Starting phenix.real_space_refine on Thu Nov 16 01:52:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9r_35281/11_2023/8i9r_35281_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9r_35281/11_2023/8i9r_35281.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9r_35281/11_2023/8i9r_35281_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9r_35281/11_2023/8i9r_35281_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9r_35281/11_2023/8i9r_35281_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9r_35281/11_2023/8i9r_35281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9r_35281/11_2023/8i9r_35281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9r_35281/11_2023/8i9r_35281_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9r_35281/11_2023/8i9r_35281_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 3 6.06 5 P 2395 5.49 5 S 183 5.16 5 C 64551 2.51 5 N 21772 2.21 5 O 28513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CA TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 117417 Number of models: 1 Model: "" Number of chains: 52 Chain: "C1" Number of atoms: 43814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2048, 43814 Classifications: {'RNA': 2048} Modifications used: {'rna2p': 1, 'rna2p_pur': 213, 'rna2p_pyr': 133, 'rna3p': 2, 'rna3p_pur': 913, 'rna3p_pyr': 786} Link IDs: {'rna2p': 346, 'rna3p': 1701} Chain breaks: 21 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Chain: "C2" Number of atoms: 4846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 4846 Classifications: {'DNA': 1, 'RNA': 227} Modifications used: {'rna2p_pur': 25, 'rna2p_pyr': 19, 'rna3p_pur': 92, 'rna3p_pyr': 91} Link IDs: {'rna2p': 44, 'rna3p': 183} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "CA" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2144 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain breaks: 2 Chain: "CB" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2063 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 20, 'TRANS': 239} Chain breaks: 1 Chain: "CC" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2258 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 37, 'TRANS': 234} Chain breaks: 3 Chain: "CE" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3673 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 21, 'TRANS': 441} Chain breaks: 1 Chain: "CH" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 891 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "CI" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1196 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "CJ" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3109 Classifications: {'peptide': 380} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 354} Chain breaks: 2 Chain: "CM" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1525 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "CN" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1856 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain: "CQ" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 960 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "CR" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain breaks: 3 Chain: "CU" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "Ch" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 562 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "LB" Number of atoms: 2708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2708 Classifications: {'peptide': 341} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 328} Chain breaks: 1 Chain: "LC" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2752 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 24, 'TRANS': 337} Chain: "LE" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1338 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 158} Chain breaks: 1 Chain: "LF" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1967 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "LG" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1470 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 1 Chain: "LL" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 964 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "LM" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1101 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "LN" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1563 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "LO" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1618 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 10, 'TRANS': 193} Chain: "LP" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1212 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 1 Chain: "LQ" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "LS" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1433 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain: "LT" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1014 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "LV" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 995 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "LY" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "Le" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1055 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "Lf" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 862 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "Lh" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "Li" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "Lj" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "Cc" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 7, 'TRANS': 228} Chain breaks: 1 Chain: "Cd" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2800 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 324} Chain breaks: 1 Chain: "Ce" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1609 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 8, 'TRANS': 185} Chain: "Cf" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1225 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "Cy" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1210 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 218} Link IDs: {'PTRANS': 17, 'TRANS': 226} Chain breaks: 1 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 805 Unresolved non-hydrogen angles: 1002 Unresolved non-hydrogen dihedrals: 685 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 14, 'PHE:plan': 17, 'GLU:plan': 14, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 416 Chain: "Cg" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1850 Classifications: {'peptide': 233} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 216} Chain breaks: 1 Chain: "CP" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 1596 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 273} Link IDs: {'PTRANS': 19, 'TRANS': 304} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 999 Unresolved non-hydrogen angles: 1278 Unresolved non-hydrogen dihedrals: 838 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 8, 'TYR:plan': 14, 'ASN:plan1': 18, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 17, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "CG" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 873 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 7, 'TRANS': 169} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 550 Unresolved non-hydrogen angles: 701 Unresolved non-hydrogen dihedrals: 460 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 289 Chain: "Lq" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1021 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 197} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 601 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 491 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 257 Chain: "Cx" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 565 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 14, 'TRANS': 87} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "LJ" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 831 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 719 Unresolved non-hydrogen dihedrals: 479 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG%COO:plan': 1, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 338 Chain: "LD" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 1346 Classifications: {'peptide': 273} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 226} Link IDs: {'PTRANS': 6, 'TRANS': 266} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 919 Unresolved non-hydrogen angles: 1165 Unresolved non-hydrogen dihedrals: 779 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 5, 'TYR:plan': 19, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 10, 'GLU:plan': 26, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 549 Chain: "C4" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2536 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 54, 'rna3p_pyr': 54} Link IDs: {'rna2p': 11, 'rna3p': 107} Chain: "CX" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 375 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain breaks: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "C1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ce" 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 97128 SG CYSLj 19 180.367 136.053 137.903 1.00 69.77 S ATOM 97156 SG CYSLj 22 181.707 137.817 140.938 1.00 62.75 S ATOM 97254 SG CYSLj 34 178.035 137.936 140.235 1.00 68.20 S ATOM 97271 SG CYSLj 37 180.274 139.891 137.982 1.00 60.38 S ATOM A022D SG CYSCe 38 210.583 184.930 196.403 1.00 73.96 S Time building chain proxies: 43.90, per 1000 atoms: 0.37 Number of scatterers: 117417 At special positions: 0 Unit cell: (270.655, 295.735, 313.5, 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 3 29.99 S 183 16.00 P 2395 15.00 O 28513 8.00 N 21772 7.00 C 64551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYSCQ 6 " - pdb=" SG CYSCQ 9 " distance=2.03 Simple disulfide: pdb=" SG CYSCQ 9 " - pdb=" SG CYSCQ 32 " distance=2.02 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: 43.79 Conformation dependent library (CDL) restraints added in 9.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNCe1000 " pdb="ZN ZNCe1000 " - pdb=" SG CYSCe 38 " pdb=" ZNLj 101 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 37 " Number of angles added : 6 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16574 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 329 helices and 76 sheets defined 47.5% alpha, 12.3% beta 800 base pairs and 1267 stacking pairs defined. Time for finding SS restraints: 64.52 Creating SS restraints... Processing helix chain 'CA' and resid 45 through 60 Proline residue: CA 60 - end of helix Processing helix chain 'CA' and resid 73 through 85 removed outlier: 4.246A pdb=" N LEUCA 77 " --> pdb=" O ARGCA 73 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYSCA 78 " --> pdb=" O LEUCA 74 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLUCA 79 " --> pdb=" O TYRCA 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEUCA 80 " --> pdb=" O GLUCA 76 " (cutoff:3.500A) Processing helix chain 'CA' and resid 143 through 149 removed outlier: 4.092A pdb=" N GLUCA 147 " --> pdb=" O ASPCA 143 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLNCA 148 " --> pdb=" O ALACA 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLUCA 149 " --> pdb=" O ALACA 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'CA' and resid 143 through 149' Processing helix chain 'CA' and resid 150 through 164 removed outlier: 4.009A pdb=" N ILECA 155 " --> pdb=" O TYRCA 151 " (cutoff:3.500A) Processing helix chain 'CA' and resid 263 through 295 removed outlier: 3.505A pdb=" N GLUCA 270 " --> pdb=" O LYSCA 266 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARGCA 272 " --> pdb=" O ARGCA 268 " (cutoff:3.500A) Processing helix chain 'CA' and resid 310 through 316 removed outlier: 4.414A pdb=" N ALACA 316 " --> pdb=" O ARGCA 312 " (cutoff:3.500A) Processing helix chain 'CB' and resid 19 through 40 removed outlier: 3.756A pdb=" N THRCB 23 " --> pdb=" O ASPCB 19 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEUCB 31 " --> pdb=" O CYSCB 27 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYSCB 35 " --> pdb=" O LEUCB 31 " (cutoff:3.500A) Processing helix chain 'CB' and resid 52 through 60 removed outlier: 4.042A pdb=" N GLUCB 59 " --> pdb=" O SERCB 55 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THRCB 60 " --> pdb=" O THRCB 56 " (cutoff:3.500A) Processing helix chain 'CB' and resid 104 through 115 removed outlier: 3.759A pdb=" N TYRCB 108 " --> pdb=" O PROCB 104 " (cutoff:3.500A) Processing helix chain 'CB' and resid 117 through 125 removed