optimal weight: 0.9990 chunk 826 optimal weight: 0.8980 chunk 669 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 494 optimal weight: 1.9990 chunk 869 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 33 ASN C 323 ASN D 272 GLN E 173 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN K 45 ASN N 149 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 137 ASN R 7 GLN R 34 ASN R 40 ASN ** U 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN X 84 HIS Y 62 ASN ** Z 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN h 13 GLN h 61 ASN h 99 GLN m 328 ASN o 27 GLN o 47 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.070 132202 Z= 0.150 Angle : 0.549 10.361 193753 Z= 0.284 Chirality : 0.035 0.278 24091 Planarity : 0.004 0.073 12950 Dihedral : 14.693 179.372 45506 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.49 % Favored : 96.32 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.01 % 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: 0.11 (0.10), residues: 6985 helix: 1.15 (0.11), residues: 2300 sheet: -0.38 (0.14), residues: 1178 loop : -0.42 (0.10), residues: 3507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 681 time to evaluate : 6.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 57 residues processed: 769 average time/residue: 2.0127 time to fit residues: 2188.9387 Evaluate side-chains 694 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 637 time to evaluate : 6.569 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 46 residues processed: 12 average time/residue: 1.2223 time to fit residues: 32.4669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 325 optimal weight: 5.9990 chunk 872 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 568 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 969 optimal weight: 50.0000 chunk 804 optimal weight: 6.9990 chunk 448 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 320 optimal weight: 10.0000 chunk 508 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 26 ASN 8 33 ASN E 173 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 ASN G 182 ASN ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN N 149 ASN O 170 GLN P 97 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 127 GLN R 7 GLN R 34 ASN ** U 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN X 84 HIS X 136 ASN Y 62 ASN ** Z 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN e 86 ASN f 18 GLN h 15 ASN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 234 ASN n 567 ASN o 27 GLN o 47 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.168 132202 Z= 0.562 Angle : 0.831 14.783 193753 Z= 0.412 Chirality : 0.051 0.392 24091 Planarity : 0.007 0.085 12950 Dihedral : 14.983 179.260 45506 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.47 % Favored : 95.30 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.10), residues: 6985 helix: 0.75 (0.11), residues: 2292 sheet: -0.49 (0.14), residues: 1187 loop : -0.62 (0.10), residues: 3506 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 634 time to evaluate : 6.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 95 residues processed: 736 average time/residue: 2.0022 time to fit residues: 2080.8038 Evaluate side-chains 718 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 623 time to evaluate : 6.657 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 61 residues processed: 34 average time/residue: 1.1834 time to fit residues: 77.1835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 934 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 552 optimal weight: 8.9990 chunk 707 optimal weight: 4.9990 chunk 548 optimal weight: 6.9990 chunk 816 optimal weight: 5.9990 chunk 541 optimal weight: 0.7980 chunk 965 optimal weight: 0.5980 chunk 604 optimal weight: 1.9990 chunk 588 optimal weight: 3.9990 chunk 445 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 117 GLN 8 33 ASN E 173 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN G 182 ASN ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 127 GLN Q 137 ASN R 34 ASN ** U 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN X 84 HIS Y 62 ASN ** Z 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN h 99 GLN o 27 GLN o 47 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 132202 Z= 0.166 Angle : 0.557 13.396 193753 Z= 0.288 Chirality : 0.035 0.250 24091 Planarity : 0.004 0.070 12950 Dihedral : 14.634 179.346 45506 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.67 % Favored : 96.13 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.01 % 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: 0.08 (0.10), residues: 6985 helix: 1.13 (0.11), residues: 2293 sheet: -0.34 (0.14), residues: 1167 loop : -0.47 (0.10), residues: 3525 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 655 time to evaluate : 6.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 72 residues processed: 742 average time/residue: 2.0612 time to fit residues: 2155.4962 Evaluate side-chains 703 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 631 time to evaluate : 6.561 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 62 residues processed: 11 average time/residue: 1.0770 time to fit residues: 28.7500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 597 optimal weight: 0.9990 chunk 385 optimal weight: 4.9990 chunk 576 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 613 optimal weight: 4.9990 chunk 657 optimal weight: 20.0000 chunk 477 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 759 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 26 ASN 8 25 GLN 8 33 ASN B 325 ASN C 272 GLN E 173 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN G 182 ASN J 161 ASN ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 170 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 127 GLN R 34 ASN U 10 ASN V 134 ASN X 84 HIS X 136 ASN Y 62 ASN ** Z 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN f 25 HIS h 15 ASN h 25 GLN h 99 GLN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 47 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.150 132202 Z= 0.440 Angle : 0.735 13.047 193753 Z= 0.369 Chirality : 0.045 0.327 24091 Planarity : 0.006 0.071 12950 Dihedral : 14.791 179.512 45506 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.41 % Favored : 95.37 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.01 % 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: -0.13 (0.10), residues: 6985 helix: 0.91 (0.11), residues: 2286 sheet: -0.44 (0.14), residues: 1185 loop : -0.57 (0.10), residues: 3514 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 633 time to evaluate : 6.