outlier: 4.421A pdb=" N ARGCB 121 " --> pdb=" O PROCB 117 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLYCB 125 " --> pdb=" O ARGCB 121 " (cutoff:3.500A) Processing helix chain 'CB' and resid 129 through 137 Processing helix chain 'CB' and resid 139 through 151 removed outlier: 3.673A pdb=" N ARGCB 144 " --> pdb=" O TYRCB 140 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHECB 147 " --> pdb=" O GLNCB 143 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HISCB 150 " --> pdb=" O LEUCB 146 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASPCB 151 " --> pdb=" O PHECB 147 " (cutoff:3.500A) Processing helix chain 'CB' and resid 156 through 167 removed outlier: 5.379A pdb=" N ASNCB 161 " --> pdb=" O THRCB 157 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ARGCB 162 " --> pdb=" O ARGCB 158 " (cutoff:3.500A) Proline residue: CB 164 - end of helix Processing helix chain 'CB' and resid 168 through 173 Processing helix chain 'CB' and resid 216 through 230 removed outlier: 3.510A pdb=" N LYSCB 226 " --> pdb=" O ALACB 222 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLYCB 229 " --> pdb=" O ARGCB 225 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALACB 230 " --> pdb=" O LYSCB 226 " (cutoff:3.500A) Processing helix chain 'CB' and resid 251 through 269 removed outlier: 3.593A pdb=" N GLUCB 268 " --> pdb=" O ARGCB 264 " (cutoff:3.500A) Processing helix chain 'CC' and resid 232 through 247 removed outlier: 3.617A pdb=" N VALCC 242 " --> pdb=" O LEUCC 238 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLYCC 245 " --> pdb=" O LYSCC 241 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILECC 247 " --> pdb=" O GLNCC 243 " (cutoff:3.500A) Processing helix chain 'CC' and resid 260 through 265 removed outlier: 5.522A pdb=" N VALCC 265 " --> pdb=" O TRPCC 261 " (cutoff:3.500A) Processing helix chain 'CC' and resid 277 through 283 removed outlier: 4.487A pdb=" N PHECC 281 " --> pdb=" O PROCC 277 " (cutoff:3.500A) Proline residue: CC 283 - end of helix Processing helix chain 'CC' and resid 284 through 301 Processing helix chain 'CC' and resid 308 through 316 removed outlier: 4.625A pdb=" N GLUCC 316 " --> pdb=" O ARGCC 312 " (cutoff:3.500A) Processing helix chain 'CC' and resid 357 through 362 Proline residue: CC 362 - end of helix Processing helix chain 'CC' and resid 363 through 374 removed outlier: 5.684A pdb=" N ASPCC 374 " --> pdb=" O TRPCC 370 " (cutoff:3.500A) Processing helix chain 'CC' and resid 389 through 394 Proline residue: CC 394 - end of helix Processing helix chain 'CC' and resid 398 through 412 Processing helix chain 'CE' and resid 112 through 117 removed outlier: 3.896A pdb=" N LEUCE 116 " --> pdb=" O GLUCE 112 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASNCE 117 " --> pdb=" O PHECE 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'CE' and resid 112 through 117' Processing helix chain 'CE' and resid 119 through 130 removed outlier: 3.556A pdb=" N ALACE 125 " --> pdb=" O LYSCE 121 " (cutoff:3.500A) Processing helix chain 'CE' and resid 135 through 148 Proline residue: CE 143 - end of helix Processing helix chain 'CE' and resid 160 through 177 removed outlier: 3.647A pdb=" N LEUCE 166 " --> pdb=" O THRCE 162 " (cutoff:3.500A) Proline residue: CE 168 - end of helix Processing helix chain 'CE' and resid 192 through 208 Processing helix chain 'CE' and resid 222 through 233 Processing helix chain 'CE' and resid 240 through 250 Processing helix chain 'CE' and resid 265 through 273 Processing helix chain 'CE' and resid 274 through 286 removed outlier: 3.770A pdb=" N LYSCE 283 " --> pdb=" O ARGCE 279 " (cutoff:3.500A) Proline residue: CE 286 - end of helix Processing helix chain 'CE' and resid 300 through 311 removed outlier: 3.818A pdb=" N GLUCE 304 " --> pdb=" O THRCE 300 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASPCE 305 " --> pdb=" O THRCE 301 " (cutoff:3.500A) Processing helix chain 'CE' and resid 343 through 356 Processing helix chain 'CE' and resid 366 through 381 Processing helix chain 'CE' and resid 392 through 406 Processing helix chain 'CE' and resid 414 through 422 removed outlier: 3.992A pdb=" N GLYCE 420 " --> pdb=" O VALCE 416 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEUCE 421 " --> pdb=" O ALACE 417 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASPCE 422 " --> pdb=" O ALACE 418 " (cutoff:3.500A) Processing helix chain 'CE' and resid 437 through 451 Processing helix chain 'CE' and resid 466 through 477 removed outlier: 4.674A pdb=" N LEUCE 470 " --> pdb=" O GLUCE 466 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALACE 471 " --> pdb=" O LEUCE 467 " (cutoff:3.500A) Processing helix chain 'CE' and resid 493 through 504 Processing helix chain 'CE' and resid 505 through 525 removed outlier: 3.655A pdb=" N HISCE 525 " --> pdb=" O ALACE 521 " (cutoff:3.500A) Processing helix chain 'CE' and resid 527 through 532 removed outlier: 3.508A pdb=" N PHECE 531 " --> pdb=" O LEUCE 527 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASPCE 532 " --> pdb=" O ARGCE 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'CE' and resid 527 through 532' Processing helix chain 'CE' and resid 537 through 546 removed outlier: 3.605A pdb=" N PHECE 545 " --> pdb=" O VALCE 541 " (cutoff:3.500A) Processing helix chain 'CH' and resid 384 through 390 removed outlier: 3.637A pdb=" N LYSCH 388 " --> pdb=" O PROCH 384 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASNCH 389 " --> pdb=" O GLUCH 385 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEUCH 390 " --> pdb=" O ALACH 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 384 through 390' Processing helix chain 'CH' and resid 403 through 412 Processing helix chain 'CH' and resid 420 through 425 removed outlier: 4.250A pdb=" N ASPCH 424 " --> pdb=" O ASPCH 420 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRPCH 425 " --> pdb=" O LEUCH 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 420 through 425' Processing helix chain 'CH' and resid 445 through 450 Processing helix chain 'CH' and resid 453 through 472 removed outlier: 4.161A pdb=" N GLUCH 464 " --> pdb=" O ALACH 460 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLUCH 465 " --> pdb=" O LEUCH 461 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLUCH 466 " --> pdb=" O GLUCH 462 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARGCH 467 " --> pdb=" O GLUCH 463 " (cutoff:3.500A) Processing helix chain 'CH' and resid 429 through 435 removed outlier: 3.791A pdb=" N LYSCH 433 " --> pdb=" O PROCH 430 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYRCH 434 " --> pdb=" O GLUCH 431 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASPCH 435 " --> pdb=" O TRPCH 432 " (cutoff:3.500A) Processing helix chain 'CI' and resid 199 through 211 removed outlier: 3.824A pdb=" N GLNCI 209 " --> pdb=" O GLYCI 205 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHECI 210 " --> pdb=" O TYRCI 206 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLYCI 211 " --> pdb=" O PHECI 207 " (cutoff:3.500A) Processing helix chain 'CI' and resid 237 through 249 Processing helix chain 'CI' and resid 284 through 295 removed outlier: 4.000A pdb=" N GLUCI 294 " --> pdb=" O GLYCI 290 " (cutoff:3.500A) Processing helix chain 'CI' and resid 298 through 324 removed outlier: 4.055A pdb=" N GLUCI 322 " --> pdb=" O GLUCI 318 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N METCI 323 " --> pdb=" O LYSCI 319 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 6 through 11 removed outlier: 3.698A pdb=" N SERCJ 10 " --> pdb=" O LYSCJ 6 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLYCJ 11 " --> pdb=" O LYSCJ 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'CJ' and resid 6 through 11' Processing helix chain 'CJ' and resid 18 through 27 Processing helix chain 'CJ' and resid 29 through 41 removed outlier: 3.983A pdb=" N ARGCJ 34 " --> pdb=" O LEUCJ 30 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 49 through 55 Processing helix chain 'CJ' and resid 65 through 75 removed outlier: 3.705A pdb=" N GLUCJ 75 " --> pdb=" O TYRCJ 71 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 76 through 98 removed outlier: 3.738A pdb=" N ALACJ 94 " --> pdb=" O LYSCJ 90 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEUCJ 95 " --> pdb=" O ILECJ 91 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 99 through 111 Processing helix chain 'CJ' and resid 112 through 117 removed outlier: 3.664A pdb=" N THRCJ 116 " --> pdb=" O LEUCJ 112 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 123 through 131 removed outlier: 3.515A pdb=" N TYRCJ 131 " --> pdb=" O ILECJ 127 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 135 through 153 removed outlier: 3.727A pdb=" N ASPCJ 142 " --> pdb=" O LEUCJ 138 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASPCJ 143 " --> pdb=" O ARGCJ 139 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SERCJ 146 " --> pdb=" O ASPCJ 142 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N METCJ 147 " --> pdb=" O ASPCJ 143 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEUCJ 148 " --> pdb=" O CYSCJ 144 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 161 through 183 Processing helix chain 'CJ' and resid 223 through 250 removed outlier: 3.545A pdb=" N THRCJ 229 " --> pdb=" O ARGCJ 225 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHECJ 230 " --> pdb=" O ILECJ 226 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 258 through 265 removed outlier: 3.987A pdb=" N GLYCJ 265 " --> pdb=" O LYSCJ 261 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 362 through 368 removed outlier: 5.455A pdb=" N PHECJ 367 " --> pdb=" O PROCJ 363 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALACJ 368 " --> pdb=" O SERCJ 364 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 379 through 391 Processing helix chain 'CJ' and resid 457 through 468 removed outlier: 4.140A pdb=" N VALCJ 461 " --> pdb=" O GLNCJ 457 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 472 through 477 Processing helix chain 'CM' and resid 53 through 78 removed outlier: 3.775A pdb=" N TYRCM 57 " --> pdb=" O ARGCM 53 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLUCM 67 " --> pdb=" O GLUCM 63 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLNCM 78 " --> pdb=" O ILECM 74 " (cutoff:3.500A) Processing helix chain 'CM' and resid 102 through 113 Processing helix chain 'CM' and resid 126 through 137 removed outlier: 3.703A pdb=" N ALACM 130 " --> pdb=" O THRCM 126 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLUCM 131 " --> pdb=" O LYSCM 127 " (cutoff:3.500A) Processing helix chain 'CM' and resid 146 through 156 Processing helix chain 'CM' and resid 171 through 179 removed outlier: 3.548A pdb=" N LEUCM 179 " --> pdb=" O ILECM 175 " (cutoff:3.500A) Processing helix chain 'CM' and resid 186 through 196 removed outlier: 4.525A pdb=" N LEUCM 190 " --> pdb=" O CYSCM 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILECM 191 " --> pdb=" O ILECM 187 " (cutoff:3.500A) Processing helix chain 'CM' and resid 200 through 209 removed outlier: 4.764A pdb=" N TRPCM 209 " --> pdb=" O ALACM 205 " (cutoff:3.500A) Processing helix chain 'CM' and resid 239 through 249 removed outlier: 4.480A pdb=" N ALACM 243 " --> pdb=" O GLUCM 239 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEUCM 244 " --> pdb=" O HISCM 240 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALACM 247 " --> pdb=" O ALACM 243 " (cutoff:3.500A) Processing helix chain 'CN' and resid 12 through 17 removed outlier: 3.775A pdb=" N PHECN 16 " --> pdb=" O GLUCN 12 " (cutoff:3.500A) Processing helix chain 'CN' and resid 32 through 43 removed outlier: 3.651A pdb=" N LEUCN 42 " --> pdb=" O PHECN 38 " (cutoff:3.500A) Processing helix chain 'CN' and resid 58 through 63 removed outlier: 3.755A pdb=" N LEUCN 62 " --> pdb=" O ILECN 58 " (cutoff:3.500A) Processing helix chain 'CN' and resid 77 through 89 removed outlier: 3.552A pdb=" N SERCN 87 " --> pdb=" O HISCN 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEUCN 88 " --> pdb=" O LEUCN 84 " (cutoff:3.500A) Proline residue: CN 89 - end of helix Processing helix chain 'CN' and resid 103 through 108 Processing helix chain 'CN' and resid 122 through 133 removed outlier: 3.843A pdb=" N GLUCN 126 " --> pdb=" O GLUCN 122 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLUCN 127 " --> pdb=" O ARGCN 123 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILECN 128 " --> pdb=" O GLUCN 124 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASPCN 131 " --> pdb=" O GLUCN 127 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VALCN 132 " --> pdb=" O ILECN 128 " (cutoff:3.500A) Processing helix chain 'CN' and resid 147 through 152 Processing helix chain 'CN' and resid 166 through 178 Processing helix chain 'CN' and resid 192 through 197 removed outlier: 3.782A pdb=" N GLYCN 196 " --> pdb=" O VALCN 192 " (cutoff:3.500A) Processing helix chain 'CN' and resid 211 through 223 removed outlier: 3.742A pdb=" N ARGCN 223 " --> pdb=" O GLUCN 219 " (cutoff:3.500A) Processing helix chain 'CN' and resid 231 through 238 Processing helix chain 'CN' and resid 239 through 246 Processing helix chain 'CQ' and resid 33 through 43 Processing helix chain 'CQ' and resid 45 through 50 removed outlier: 5.770A pdb=" N LYSCQ 50 " --> pdb=" O PROCQ 46 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 52 through 60 removed outlier: 3.674A pdb=" N ARGCQ 56 " --> pdb=" O THRCQ 52 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 66 through 73 removed outlier: 3.690A pdb=" N GLNCQ 70 " --> pdb=" O ASPCQ 66 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALACQ 73 " --> pdb=" O LEUCQ 69 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 82 through 112 removed outlier: 3.692A pdb=" N TRPCQ 86 " --> pdb=" O ASNCQ 82 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLNCQ 87 " --> pdb=" O ARGCQ 83 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALACQ 92 " --> pdb=" O LYSCQ 88 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLUCQ 94 " --> pdb=" O LEUCQ 90 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARGCQ 95 " --> pdb=" O LYSCQ 91 " (cutoff:3.500A) Processing helix chain 'CR' and resid 3 through 12 removed outlier: 3.739A pdb=" N ARGCR 8 " --> pdb=" O GLUCR 4 " (cutoff:3.500A) Processing helix chain 'CR' and resid 33 through 39 Processing helix chain 'CR' and resid 44 through 53 Processing helix chain 'CR' and resid 166 through 178 Processing helix chain 'CR' and resid 188 through 202 Processing helix chain 'CR' and resid 205 through 212 Processing helix chain 'CR' and resid 221 through 233 Processing helix chain 'CU' and resid 192 through 204 removed outlier: 3.748A pdb=" N ARGCU 202 " --> pdb=" O THRCU 198 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILECU 203 " --> pdb=" O ALACU 199 " (cutoff:3.500A) Processing helix chain 'CU' and resid 213 through 218 removed outlier: 4.208A pdb=" N HISCU 217 " --> pdb=" O PROCU 213 " (cutoff:3.500A) Processing helix chain 'CU' and resid 225 through 231 removed outlier: 6.323A pdb=" N SERCU 229 " --> pdb=" O ARGCU 225 " (cutoff:3.500A) Proline residue: CU 231 - end of helix Processing helix chain 'CU' and resid 235 through 262 Processing helix chain 'CU' and resid 278 through 310 Processing helix chain 'Ch' and resid 270 through 315 removed outlier: 4.443A pdb=" N GLNCh 274 " --> pdb=" O VALCh 270 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILECh 275 " --> pdb=" O THRCh 271 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILECh 276 " --> pdb=" O THRCh 272 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLUCh 277 " --> pdb=" O GLUCh 273 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEUCh 282 " --> pdb=" O ARGCh 278 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILECh 285 " --> pdb=" O LYSCh 281 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALACh 311 " --> pdb=" O ALACh 307 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARGCh 312 " --> pdb=" O GLUCh 308 " (cutoff:3.500A) Processing helix chain 'Ch' and resid 319 through 340 removed outlier: 4.459A pdb=" N THRCh 327 " --> pdb=" O GLUCh 323 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILECh 338 " --> pdb=" O PHECh 334 " (cutoff:3.500A) Processing helix chain 'LB' and resid 111 through 120 removed outlier: 3.868A pdb=" N LYSLB 115 " --> pdb=" O SERLB 111 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARGLB 116 " --> pdb=" O ASPLB 112 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 140 removed outlier: 4.110A pdb=" N ASNLB 140 " --> pdb=" O LYSLB 136 " (cutoff:3.500A) Processing helix chain 'LB' and resid 141 through 155 Processing helix chain 'LB' and resid 166 through 171 removed outlier: 3.899A pdb=" N THRLB 170 " --> pdb=" O GLNLB 166 " (cutoff:3.500A) Proline residue: LB 171 - end of helix No H-bonds generated for 'chain 'LB' and resid 166 through 171' Processing helix chain 'LB' and resid 188 through 200 removed outlier: 3.848A pdb=" N VALLB 193 " --> pdb=" O VALLB 189 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLULB 194 " --> pdb=" O ALALB 190 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHELB 200 " --> pdb=" O GLYLB 196 " (cutoff:3.500A) Processing helix chain 'LB' and resid 205 through 210 removed outlier: 3.542A pdb=" N ILELB 209 " --> pdb=" O THRLB 205 " (cutoff:3.500A) Processing helix chain 'LB' and resid 348 through 353 Processing helix chain 'LB' and resid 373 through 382 removed outlier: 3.723A pdb=" N GLNLB 379 " --> pdb=" O ALALB 375 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHELB 380 " --> pdb=" O GLULB 376 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLYLB 382 " --> pdb=" O LYSLB 378 " (cutoff:3.500A) Processing helix chain 'LB' and resid 384 through 391 Processing helix chain 'LC' and resid 24 through 30 removed outlier: 4.317A pdb=" N SERLC 28 " --> pdb=" O PROLC 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALALC 29 " --> pdb=" O LYSLC 25 " (cutoff:3.500A) Proline residue: LC 30 - end of helix No H-bonds generated for 'chain 'LC' and resid 24 through 30' Processing helix chain 'LC' and resid 32 through 48 removed outlier: 3.541A pdb=" N GLYLC 42 " --> pdb=" O HISLC 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSLC 45 " --> pdb=" O THRLC 41 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASNLC 46 " --> pdb=" O GLYLC 42 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYSLC 47 " --> pdb=" O METLC 43 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ARGLC 48 " --> pdb=" O ALALC 44 " (cutoff:3.500A) Processing helix chain 'LC' and resid 115 through 133 removed outlier: 3.546A pdb=" N ALALC 131 " --> pdb=" O LEULC 127 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALLC 132 " --> pdb=" O ALALC 128 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALALC 133 " --> pdb=" O ALALC 129 " (cutoff:3.500A) Processing helix chain 'LC' and resid 134 through 140 removed outlier: 3.660A pdb=" N GLYLC 140 " --> pdb=" O LEULC 136 " (cutoff:3.500A) Processing helix chain 'LC' and resid 154 through 159 removed outlier: 3.900A pdb=" N VALLC 158 " --> pdb=" O ASPLC 154 " (cutoff:3.500A) Processing helix chain 'LC' and resid 160 through 165 removed outlier: 4.454A pdb=" N ALALC 164 " --> pdb=" O GLYLC 160 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYSLC 165 " --> pdb=" O ASPLC 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 160 through 165' Processing helix chain 'LC' and resid 166 through 177 Processing helix chain 'LC' and resid 178 through 189 removed outlier: 3.648A pdb=" N LYSLC 186 " --> pdb=" O VALLC 182 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYSLC 189 " --> pdb=" O VALLC 185 " (cutoff:3.500A) Processing helix chain 'LC' and resid 195 through 200 removed outlier: 4.069A pdb=" N ARGLC 199 " --> pdb=" O LYSLC 195 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLYLC 200 " --> pdb=" O GLYLC 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 195 through 200' Processing helix chain 'LC' and resid 220 through 228 removed outlier: 4.140A pdb=" N LYSLC 224 " --> pdb=" O LYSLC 220 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLYLC 225 " --> pdb=" O GLULC 221 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASNLC 228 " --> pdb=" O LYSLC 224 " (cutoff:3.500A) Processing helix chain 'LC' and resid 241 through 247 Proline residue: LC 247 - end of helix Processing helix chain 'LC' and resid 258 through 272 removed outlier: 4.322A pdb=" N ASPLC 266 " --> pdb=" O ILELC 262 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALALC 267 " --> pdb=" O LYSLC 263 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYRLC 269 " --> pdb=" O LEULC 265 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYSLC 272 " --> pdb=" O VALLC 268 " (cutoff:3.500A) Processing helix chain 'LC' and resid 286 through 292 removed outlier: 3.501A pdb=" N LEULC 290 " --> pdb=" O ASPLC 286 " (cutoff:3.500A) Processing helix chain 'LC' and resid 293 through 300 removed outlier: 4.248A pdb=" N VALLC 299 " --> pdb=" O GLULC 295 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEULC 300 " --> pdb=" O ILELC 296 " (cutoff:3.500A) Processing helix chain 'LC' and resid 318 through 323 removed outlier: 4.510A pdb=" N LYSLC 323 " --> pdb=" O PROLC 319 " (cutoff:3.500A) Processing helix chain 'LC' and resid 324 through 330 Processing helix chain 'LC' and resid 332 through 340 removed outlier: 3.708A pdb=" N ALALC 337 " --> pdb=" O ALALC 333 " (cutoff:3.500A) Processing helix chain 'LC' and resid 355 through 364 removed outlier: 3.602A pdb=" N LYSLC 359 " --> pdb=" O PROLC 355 " (cutoff:3.500A) Processing helix chain 'LC' and resid 214 through 219 removed outlier: 3.654A pdb=" N GLYLC 219 " --> pdb=" O SERLC 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 214 through 219' Processing helix chain 'LE' and resid 98 through 103 removed outlier: 3.822A pdb=" N VALLE 102 " --> pdb=" O ASNLE 98 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILELE 103 " --> pdb=" O ALALE 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 98 through 103' Processing helix chain 'LE' and resid 115 through 124 removed outlier: 4.073A pdb=" N GLNLE 124 " --> pdb=" O ASPLE 120 " (cutoff:3.500A) Processing helix chain 'LE' and resid 125 through 130 removed outlier: 3.862A pdb=" N THRLE 129 " --> pdb=" O PROLE 125 " (cutoff:3.500A) Processing helix chain 'LE' and resid 138 through 145 removed outlier: 4.141A pdb=" N GLNLE 145 " --> pdb=" O ALALE 141 " (cutoff:3.500A) Processing helix chain 'LE' and resid 155 through 174 removed outlier: 4.637A pdb=" N ALALE 168 " --> pdb=" O ALALE 164 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEULE 169 " --> pdb=" O ILELE 165 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALALE 171 " --> pdb=" O LYSLE 167 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASNLE 172 " --> pdb=" O ALALE 168 " (cutoff:3.500A) Processing helix chain 'LE' and resid 178 through 185 Processing helix chain 'LF' and resid 15 through 79 removed outlier: 3.641A pdb=" N LYSLF 20 " --> pdb=" O GLULF 16 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLNLF 48 " --> pdb=" O LYSLF 44 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYSLF 59 " --> pdb=" O GLULF 55 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALALF 72 " --> pdb=" O LYSLF 68 " (cutoff:3.500A) Processing helix chain 'LF' and resid 102 through 113 removed outlier: 3.512A pdb=" N ILELF 108 " --> pdb=" O LYSLF 104 " (cutoff:3.500A) Processing helix chain 'LF' and resid 126 through 137 removed outlier: 3.676A pdb=" N GLULF 131 " --> pdb=" O LYSLF 127 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N METLF 132 " --> pdb=" O ALALF 128 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILELF 135 " --> pdb=" O GLULF 131 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VALLF 136 " --> pdb=" O METLF 132 " (cutoff:3.500A) Processing helix chain 'LF' and resid 146 through 156 Processing helix chain 'LF' and resid 171 through 179 removed outlier: 4.448A pdb=" N ILELF 175 " --> pdb=" O ASPLF 171 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLULF 176 " --> pdb=" O ASNLF 172 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASNLF 178 " --> pdb=" O ILELF 174 " (cutoff:3.500A) Processing helix chain 'LF' and resid 186 through 197 removed outlier: 3.926A pdb=" N VALLF 197 " --> pdb=" O GLULF 193 " (cutoff:3.500A) Processing helix chain 'LF' and resid 200 through 209 removed outlier: 3.601A pdb=" N LEULF 208 " --> pdb=" O ALALF 204 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TRPLF 209 " --> pdb=" O ALALF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 239 through 249 removed outlier: 4.553A pdb=" N ALALF 243 " --> pdb=" O GLULF 239 " (cutoff:3.500A) Processing helix chain 'LG' and resid 56 through 72 removed outlier: 3.587A pdb=" N ARGLG 63 " --> pdb=" O ILELG 59 " (cutoff:3.500A) Processing helix chain 'LG' and resid 75 through 84 removed outlier: 5.010A pdb=" N GLNLG 80 " --> pdb=" O PROLG 76 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHELG 81 " --> pdb=" O ALALG 77 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLNLG 82 " --> pdb=" O ILELG 78 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYRLG 83 " --> pdb=" O ALALG 79 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THRLG 84 " --> pdb=" O GLNLG 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 86 through 101 removed outlier: 3.596A pdb=" N LEULG 96 " --> pdb=" O GLNLG 92 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYSLG 99 " --> pdb=" O LYSLG 95 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYRLG 100 " --> pdb=" O LEULG 96 " (cutoff:3.500A) Processing helix chain 'LG' and resid 104 through 121 Processing helix chain 'LG' and resid 138 through 149 removed outlier: 3.548A pdb=" N GLYLG 144 " --> pdb=" O ASNLG 140 " (cutoff:3.500A) Processing helix chain 'LG' and resid 162 through 177 removed outlier: 4.843A pdb=" N VALLG 166 " --> pdb=" O PROLG 162 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHELG 168 " --> pdb=" O GLULG 164 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEULG 169 " --> pdb=" O LEULG 165 " (cutoff:3.500A) Proline residue: LG 170 - end of helix Processing helix chain 'LG' and resid 185 through 194 removed outlier: 3.618A pdb=" N LEULG 189 " --> pdb=" O GLYLG 185 " (cutoff:3.500A) Processing helix chain 'LG' and resid 210 through 233 removed outlier: 3.666A pdb=" N LEULG 214 " --> pdb=" O ASPLG 210 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEULG 226 " --> pdb=" O LYSLG 222 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLULG 227 " --> pdb=" O GLULG 223 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYSLG 228 " --> pdb=" O GLYLG 224 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLULG 230 " --> pdb=" O LEULG 226 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASPLG 231 " --> pdb=" O GLULG 227 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THRLG 232 " --> pdb=" O LYSLG 228 " (cutoff:3.500A) Processing helix chain 'LL' and resid 17 through 22 removed outlier: 3.936A pdb=" N ARGLL 21 " --> pdb=" O HISLL 17 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VALLL 22 " --> pdb=" O TRPLL 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'LL' and resid 17 through 22' Processing helix chain 'LL' and resid 27 through 47 removed outlier: 3.539A pdb=" N ALALL 45 " --> pdb=" O ALALL 41 " (cutoff:3.500A) Processing helix chain 'LL' and resid 76 through 84 Processing helix chain 'LL' and resid 86 through 94 Proline residue: LL 91 - end of helix Processing helix chain 'LL' and resid 105 through 123 removed outlier: 3.668A pdb=" N ASNLL 112 " --> pdb=" O SERLL 108 " (cutoff:3.500A) Processing helix chain 'LM' and resid 58 through 63 removed outlier: 3.632A pdb=" N ALALM 62 " --> pdb=" O PROLM 58 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEULM 63 " --> pdb=" O LEULM 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'LM' and resid 58 through 63' Processing helix chain 'LM' and resid 77 through 89 Processing helix chain 'LM' and resid 90 through 98 removed outlier: 5.332A pdb=" N ASNLM 98 " --> pdb=" O TRPLM 94 " (cutoff:3.500A) Processing helix chain 'LM' and resid 99 through 112 removed outlier: 3.718A pdb=" N LEULM 112 " --> pdb=" O ARGLM 108 " (cutoff:3.500A) Processing helix chain 'LM' and resid 114 through 136 removed outlier: 3.554A pdb=" N VALLM 120 " --> pdb=" O ASPLM 116 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYSLM 125 " --> pdb=" O METLM 121 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLULM 130 " --> pdb=" O GLNLM 126 " (cutoff:3.500A) Processing helix chain 'LN' and resid 2 through 14 removed outlier: 4.141A pdb=" N TYRLN 6 " --> pdb=" O GLYLN 2 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 3.833A pdb=" N GLNLN 32 " --> pdb=" O TRPLN 28 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEULN 33 " --> pdb=" O GLULN 29 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASNLN 34 " --> pdb=" O TYRLN 30 " (cutoff:3.500A) Processing helix chain 'LN' and resid 44 through 52 Processing helix chain 'LN' and resid 97 through 111 removed outlier: 3.522A pdb=" N VALLN 106 " --> pdb=" O ALALN 102 " (cutoff:3.500A) Processing helix chain 'LN' and resid 139 through 146 removed outlier: 3.788A pdb=" N ASPLN 145 " --> pdb=" O ALALN 141 " (cutoff:3.500A) Proline residue: LN 146 - end of helix Processing helix chain 'LN' and resid 148 through 153 removed outlier: 4.439A pdb=" N CYSLN 152 " --> pdb=" O ILELN 148 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASNLN 153 " --> pdb=" O ASNLN 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 148 through 153' Processing helix chain 'LN' and resid 158 through 163 removed outlier: 3.640A pdb=" N ARGLN 162 " --> pdb=" O HISLN 158 " (cutoff:3.500A) Processing helix chain 'LN' and resid 165 through 173 Processing helix chain 'LN' and resid 186 through 196 Processing helix chain 'LO' and resid 16 through 31 Processing helix chain 'LO' and resid 47 through 63 removed outlier: 3.625A pdb=" N ALALO 51 " --> pdb=" O GLULO 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYSLO 54 " --> pdb=" O ARGLO 50 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N METLO 62 " --> pdb=" O TYRLO 58 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N THRLO 63 " --> pdb=" O LEULO 59 " (cutoff:3.500A) Processing helix chain 'LO' and resid 71 through 77 removed outlier: 4.777A pdb=" N PHELO 75 " --> pdb=" O GLYLO 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARGLO 76 " --> pdb=" O PROLO 72 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALALO 77 " --> pdb=" O PHELO 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'LO' and resid 71 through 77' Processing helix chain 'LO' and resid 78 through 91 removed outlier: 3.658A pdb=" N METLO 89 " --> pdb=" O ALALO 85 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILELO 90 " --> pdb=" O VALLO 86 " (cutoff:3.500A) Proline residue: LO 91 - end of helix Processing helix chain 'LO' and resid 94 through 105 removed outlier: 5.029A pdb=" N LYSLO 105 " --> pdb=" O LEULO 101 " (cutoff:3.500A) Processing helix chain 'LO' and resid 111 through 118 removed outlier: 4.515A pdb=" N LYSLO 116 " --> pdb=" O PROLO 112 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYSLO 117 " --> pdb=" O PROLO 113 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYSLO 118 " --> pdb=" O TYRLO 114 " (cutoff:3.500A) Processing helix chain 'LO' and resid 126 through 131 Processing helix chain 'LO' and resid 139 through 148 Processing helix chain 'LO' and resid 151 through 189 removed outlier: 3.500A pdb=" N ALALO 164 " --> pdb=" O GLULO 160 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEULO 175 " --> pdb=" O GLULO 171 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALALO 189 " --> pdb=" O LYSLO 185 " (cutoff:3.500A) Processing helix chain 'LO' and resid 192 through 203 removed outlier: 3.778A pdb=" N SERLO 196 " --> pdb=" O ASPLO 192 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLULO 197 " --> pdb=" O PROLO 193 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALALO 198 " --> pdb=" O LYSLO 194 " (cutoff:3.500A) Processing helix chain 'LP' and resid 10 through 15 removed outlier: 4.757A pdb=" N ALALP 15 " --> pdb=" O PROLP 11 " (cutoff:3.500A) Processing helix chain 'LP' and resid 25 through 37 removed outlier: 3.529A pdb=" N ALALP 35 " --> pdb=" O GLULP 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILELP 36 " --> pdb=" O THRLP 32 " (cutoff:3.500A) Processing helix chain 'LP' and resid 40 through 54 Processing helix chain 'LP' and resid 70 through 77 removed outlier: 4.835A pdb=" N LYSLP 74 " --> pdb=" O THRLP 70 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLNLP 75 " --> pdb=" O ALALP 71 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRPLP 76 " --> pdb=" O GLNLP 72 " (cutoff:3.500A) Processing helix chain 'LP' and resid 84 through 106 Processing helix chain 'LQ' and resid 51 through 68 Processing helix chain 'LQ' and resid 70 through 83 removed outlier: 3.907A pdb=" N LYSLQ 74 " --> pdb=" O ALALQ 70 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N METLQ 82 " --> pdb=" O ARGLQ 78 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SERLQ 83 " --> pdb=" O ARGLQ 79 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 91 through 101 removed outlier: 5.537A pdb=" N ASNLQ 101 " --> pdb=" O ARGLQ 97 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 134 through 145 removed outlier: 3.683A pdb=" N GLYLQ 145 " --> pdb=" O ILELQ 141 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 150 through 158 Processing helix chain 'LS' and resid 33 through 49 Processing helix chain 'LS' and resid 98 through 114 Processing helix chain 'LS' and resid 117 through 122 removed outlier: 5.446A pdb=" N HISLS 122 " --> pdb=" O PHELS 118 " (cutoff:3.500A) Processing helix chain 'LS' and resid 137 through 145 removed outlier: 3.901A pdb=" N LEULS 143 " --> pdb=" O TYRLS 139 " (cutoff:3.500A) Processing helix chain 'LT' and resid 54 through 59 removed outlier: 6.334A pdb=" N GLYLT 59 " --> pdb=" O LYSLT 55 " (cutoff:3.500A) Processing helix chain 'LT' and resid 92 through 97 removed outlier: 4.030A pdb=" N VALLT 96 " --> pdb=" O ARGLT 92 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYSLT 97 " --> pdb=" O ILELT 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 92 through 97' Processing helix chain 'LT' and resid 102 through 123 removed outlier: 3.549A pdb=" N LYSLT 116 " --> pdb=" O ASNLT 112 " (cutoff:3.500A) Processing helix chain 'LV' and resid 121 through 129 Proline residue: LV 129 - end of helix Processing helix chain 'LV' and resid 130 through 136 removed outlier: 5.535A pdb=" N GLYLV 136 " --> pdb=" O ALALV 132 " (cutoff:3.500A) Processing helix chain 'LY' and resid 10 through 21 Processing helix chain 'LY' and resid 22 through 31 removed outlier: 3.941A pdb=" N VALLY 28 " --> pdb=" O SERLY 24 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SERLY 31 " --> pdb=" O ARGLY 27 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 99 through 104 removed outlier: 4.346A pdb=" N VALLY 103 " --> pdb=" O HISLY 99 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VALLY 104 " --> pdb=" O PROLY 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'LY' and resid 99 through 104' Processing helix chain 'LY' and resid 111 through 134 Processing helix chain 'Le' and resid 22 through 27 removed outlier: 5.149A pdb=" N LYSLe 27 " --> pdb=" O SERLe 23 " (cutoff:3.500A) Processing helix chain 'Le' and resid 41 through 46 Processing helix chain 'Le' and resid 79 through 88 removed outlier: 3.809A pdb=" N VALLe 83 " --> pdb=" O ASNLe 79 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEULe 85 " --> pdb=" O LYSLe 81 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEULe 86 " --> pdb=" O ASPLe 82 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEULe 87 " --> pdb=" O VALLe 83 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N METLe 88 " --> pdb=" O GLULe 84 " (cutoff:3.500A) Processing helix chain 'Le' and resid 102 through 117 Processing helix chain 'Lf' and resid 39 through 47 removed outlier: 3.967A pdb=" N PHELf 45 " --> pdb=" O ALALf 41 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYRLf 46 " --> pdb=" O ALALf 42 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEULf 47 " --> pdb=" O ALALf 43 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 8 through 15 removed outlier: 3.581A pdb=" N LEULh 12 " --> pdb=" O LYSLh 8 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SERLh 14 " --> pdb=" O GLYLh 10 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYSLh 15 " --> pdb=" O GLNLh 11 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 16 through 42 removed outlier: 3.544A pdb=" N ILELh 36 " --> pdb=" O SERLh 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLNLh 37 " --> pdb=" O GLNLh 33 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILELh 39 " --> pdb=" O ARGLh 35 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SERLh 40 " --> pdb=" O ILELh 36 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SERLh 41 " --> pdb=" O GLNLh 37 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SERLh 42 " --> pdb=" O LYSLh 38 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 43 through 76 removed outlier: 3.542A pdb=" N ASNLh 47 " --> pdb=" O GLYLh 43 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYSLh 76 " --> pdb=" O ARGLh 72 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 82 through 87 Proline residue: Lh 87 - end of helix Processing helix chain 'Lh' and resid 90 through 96 Processing helix chain 'Lh' and resid 98 through 104 Processing helix chain 'Lh' and resid 106 through 116 Processing helix chain 'Li' and resid 43 through 58 removed outlier: 3.606A pdb=" N GLNLi 47 " --> pdb=" O SERLi 43 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLULi 55 " --> pdb=" O SERLi 51 " (cutoff:3.500A) Processing helix chain 'Li' and resid 60 through 73 Processing helix chain 'Li' and resid 74 through 87 removed outlier: 3.591A pdb=" N LYSLi 80 " --> pdb=" O LYSLi 76 " (cutoff:3.500A) Processing helix chain 'Li' and resid 88 through 110 removed outlier: 3.508A pdb=" N ALALi 109 " --> pdb=" O GLULi 105 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.663A pdb=" N LYSLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 65 through 77 removed outlier: 5.098A pdb=" N THRLj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VALLj 70 " --> pdb=" O TYRLj 66 " (cutoff:3.500A) Proline residue: Lj 71 - end of helix Processing helix chain 'Cc' and resid 9 through 17 removed outlier: 4.694A pdb=" N HISCc 13 " --> pdb=" O PROCc 9 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALACc 15 " --> pdb=" O ILECc 11 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SERCc 16 " --> pdb=" O LYSCc 12 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N SERCc 17 " --> pdb=" O HISCc 13 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 18 through 36 removed outlier: 3.570A pdb=" N ALACc 31 " --> pdb=" O ASNCc 27 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARGCc 36 " --> pdb=" O PHECc 32 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 37 through 42 removed outlier: 3.681A pdb=" N ALACc 41 " --> pdb=" O GLNCc 37 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 43 through 62 removed outlier: 3.614A pdb=" N LYSCc 49 " --> pdb=" O LEUCc 45 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYSCc 61 " --> pdb=" O ALACc 57 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASPCc 62 " --> pdb=" O LEUCc 58 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 63 through 82 removed outlier: 3.946A pdb=" N LEUCc 77 " --> pdb=" O GLUCc 73 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ILECc 78 " --> pdb=" O LEUCc 74 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TRPCc 79 " --> pdb=" O ALACc 75 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLNCc 80 " --> pdb=" O ASPCc 76 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEUCc 81 " --> pdb=" O LEUCc 77 " (cutoff:3.500A) Proline residue: Cc 82 - end of helix Processing helix chain 'Cc' and resid 83 through 101 removed outlier: 5.054A pdb=" N ALACc 87 " --> pdb=" O ARGCc 83 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THRCc 88 " --> pdb=" O GLUCc 84 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 105 through 128 removed outlier: 4.796A pdb=" N GLUCc 110 " --> pdb=" O VALCc 106 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LYSCc 111 " --> pdb=" O LEUCc 107 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHECc 112 " --> pdb=" O ARGCc 108 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYSCc 128 " --> pdb=" O PHECc 124 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 151 through 166 removed outlier: 3.816A pdb=" N GLUCc 157 " --> pdb=" O SERCc 153 " (cutoff:3.500A) Proline residue: Cc 166 - end of helix Processing helix chain 'Cc' and resid 190 through 209 removed outlier: 3.750A pdb=" N ARGCc 194 " --> pdb=" O PROCc 190 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASPCc 199 " --> pdb=" O LEUCc 195 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VALCc 202 " --> pdb=" O LEUCc 198 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASPCc 203 " --> pdb=" O ASPCc 199 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 215 through 236 removed outlier: 3.540A pdb=" N ILECc 225 " --> pdb=" O ILECc 221 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 238 through 251 removed outlier: 3.569A pdb=" N ASPCc 251 " --> pdb=" O ASPCc 247 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 13 through 18 Processing helix chain 'Cd' and resid 20 through 54 removed outlier: 3.562A pdb=" N GLNCd 26 " --> pdb=" O LEUCd 22 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYSCd 52 " --> pdb=" O LYSCd 48 " (cutoff:3.500A) Proline residue: Cd 54 - end of helix Processing helix chain 'Cd' and resid 55 through 64 Processing helix chain 'Cd' and resid 68 through 73 Processing helix chain 'Cd' and resid 88 through 98 Processing helix chain 'Cd' and resid 180 through 188 Proline residue: Cd 188 - end of helix Processing helix chain 'Cd' and resid 211 through 223 removed outlier: 3.751A pdb=" N PHECd 222 " --> pdb=" O ILECd 218 " (cutoff:3.500A) Proline residue: Cd 223 - end of helix Processing helix chain 'Cd' and resid 240 through 252 Processing helix chain 'Cd' and resid 294 through 299 removed outlier: 3.580A pdb=" N ILECd 298 " --> pdb=" O PROCd 294 " (cutoff:3.500A) Proline residue: Cd 299 - end of helix No H-bonds generated for 'chain 'Cd' and resid 294 through 299' Processing helix chain 'Cd' and resid 318 through 333 removed outlier: 3.577A pdb=" N LEUCd 331 " --> pdb=" O SERCd 327 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHECd 332 " --> pdb=" O METCd 328 " (cutoff:3.500A) Proline residue: Cd 333 - end of helix Processing helix chain 'Cd' and resid 409 through 414 removed outlier: 5.127A pdb=" N GLUCd 414 " --> pdb=" O ARGCd 410 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 424 through 430 removed outlier: 4.293A pdb=" N GLUCd 428 " --> pdb=" O LYSCd 424 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYSCd 429 " --> pdb=" O ALACd 425 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYSCd 430 " --> pdb=" O LYSCd 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cd' and resid 424 through 430' Processing helix chain 'Ce' and resid 2 through 12 Processing helix chain 'Ce' and resid 43 through 48 removed outlier: 5.363A pdb=" N SERCe 48 " --> pdb=" O PROCe 44 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 67 through 72 removed outlier: 3.945A pdb=" N SERCe 71 " --> pdb=" O THRCe 67 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N HISCe 72 " --> pdb=" O ILECe 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ce' and resid 67 through 72' Processing helix chain 'Ce' and resid 86 through 99 removed outlier: 3.668A pdb=" N GLNCe 99 " --> pdb=" O ASPCe 95 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 102 through 134 Processing helix chain 'Ce' and resid 142 through 161 removed outlier: 3.761A pdb=" N LYSCe 161 " --> pdb=" O LEUCe 157 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 162 through 177 Processing helix chain 'Ce' and resid 187 through 195 removed outlier: 3.515A pdb=" N LYSCe 192 " --> pdb=" O PROCe 188 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYSCe 193 " --> pdb=" O GLNCe 189 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VALCe 194 " --> pdb=" O ILECe 190 " (cutoff:3.500A) Processing helix chain 'Cf' and resid 428 through 437 removed outlier: 3.730A pdb=" N LYSCf 434 " --> pdb=" O ASPCf 430 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYSCf 436 " --> pdb=" O GLUCf 432 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLYCf 437 " --> pdb=" O LYSCf 433 " (cutoff:3.500A) Processing helix chain 'Cf' and resid 440 through 458 removed outlier: 4.651A pdb=" N LEUCf 458 " --> pdb=" O ARGCf 454 " (cutoff:3.500A) Processing helix chain 'Cf' and resid 460 through 481 removed outlier: 3.560A pdb=" N LYSCf 464 " --> pdb=" O GLUCf 460 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLUCf 465 " --> pdb=" O GLUCf 461 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLYCf 481 " --> pdb=" O ARGCf 477 " (cutoff:3.500A) Processing helix chain 'Cf' and resid 487 through 544 removed outlier: 3.958A pdb=" N GLUCf 499 " --> pdb=" O LEUCf 495 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARGCf 527 " --> pdb=" O ARGCf 523 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLUCf 528 " --> pdb=" O GLNCf 524 " (cutoff:3.500A) Processing helix chain 'Cy' and resid 9 through 20 Processing helix chain 'Cy' and resid 39 through 54 removed outlier: 3.605A pdb=" N METCy 52 " --> pdb=" O ASPCy 48 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARGCy 53 " --> pdb=" O LEUCy 49 " (cutoff:3.500A) Processing helix chain 'Cy' and resid 72 through 83 Processing helix chain 'Cy' and resid 125 through 130 removed outlier: 3.584A pdb=" N PHECy 129 " --> pdb=" O SERCy 125 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LYSCy 130 " --> pdb=" O ILECy 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cy' and resid 125 through 130' Processing helix chain 'Cy' and resid 155 through 169 Processing helix chain 'Cy' and resid 177 through 182 removed outlier: 4.358A pdb=" N LEUCy 181 " --> pdb=" O ASPCy 177 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARGCy 182 " --> pdb=" O VALCy 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cy' and resid 177 through 182' Processing helix chain 'Cy' and resid 264 through 273 Processing helix chain 'Cg' and resid 45 through 60 Processing helix chain 'Cg' and resid 74 through 86 removed outlier: 3.557A pdb=" N METCg 81 " --> pdb=" O ASPCg 77 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLYCg 83 " --> pdb=" O VALCg 79 " (cutoff:3.500A) Proline residue: Cg 84 - end of helix Processing helix chain 'Cg' and resid 123 through 132 removed outlier: 3.518A pdb=" N ALACg 130 " --> pdb=" O ASPCg 126 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ARGCg 132 " --> pdb=" O ARGCg 128 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 164 through 180 removed outlier: 4.459A pdb=" N LEUCg 170 " --> pdb=" O HISCg 166 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHECg 179 " --> pdb=" O PHECg 175 " (cutoff:3.500A) Proline residue: Cg 180 - end of helix Processing helix chain 'Cg' and resid 188 through 193 removed outlier: 3.715A pdb=" N ILECg 192 " --> pdb=" O PROCg 188 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ARGCg 193 " --> pdb=" O LEUCg 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cg' and resid 188 through 193' Processing helix chain 'CP' and resid 262 through 274 Processing helix chain 'CP' and resid 277 through 288 Processing helix chain 'CP' and resid 289 through 303 removed outlier: 3.703A pdb=" N GLUCP 301 " --> pdb=" O PHECP 297 " (cutoff:3.500A) Proline residue: CP 303 - end of helix Processing helix chain 'CP' and resid 316 through 328 Processing helix chain 'CP' and resid 354 through 360 Processing helix chain 'CP' and resid 366 through 377 removed outlier: 3.569A pdb=" N PHECP 370 " --> pdb=" O ALACP 366 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEUCP 371 " --> pdb=" O ALACP 367 " (cutoff:3.500A) Proline residue: CP 372 - end of helix removed outlier: 4.667A pdb=" N CYSCP 377 " --> pdb=" O VALCP 373 " (cutoff:3.500A) Processing helix chain 'CP' and resid 392 through 403 removed outlier: 3.653A pdb=" N METCP 398 " --> pdb=" O LYSCP 394 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALACP 399 " --> pdb=" O THRCP 395 " (cutoff:3.500A) Processing helix chain 'CP' and resid 414 through 429 removed outlier: 3.520A pdb=" N ILECP 422 " --> pdb=" O ALACP 418 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLYCP 423 " --> pdb=" O LYSCP 419 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASNCP 424 " --> pdb=" O GLYCP 420 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HISCP 426 " --> pdb=" O ILECP 422 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARGCP 427 " --> pdb=" O GLYCP 423 " (cutoff:3.500A) Processing helix chain 'CP' and resid 439 through 447 Proline residue: CP 444 - end of helix Processing helix chain 'CP' and resid 464 through 469 removed outlier: 3.904A pdb=" N ASPCP 468 " --> pdb=" O VALCP 464 " (cutoff:3.500A) Proline residue: CP 469 - end of helix No H-bonds generated for 'chain 'CP' and resid 464 through 469' Processing helix chain 'CP' and resid 476 through 499 removed outlier: 3.665A pdb=" N PHECP 480 " --> pdb=" O ASPCP 476 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N METCP 481 " --> pdb=" O ALACP 477 " (cutoff:3.500A) Proline residue: CP 484 - end of helix removed outlier: 3.505A pdb=" N GLNCP 489 " --> pdb=" O HISCP 485 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASNCP 499 " --> pdb=" O ILECP 495 " (cutoff:3.500A) Processing helix chain 'CP' and resid 516 through 532 removed outlier: 4.888A pdb=" N GLUCP 521 " --> pdb=" O VALCP 517 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLUCP 522 " --> pdb=" O GLUCP 518 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VALCP 523 " --> pdb=" O GLUCP 519 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VALCP 524 " --> pdb=" O ASNCP 520 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASNCP 525 " --> pdb=" O GLUCP 521 " (cutoff:3.500A) Proline residue: CP 532 - end of helix Processing helix chain 'CG' and resid 5 through 20 removed outlier: 3.693A pdb=" N TYRCG 19 " --> pdb=" O LYSCG 15 " (cutoff:3.500A) Processing helix chain 'CG' and resid 22 through 28 removed outlier: 3.602A pdb=" N LEUCG 26 " --> pdb=" O ASPCG 22 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALACG 28 " --> pdb=" O LYSCG 24 " (cutoff:3.500A) Processing helix chain 'CG' and resid 49 through 58 removed outlier: 4.185A pdb=" N CYSCG 58 " --> pdb=" O ASNCG 54 " (cutoff:3.500A) Processing helix chain 'CG' and resid 60 through 65 removed outlier: 5.325A pdb=" N LEUCG 65 " --> pdb=" O ARGCG 61 " (cutoff:3.500A) Processing helix chain 'CG' and resid 83 through 94 removed outlier: 4.127A pdb=" N LEUCG 87 " --> pdb=" O HISCG 83 " (cutoff:3.500A) Proline residue: CG 88 - end of helix removed outlier: 4.112A pdb=" N ASNCG 93 " --> pdb=" O ILECG 89 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALACG 94 " --> pdb=" O LEUCG 90 " (cutoff:3.500A) Processing helix chain 'CG' and resid 101 through 111 Proline residue: CG 107 - end of helix Processing helix chain 'CG' and resid 150 through 157 removed outlier: 3.570A pdb=" N ARGCG 156 " --> pdb=" O ALACG 152 " (cutoff:3.500A) Processing helix chain 'CG' and resid 170 through 177 removed outlier: 4.650A pdb=" N GLUCG 177 " --> pdb=" O TYRCG 173 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 5 through 25 removed outlier: 3.575A pdb=" N ASPLq 18 " --> pdb=" O ALALq 14 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYRLq 19 " --> pdb=" O GLULq 15 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASNLq 21 " --> pdb=" O LEULq 17 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 72 through 81 removed outlier: 5.784A pdb=" N ARGLq 76 " --> pdb=" O HISLq 72 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 86 through 97 removed outlier: 3.633A pdb=" N ASNLq 96 " --> pdb=" O LYSLq 92 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYSLq 97 " --> pdb=" O LEULq 93 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 98 through 108 removed outlier: 4.984A pdb=" N ASPLq 108 " --> pdb=" O ALALq 104 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 113 through 121 removed outlier: 3.582A pdb=" N LYSLq 118 " --> pdb=" O GLULq 114 " (cutoff:3.500A) Proline residue: Lq 121 - end of helix Processing helix chain 'Lq' and resid 122 through 129 Proline residue: Lq 126 - end of helix Processing helix chain 'Lq' and resid 143 through 153 removed outlier: 3.566A pdb=" N LYSLq 147 " --> pdb=" O ASPLq 143 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASNLq 149 " --> pdb=" O SERLq 145 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLULq 150 " --> pdb=" O ALALq 146 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SERLq 153 " --> pdb=" O ASNLq 149 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 175 through 195 removed outlier: 3.816A pdb=" N LEULq 179 " --> pdb=" O THRLq 175 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LYSLq 195 " --> pdb=" O VALLq 191 " (cutoff:3.500A) Processing helix chain 'Cx' and resid 43 through 69 Processing helix chain 'LJ' and resid 28 through 43 Processing helix chain 'LJ' and resid 74 through 89 removed outlier: 3.996A pdb=" N GLULJ 78 " --> pdb=" O GLYLJ 74 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 109 through 114 removed outlier: 3.942A pdb=" N LEULJ 113 " --> pdb=" O GLULJ 109 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLYLJ 114 " --> pdb=" O HISLJ 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 109 through 114' Processing helix chain 'LJ' and resid 136 through 142 removed outlier: 4.617A pdb=" N ALALJ 140 " --> pdb=" O GLYLJ 136 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYSLJ 141 " --> pdb=" O GLULJ 137 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 150 through 155 removed outlier: 5.585A pdb=" N ILELJ 155 " --> pdb=" O ALALJ 151 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 156 through 168 Processing helix chain 'LD' and resid 9 through 16 Processing helix chain 'LD' and resid 20 through 26 Processing helix chain 'LD' and resid 29 through 38 Processing helix chain 'LD' and resid 79 through 87 removed outlier: 3.676A pdb=" N LEULD 83 " --> pdb=" O TYRLD 79 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARGLD 84 " --> pdb=" O SERLD 80 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALALD 85 " --> pdb=" O HISLD 81 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYRLD 86 " --> pdb=" O GLULD 82 " (cutoff:3.500A) Processing helix chain 'LD' and resid 94 through 114 Processing helix chain 'LD' and resid 130 through 136 Processing helix chain 'LD' and resid 160 through 173 removed outlier: 3.755A pdb=" N GLYLD 164 " --> pdb=" O ALALD 160 " (cutoff:3.500A) Processing helix chain 'LD' and resid 194 through 204 Processing helix chain 'LD' and resid 205 through 218 Processing helix chain 'LD' and resid 219 through 227 Processing helix chain 'LD' and resid 228 through 233 Processing helix chain 'LD' and resid 236 through 253 removed outlier: 4.573A pdb=" N GLULD 240 " --> pdb=" O ALALD 236 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLULD 241 " --> pdb=" O ASPLD 237 " (cutoff:3.500A) Processing helix chain 'LD' and resid 266 through 278 Processing helix chain 'CX' and resid 65 through 70 removed outlier: 3.610A pdb=" N LEUCX 69 " --> pdb=" O SERCX 65 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLYCX 70 " --> pdb=" O GLUCX 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'CX' and resid 65 through 70' Processing helix chain 'CX' and resid 97 through 134 removed outlier: 3.568A pdb=" N LEUCX 126 " --> pdb=" O ARGCX 122 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLUCX 127 " --> pdb=" O ALACX 123 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLUCX 128 " --> pdb=" O ARGCX 124 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'CA' and resid 61 through 66 removed outlier: 3.534A pdb=" N SERCA 40 " --> pdb=" O ASPCA 65 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEUCA 100 " --> pdb=" O ALACA 117 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYSCA 114 " --> pdb=" O ILECA 243 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLYCA 235 " --> pdb=" O METCA 123 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N METCA 123 " --> pdb=" O GLYCA 235 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'CA' and resid 138 through 142 removed outlier: 5.813A pdb=" N ASPCA 177 " --> pdb=" O ILECA 196 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LYSCA 188 " --> pdb=" O ALACA 185 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'CA' and resid 193 through 198 removed outlier: 7.442A pdb=" N ASNCA 193 " --> pdb=" O ILECA 234 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'CB' and resid 64 through 68 removed outlier: 4.328A pdb=" N ARGCB 279 " --> pdb=" O GLNCB 295 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLNCB 295 " --> pdb=" O ARGCB 279 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'CB' and resid 80 through 83 Processing sheet with id= 6, first strand: chain 'CB' and resid 97 through 100 Processing sheet with id= 7, first strand: chain 'CC' and resid 137 through 141 Processing sheet with id= 8, first strand: chain 'CE' and resid 150 through 155 removed outlier: 3.719A pdb=" N VALCE 151 " --> pdb=" O THRCE 292 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALACE 155 " --> pdb=" O SERCE 296 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'CE' and resid 384 through 387 removed outlier: 4.993A pdb=" N SERCE 458 " --> pdb=" O GLUCE 333 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VALCE 338 " --> pdb=" O TYRCE 483 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'CI' and resid 214 through 219 removed outlier: 3.574A pdb=" N ARGCI 215 " --> pdb=" O GLUCI 234 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARGCI 230 " --> pdb=" O VALCI 219 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLYCI 187 " --> pdb=" O PHECI 235 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VALCI 188 " --> pdb=" O VALCI 263 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'CJ' and resid 186 through 191 Processing sheet with id= 12, first strand: chain 'CJ' and resid 394 through 397 removed outlier: 3.509A pdb=" N VALCJ 456 " --> pdb=" O GLNCJ 418 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'CM' and resid 119 through 124 removed outlier: 5.446A pdb=" N ASNCM 119 " --> pdb=" O ARGCM 94 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLYCM 143 " --> pdb=" O PHECM 91 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'CN' and resid 1 through 5 removed outlier: 3.716A pdb=" N ALACN 204 " --> pdb=" O METCN 1 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'CN' and resid 23 through 27 Processing sheet with id= 16, first strand: chain 'CN' and resid 69 through 73 Processing sheet with id= 17, first strand: chain 'CN' and resid 114 through 117 Processing sheet with id= 18, first strand: chain 'CN' and resid 158 through 161 removed outlier: 3.709A pdb=" N GLYCN 159 " --> pdb=" O PROCN 180 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'CQ' and resid 18 through 22 Processing sheet with id= 20, first strand: chain 'LB' and resid 53 through 59 removed outlier: 6.727A pdb=" N ILELB 78 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARGLB 335 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILELB 336 " --> pdb=" O VALLB 221 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VALLB 221 " --> pdb=" O ILELB 336 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N HISLB 274 " --> pdb=" O THRLB 222 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LB' and resid 84 through 87 removed outlier: 6.674A pdb=" N LEULB 162 " --> pdb=" O VALLB 87 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LB' and resid 285 through 288 removed outlier: 3.588A pdb=" N ARGLB 285 " --> pdb=" O METLB 324 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYRLB 322 " --> pdb=" O GLYLB 287 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LB' and resid 77 through 80 Processing sheet with id= 24, first strand: chain 'LB' and resid 88 through 91 removed outlier: 3.846A pdb=" N THRLB 103 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LB' and resid 214 through 217 removed outlier: 3.824A pdb=" N GLULB 214 " --> pdb=" O ILELB 283 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LC' and resid 209 through 212 Processing sheet with id= 27, first strand: chain 'LE' and resid 56 through 61 removed outlier: 4.580A pdb=" N THRLE 56 " --> pdb=" O LEULE 72 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYSLE 68 " --> pdb=" O LEULE 60 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LF' and resid 140 through 144 removed outlier: 3.624A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASNLF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LG' and resid 178 through 184 removed outlier: 3.506A pdb=" N LEULG 153 " --> pdb=" O ILELG 203 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LL' and resid 55 through 59 Processing sheet with id= 31, first strand: chain 'LM' and resid 18 through 21 removed outlier: 4.647A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LM' and resid 39 through 42 Processing sheet with id= 33, first strand: chain 'LN' and resid 35 through 39 removed outlier: 6.730A pdb=" N VALLN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLYLN 58 " --> pdb=" O ASPLN 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LN' and resid 117 through 121 removed outlier: 3.502A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LO' and resid 7 through 11 Processing sheet with id= 36, first strand: chain 'LP' and resid 16 through 20 removed outlier: 3.505A pdb=" N HISLP 116 " --> pdb=" O ILELP 149 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LP' and resid 57 through 60 removed outlier: 5.127A pdb=" N ARGLP 80 " --> pdb=" O METLP 60 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LQ' and resid 106 through 110 Processing sheet with id= 39, first strand: chain 'LQ' and resid 126 through 129 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'LS' and resid 24 through 30 removed outlier: 6.615A pdb=" N ILELS 10 " --> pdb=" O VALLS 59 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LS' and resid 86 through 95 removed outlier: 3.617A pdb=" N GLYLS 86 " --> pdb=" O SERLS 83 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASNLS 74 " --> pdb=" O LEULS 129 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYSLS 125 " --> pdb=" O TRPLS 78 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LS' and resid 6 through 10 removed outlier: 4.559A pdb=" N GLULS 6 " --> pdb=" O ILELS 64 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LT' and resid 73 through 79 Processing sheet with id= 44, first strand: chain 'LV' and resid 22 through 26 removed outlier: 3.569A pdb=" N ALALV 23 " --> pdb=" O ILELV 38 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N METLV 61 " --> pdb=" O ILELV 39 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYSLV 74 " --> pdb=" O VALLV 64 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LV' and resid 81 through 84 removed outlier: 6.448A pdb=" N ASPLV 99 " --> pdb=" O ALALV 84 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LY' and resid 55 through 58 removed outlier: 3.709A pdb=" N LYSLY 65 " --> pdb=" O ILELY 57 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LY' and