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 150 outliers final: 89 residues processed: 728 average time/residue: 2.0270 time to fit residues: 2097.7273 Evaluate side-chains 717 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 628 time to evaluate : 6.572 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 68 residues processed: 21 average time/residue: 1.1214 time to fit residues: 48.9311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 878 optimal weight: 0.9990 chunk 925 optimal weight: 3.9990 chunk 844 optimal weight: 0.8980 chunk 899 optimal weight: 7.9990 chunk 924 optimal weight: 3.9990 chunk 541 optimal weight: 1.9990 chunk 392 optimal weight: 0.9980 chunk 706 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 813 optimal weight: 3.9990 chunk 851 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 33 ASN E 173 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN G 182 ASN ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 127 GLN Q 137 ASN R 34 ASN V 134 ASN X 84 HIS Y 62 ASN ** Z 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN h 15 ASN h 99 GLN o 27 GLN o 47 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.104 132202 Z= 0.238 Angle : 0.593 12.337 193753 Z= 0.304 Chirality : 0.038 0.264 24091 Planarity : 0.005 0.071 12950 Dihedral : 14.617 179.258 45506 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.84 % Favored : 95.96 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.01 % 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: 0.00 (0.10), residues: 6985 helix: 1.04 (0.11), residues: 2301 sheet: -0.36 (0.14), residues: 1177 loop : -0.50 (0.10), residues: 3507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 632 time to evaluate : 6.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 81 residues processed: 719 average time/residue: 2.0276 time to fit residues: 2073.8687 Evaluate side-chains 695 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 614 time to evaluate : 6.544 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 71 residues processed: 11 average time/residue: 1.2325 time to fit residues: 30.5981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 896 optimal weight: 0.0670 chunk 590 optimal weight: 0.9990 chunk 951 optimal weight: 20.0000 chunk 580 optimal weight: 6.9990 chunk 451 optimal weight: 8.9990 chunk 661 optimal weight: 0.9990 chunk 998 optimal weight: 10.0000 chunk 918 optimal weight: 9.9990 chunk 794 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 614 optimal weight: 0.9990 overall best weight: 0.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 26 ASN 8 25 GLN 8 33 ASN E 173 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN G 182 ASN ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 170 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 127 GLN R 34 ASN V 134 ASN X 84 HIS X 136 ASN Y 62 ASN d 50 GLN h 15 ASN h 99 GLN o 27 GLN o 47 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.079 132202 Z= 0.155 Angle : 0.563 13.074 193753 Z= 0.292 Chirality : 0.035 0.343 24091 Planarity : 0.004 0.070 12950 Dihedral : 14.606 179.288 45506 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.81 % Favored : 96.00 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.01 % 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: 0.11 (0.10), residues: 6985 helix: 1.16 (0.11), residues: 2300 sheet: -0.33 (0.14), residues: 1167 loop : -0.45 (0.10), residues: 3518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13970 Ramachandran restraints generated. 6985 Oldfield, 0 Emsley, 6985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 626 time to evaluate : 6.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 76 residues processed: 705 average time/residue: 2.0270 time to fit residues: 2043.1684 Evaluate side-chains 696 residues out of total 6037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 620 time to evaluate : 6.569 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 71 residues processed: 6 average time/residue: 1.8576 time to fit residues: 24.3312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 487 optimal weight: 3.9990 chunk 631 optimal weight: 2.9990 chunk 846 optimal weight: 0.0050 chunk 243 optimal weight: 5.9990 chunk 732 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 796 optimal weight: 0.6980 chunk 333 optimal weight: 0.9990 chunk 817 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 26 ASN 8 33 ASN C 272 GLN E 173 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN G 182 ASN ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 127 GLN R 7 GLN R 34 ASN V 134 ASN X 84 HIS X 136 ASN Y 62 ASN ** Z 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN h 15 ASN h 99 GLN o 27 GLN o 47 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.142906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.125792 restraints weight = 183040.062| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 0.89 r_work: 0.3368 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 132202 Z= 0.234 Angle : 0.581 12.778 193753 Z= 0.299 Chirality : 0.037 0.332 24091 Planarity : 0.005 0.071 12950 Dihedral : 14.506 179.941 45506 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.05 % Favored : 95.76 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.01 % 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: 0.13 (0.10), residues: 6985 helix: 1.16 (0.11), residues: 2297 sheet: -0.26 (0.14), residues: 1147 loop : -0.44 (0.10), residues: 3541 =============================================================================== Job complete usr+sys time: 30474.05 seconds wall clock time: 534 minutes 39.08 seconds (32079.08 seconds total)