resid 71 through 74 removed outlier: 3.582A pdb=" N SERLY 71 " --> pdb=" O HISLY 80 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'LY' and resid 85 through 88 removed outlier: 5.004A pdb=" N GLNLY 92 " --> pdb=" O LYSLY 88 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Le' and resid 72 through 78 Processing sheet with id= 50, first strand: chain 'Lf' and resid 12 through 17 removed outlier: 5.649A pdb=" N LYSLf 12 " --> pdb=" O GLULf 35 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEULf 31 " --> pdb=" O LEULf 16 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARGLf 84 " --> pdb=" O THRLf 74 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LYSLf 65 " --> pdb=" O ALALf 57 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYSLf 49 " --> pdb=" O ILELf 73 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARGLf 50 " --> pdb=" O METLf 103 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'Lf' and resid 10 through 16 removed outlier: 4.093A pdb=" N ALALf 98 " --> pdb=" O HISLf 15 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'Cc' and resid 172 through 175 removed outlier: 3.752A pdb=" N ILECc 185 " --> pdb=" O ILECc 175 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'Cd' and resid 224 through 228 removed outlier: 4.379A pdb=" N THRCd 205 " --> pdb=" O ILECd 228 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLUCd 261 " --> pdb=" O GLYCd 206 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THRCd 254 " --> pdb=" O LEUCd 274 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SERCd 267 " --> pdb=" O ILECd 289 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYSCd 400 " --> pdb=" O THRCd 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THRCd 398 " --> pdb=" O ARGCd 290 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Cd' and resid 309 through 314 removed outlier: 5.672A pdb=" N ARGCd 341 " --> pdb=" O TYRCd 360 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARGCd 357 " --> pdb=" O ILECd 393 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VALCd 361 " --> pdb=" O GLYCd 389 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Cd' and resid 283 through 286 removed outlier: 3.815A pdb=" N ARGCd 403 " --> pdb=" O THRCd 286 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Ce' and resid 17 through 20 removed outlier: 6.762A pdb=" N PHECe 17 " --> pdb=" O ARGCe 29 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Ce' and resid 50 through 56 removed outlier: 3.857A pdb=" N THRCe 60 " --> pdb=" O SERCe 56 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILECe 61 " --> pdb=" O LEUCe 83 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Cy' and resid 56 through 60 removed outlier: 4.724A pdb=" N ARGCy 34 " --> pdb=" O PHECy 60 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N SERCy 92 " --> pdb=" O GLYCy 35 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N SERCy 85 " --> pdb=" O METCy 105 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASNCy 93 " --> pdb=" O PROCy 97 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N HISCy 98 " --> pdb=" O LEUCy 118 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASPCy 254 " --> pdb=" O ASPCy 119 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'Cy' and resid 111 through 115 removed outlier: 8.840A pdb=" N LEUCy 111 " --> pdb=" O PROCy 263 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N METCy 113 " --> pdb=" O ARGCy 261 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARGCy 259 " --> pdb=" O GLUCy 115 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Cg' and resid 33 through 38 removed outlier: 4.551A pdb=" N ASNCg 100 " --> pdb=" O SERCg 96 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VALCg 101 " --> pdb=" O VALCg 118 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N HISCg 115 " --> pdb=" O THRCg 338 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARGCg 334 " --> pdb=" O GLUCg 119 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N PHECg 210 " --> pdb=" O METCg 337 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VALCg 211 " --> pdb=" O GLUCg 201 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEUCg 198 " --> pdb=" O VALCg 148 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Cg' and resid 112 through 115 removed outlier: 3.700A pdb=" N LYSCg 339 " --> pdb=" O HISCg 115 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Cg' and resid 215 through 221 removed outlier: 6.866A pdb=" N HISCg 216 " --> pdb=" O LEUCg 329 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'CP' and resid 330 through 334 removed outlier: 6.723A pdb=" N THRCP 330 " --> pdb=" O PHECP 345 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLYCP 341 " --> pdb=" O VALCP 334 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VALCP 340 " --> pdb=" O THRCP 310 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VALCP 306 " --> pdb=" O VALCP 344 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N HISCP 361 " --> pdb=" O ASNCP 311 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'CP' and resid 432 through 437 removed outlier: 6.043A pdb=" N ASNCP 432 " --> pdb=" O GLYCP 406 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASPCP 456 " --> pdb=" O METCP 387 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N CYSCP 513 " --> pdb=" O ALACP 457 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASNCP 533 " --> pdb=" O ILECP 584 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'CP' and resid 544 through 547 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 'CP' and resid 563 through 568 removed outlier: 6.676A pdb=" N ASPCP 574 " --> pdb=" O PROCP 568 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'CG' and resid 37 through 40 removed outlier: 3.548A pdb=" N VALCG 48 " --> pdb=" O VALCG 37 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'CG' and resid 96 through 100 removed outlier: 5.066A pdb=" N TYRCG 96 " --> pdb=" O GLYCG 131 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'Lq' and resid 30 through 37 removed outlier: 7.999A pdb=" N GLULq 30 " --> pdb=" O ASNLq 171 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASNLq 171 " --> pdb=" O GLULq 30 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VALLq 32 " --> pdb=" O VALLq 169 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Lq' and resid 50 through 54 Processing sheet with id= 71, first strand: chain 'Lq' and resid 65 through 68 removed outlier: 3.560A pdb=" N CYSLq 66 " --> pdb=" O ALALq 109 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'Cx' and resid 21 through 25 Processing sheet with id= 73, first strand: chain 'Cx' and resid 71 through 75 removed outlier: 4.219A pdb=" N THRCx 71 " --> pdb=" O THRCx 82 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'LJ' and resid 46 through 50 removed outlier: 5.331A pdb=" N SERLJ 23 " --> pdb=" O GLYLJ 125 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLYLJ 125 " --> pdb=" O SERLJ 23 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'LJ' and resid 90 through 93 Processing sheet with id= 76, first strand: chain 'LD' and resid 60 through 66 3008 hydrogen bonds defined for protein. 8961 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2010 hydrogen bonds 3338 hydrogen bond angles 0 basepair planarities 800 basepair parallelities 1267 stacking parallelities Total time for adding SS restraints: 91.60 Time building geometry restraints manager: 47.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.17: 1 1.17 - 1.33: 22831 1.33 - 1.50: 59326 1.50 - 1.66: 42124 1.66 - 1.83: 307 Bond restraints: 124589 Sorted by residual: bond pdb=" CG PROCg 204 " pdb=" CD PROCg 204 " ideal model delta sigma weight residual 1.503 1.000 0.503 3.40e-02 8.65e+02 2.19e+02 bond pdb=" N PROCg 204 " pdb=" CD PROCg 204 " ideal model delta sigma weight residual 1.473 1.571 -0.098 1.40e-02 5.10e+03 4.89e+01 bond pdb=" C1' UC13215 " pdb=" N1 UC13215 " ideal model delta sigma weight residual 1.480 1.583 -0.103 1.50e-02 4.44e+03 4.69e+01 bond pdb=" N PROCG 3 " pdb=" CA PROCG 3 " ideal model delta sigma weight residual 1.469 1.425 0.044 1.28e-02 6.10e+03 1.16e+01 bond pdb=" C ASPCJ 362 " pdb=" N PROCJ 363 " ideal model delta sigma weight residual 1.336 1.374 -0.038 1.20e-02 6.94e+03 1.03e+01 ... (remaining 124584 not shown) Histogram of bond angle deviations from ideal: 78.39 - 92.07: 2 92.07 - 105.75: 13495 105.75 - 119.43: 106720 119.43 - 133.12: 59750 133.12 - 146.80: 115 Bond angle restraints: 180082 Sorted by residual: angle pdb=" C CYSCe 186 " pdb=" N ASNCe 187 " pdb=" CA ASNCe 187 " ideal model delta sigma weight residual 121.20 146.80 -25.60 1.40e+00 5.10e-01 3.34e+02 angle pdb=" N PROCg 204 " pdb=" CD PROCg 204 " pdb=" CG PROCg 204 " ideal model delta sigma weight residual 103.20 78.39 24.81 1.50e+00 4.44e-01 2.74e+02 angle pdb=" CA PROCg 204 " pdb=" N PROCg 204 " pdb=" CD PROCg 204 " ideal model delta sigma weight residual 112.00 97.49 14.51 1.40e+00 5.10e-01 1.07e+02 angle pdb=" CA PROCg 204 " pdb=" CB PROCg 204 " pdb=" CG PROCg 204 " ideal model delta sigma weight residual 104.50 85.28 19.22 1.90e+00 2.77e-01 1.02e+02 angle pdb=" N VALLC 163 " pdb=" CA VALLC 163 " pdb=" C VALLC 163 " ideal model delta sigma weight residual 113.20 105.90 7.30 9.60e-01 1.09e+00 5.78e+01 ... (remaining 180077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 66871 35.82 - 71.63: 3052 71.63 - 107.45: 217 107.45 - 143.27: 12 143.27 - 179.08: 18 Dihedral angle restraints: 70170 sinusoidal: 44629 harmonic: 25541 Sorted by residual: dihedral pdb=" CA ARGLq 60 " pdb=" C ARGLq 60 " pdb=" N PROLq 61 " pdb=" CA PROLq 61 " ideal model delta harmonic sigma weight residual -180.00 -125.42 -54.58 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CB CYSCQ 9 " pdb=" SG CYSCQ 9 " pdb=" SG CYSCQ 32 " pdb=" CB CYSCQ 32 " ideal model delta sinusoidal sigma weight residual -86.00 -175.69 89.69 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" O4' UC13158 " pdb=" C1' UC13158 " pdb=" N1 UC13158 " pdb=" C2 UC13158 " ideal model delta sinusoidal sigma weight residual 200.00 28.97 171.03 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 70167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 21268 0.106 - 0.212: 843 0.212 - 0.319: 47 0.319 - 0.425: 8 0.425 - 0.531: 2 Chirality restraints: 22168 Sorted by residual: chirality pdb=" C1' UC11841 " pdb=" O4' UC11841 " pdb=" C2' UC11841 " pdb=" N1 UC11841 " both_signs ideal model delta sigma weight residual False 2.47 1.93 0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" P GC12931 " pdb=" OP1 GC12931 " pdb=" OP2 GC12931 " pdb=" O5' GC12931 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" P UC12932 " pdb=" OP1 UC12932 " pdb=" OP2 UC12932 " pdb=" O5' UC12932 " both_signs ideal model delta sigma weight residual True 2.41 -2.81 -0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 22165 not shown) Planarity restraints: 14231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLNCE 463 " 0.098 5.00e-02 4.00e+02 1.45e-01 3.39e+01 pdb=" N PROCE 464 " -0.251 5.00e-02 4.00e+02 pdb=" CA PROCE 464 " 0.080 5.00e-02 4.00e+02 pdb=" CD PROCE 464 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASPLB 36 " 0.097 5.00e-02 4.00e+02 1.44e-01 3.30e+01 pdb=" N PROLB 37 " -0.248 5.00e-02 4.00e+02 pdb=" CA PROLB 37 " 0.077 5.00e-02 4.00e+02 pdb=" CD PROLB 37 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRPCe 191 " -0.033 2.00e-02 2.50e+03 3.13e-02 2.44e+01 pdb=" CG TRPCe 191 " 0.084 2.00e-02 2.50e+03 pdb=" CD1 TRPCe 191 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRPCe 191 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRPCe 191 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRPCe 191 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRPCe 191 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRPCe 191 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRPCe 191 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRPCe 191 " -0.004 2.00e-02 2.50e+03 ... (remaining 14228 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 11539 2.73 - 3.27: 103558 3.27 - 3.82: 224829 3.82 - 4.36: 266942 4.36 - 4.90: 385616 Nonbonded interactions: 992484 Sorted by model distance: nonbonded pdb=" O6 GC12922 " pdb=" O6 GC12926 " model vdw 2.191 3.040 nonbonded pdb=" OD1 ASNCe 39 " pdb=" OG SERCe 42 " model vdw 2.194 2.440 nonbonded pdb=" N2 GC1 631 " pdb=" N6 AC11135 " model vdw 2.208 3.200 nonbonded pdb=" OH TYRLE 182 " pdb=" OD2 ASPLM 114 " model vdw 2.209 2.440 nonbonded pdb=" O ARGCN 96 " pdb=" ND2 ASNCQ 76 " model vdw 2.211 2.520 ... (remaining 992479 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 18.560 Check model and map are aligned: 1.300 Set scattering table: 0.790 Process input model: 348.050 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.300 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 379.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.503 124589 Z= 0.342 Angle : 0.862 25.598 180082 Z= 0.446 Chirality : 0.047 0.531 22168 Planarity : 0.008 0.172 14231 Dihedral : 17.056 179.084 53590 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.82 % Rotamer: Outliers : 1.07 % Allowed : 29.41 % Favored : 69.52 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.01 % Twisted Proline : 0.88 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.08), residues: 8678 helix: -2.63 (0.06), residues: 3421 sheet: -0.26 (0.15), residues: 1151 loop : -1.17 (0.09), residues: 4106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2053 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1986 time to evaluate : 6.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 17 residues processed: 2016 average time/residue: 1.2423 time to fit residues: 4117.4481 Evaluate side-chains 1157 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1140 time to evaluate : 6.904 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.8791 time to fit residues: 36.9506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1100 random chunks: chunk 928 optimal weight: 20.0000 chunk 833 optimal weight: 0.8980 chunk 462 optimal weight: 3.9990 chunk 284 optimal weight: 7.9990 chunk 562 optimal weight: 0.0770 chunk 445 optimal weight: 20.0000 chunk 862 optimal weight: 4.9990 chunk 333 optimal weight: 0.9980 chunk 524 optimal weight: 20.0000 chunk 641 optimal weight: 2.9990 chunk 998 optimal weight: 50.0000 overall best weight: 1.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 121 HIS CA 167 GLN CA 246 GLN CB 90 ASN CB 150 HIS CC 144 ASN CC 166 ASN CE 576 GLN ** CH 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CI 209 GLN CJ 153 ASN CM 249 ASN ** CN 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 134 GLN CR 137 GLN CR 219 GLN CU 246 GLN Ch 301 GLN LB 68 HIS LB 166 GLN LB 270 GLN LC 59 HIS LC 284 GLN ** LE 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 145 GLN LF 77 GLN LF 78 GLN LF 110 GLN LF 206 ASN LG 92 GLN LP 28 ASN LQ 98 ASN LS 13 HIS LT 82 HIS Le 7 HIS ** Lh 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 64 ASN ** Lh 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 118 GLN Cc 27 ASN Cd 30 GLN Cd 263 GLN Ce 93 GLN ** Ce 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 412 ASN Cg 73 ASN Cg 133 HIS ** Cg 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 124589 Z= 0.231 Angle : 0.613 10.378 180082 Z= 0.317 Chirality : 0.038 0.544 22168 Planarity : 0.006 0.120 14231 Dihedral : 14.729 179.805 38299 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.54 % Favored : 96.34 % Rotamer: Outliers : 3.94 % Allowed : 23.31 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.01 % Twisted Proline : 0.22 % Twisted General : 0.02 % 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: -0.93 (0.08), residues: 8678 helix: -0.29 (0.08), residues: 3496 sheet: -0.12 (0.15), residues: 1194 loop : -0.96 (0.09), residues: 3988 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1184 time to evaluate : 6.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 246 outliers final: 125 residues processed: 1359 average time/residue: 1.0836 time to fit residues: 2473.5666 Evaluate side-chains 1155 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1030 time to evaluate : 6.892 Switching outliers to nearest non-outliers outliers start: 125 outliers final: 0 residues processed: 125 average time/residue: 0.8620 time to fit residues: 208.8489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1100 random chunks: chunk 555 optimal weight: 0.8980 chunk 310 optimal weight: 0.9980 chunk 831 optimal weight: 4.9990 chunk 680 optimal weight: 3.9990 chunk 275 optimal weight: 10.0000 chunk 1000 optimal weight: 0.8980 chunk 1081 optimal weight: 50.0000 chunk 891 optimal weight: 1.9990 chunk 992 optimal weight: 50.0000 chunk 341 optimal weight: 0.8980 chunk 802 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 121 HIS CA 246 GLN CC 144 ASN CC 166 ASN CC 191 ASN CE 405 ASN CJ 153 ASN ** CN 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CN 83 HIS ** CN 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 246 GLN CU 287 GLN LB 68 HIS ** LB 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 59 HIS LC 284 GLN LE 25 GLN LF 41 GLN LF 110 GLN LG 92 GLN LN 57 GLN LO 32 GLN LS 88 HIS LT 82 HIS ** Lh 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 77 ASN Cc 30 HIS ** Cc 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 263 GLN Ce 88 GLN Ce 185 ASN Cf 412 ASN ** Cg 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 124589 Z= 0.173 Angle : 0.558 12.889 180082 Z= 0.287 Chirality : 0.036 0.555 22168 Planarity : 0.005 0.098 14231 Dihedral : 14.604 179.644 38299 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 2.19 % Allowed : 23.28 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.01 % Twisted Proline : 0.22 % Twisted General : 0.01 % 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: -0.24 (0.09), residues: 8678 helix: 0.61 (0.09), residues: 3527 sheet: -0.09 (0.15), residues: 1201 loop : -0.83 (0.10), residues: 3950 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1103 time to evaluate : 6.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 51 residues processed: 1208 average time/residue: 1.0858 time to fit residues: 2205.0526 Evaluate side-chains 1076 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1025 time to evaluate : 6.861 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.8826 time to fit residues: 90.7878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1100 random chunks: chunk 988 optimal weight: 40.0000 chunk 752 optimal weight: 1.9990 chunk 519 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 477 optimal weight: 7.9990 chunk 671 optimal weight: 0.0070 chunk 1004 optimal weight: 30.0000 chunk 1063 optimal weight: 40.0000 chunk 524 optimal weight: 20.0000 chunk 951 optimal weight: 20.0000 chunk 286 optimal weight: 0.6980 overall best weight: 2.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 121 HIS CC 144 ASN CC 166 ASN CC 191 ASN CI 209 GLN CJ 70 GLN CJ 485 HIS CM 236 ASN CN 79 GLN ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CN 234 ASN ** CQ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 196 GLN CR 216 ASN LB 68 HIS LB 183 GLN LB 225 HIS ** LB 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 111 HIS LC 284 GLN ** LE 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 110 GLN LF 116 GLN LM 36 HIS LM 106 GLN LN 57 GLN LS 88 HIS LT 82 HIS ** Lh 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 77 ASN Cc 80 GLN Cc 223 GLN ** Cd 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 88 GLN Cf 412 ASN Cg 183 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 124589 Z= 0.243 Angle : 0.572 11.656 180082 Z= 0.294 Chirality : 0.038 0.571 22168 Planarity : 0.005 0.099 14231 Dihedral : 14.566 179.899 38299 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 2.29 % Allowed : 23.84 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.05 (0.09), residues: 8678 helix: 0.97 (0.09), residues: 3536 sheet: -0.03 (0.15), residues: 1185 loop : -0.76 (0.10), residues: 3957 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1036 time to evaluate : 6.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 86 residues processed: 1127 average time/residue: 1.1407 time to fit residues: 2181.8588 Evaluate side-chains 1063 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 977 time to evaluate : 6.901 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 0.8889 time to fit residues: 153.0025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1100 random chunks: chunk 885 optimal weight: 0.9980 chunk 603 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 791 optimal weight: 2.9990 chunk 438 optimal weight: 40.0000 chunk 907 optimal weight: 10.0000 chunk 734 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 542 optimal weight: 0.0980 chunk 954 optimal weight: 20.0000 chunk 268 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 121 HIS ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 144 ASN CC 166 ASN CC 191 ASN CE 393 GLN CM 118 ASN ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 68 HIS LB 183 GLN LB 225 HIS ** LB 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 110 GLN ** LM 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 88 HIS LT 82 HIS ** LT 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 77 ASN Cc 80 GLN Cc 234 GLN ** Cd 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 88 GLN Cf 412 ASN Cg 183 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 124589 Z= 0.227 Angle : 0.559 12.024 180082 Z= 0.287 Chirality : 0.037 0.570 22168 Planarity : 0.005 0.097 14231 Dihedral : 14.529 179.781 38299 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.17 % Rotamer: Outliers : 1.79 % Allowed : 24.11 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.24 (0.09), residues: 8678 helix: 1.19 (0.09), residues: 3536 sheet: 0.02 (0.15), residues: 1187 loop : -0.70 (0.10), residues: 3955 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1002 time to evaluate : 6.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 44 residues processed: 1085 average time/residue: 1.0888 time to fit residues: 1989.4804 Evaluate side-chains 1003 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 959 time to evaluate : 6.872 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.8446 time to fit residues: 78.0569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1100 random chunks: chunk 357 optimal weight: 0.3980 chunk 957 optimal weight: 40.0000 chunk 210 optimal weight: 6.9990 chunk 624 optimal weight: 0.9980 chunk 262 optimal weight: 0.8980 chunk 1064 optimal weight: 40.0000 chunk 883 optimal weight: 2.9990 chunk 492 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 352 optimal weight: 0.0670 chunk 558 optimal weight: 0.4980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 121 HIS ** CA 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 105 GLN CC 191 ASN ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 68 HIS LB 183 GLN LB 372 GLN LF 110 GLN LG 141 HIS LN 57 GLN ** LQ 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 77 ASN ** Cc 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 234 GLN Ce 88 GLN Cf 412 ASN Cg 183 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 124589 Z= 0.132 Angle : 0.521 15.852 180082 Z= 0.267 Chirality : 0.035 0.576 22168 Planarity : 0.005 0.094 14231 Dihedral : 14.430 179.150 38299 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 1.34 % Allowed : 24.64 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.47 (0.09), residues: 8678 helix: 1.41 (0.09), residues: 3556 sheet: 0.11 (0.15), residues: 1201 loop : -0.60 (0.10), residues: 3921 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1021 time to evaluate : 6.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 45 residues processed: 1068 average time/residue: 1.1649 time to fit residues: 2110.6171 Evaluate side-chains 1004 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 959 time to evaluate : 6.882 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.8246 time to fit residues: 78.1794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1100 random chunks: chunk 1026 optimal weight: 50.0000 chunk 119 optimal weight: 4.9990 chunk 606 optimal weight: 2.9990 chunk 777 optimal weight: 2.9990 chunk 602 optimal weight: 0.9980 chunk 895 optimal weight: 0.8980 chunk 594 optimal weight: 0.9990 chunk 1060 optimal weight: 20.0000 chunk 663 optimal weight: 3.9990 chunk 646 optimal weight: 4.9990 chunk 489 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 246 GLN ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 191 ASN CE 378 GLN ** CN 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 68 HIS LB 109 HIS LB 183 GLN LF 110 GLN LM 106 GLN ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 77 ASN Ce 88 GLN Cf 412 ASN Cg 183 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 124589 Z= 0.210 Angle : 0.545 13.610 180082 Z= 0.278 Chirality : 0.037 0.584 22168 Planarity : 0.005 0.094 14231 Dihedral : 14.394 179.109 38299 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.63 % Favored : 96.30 % Rotamer: Outliers : 0.99 % Allowed : 25.17 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.51 (0.09), residues: 8678 helix: 1.47 (0.09), residues: 3547 sheet: 0.07 (0.15), residues: 1200 loop : -0.58 (0.10), residues: 3931 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 963 time to evaluate : 6.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 37 residues processed: 1000 average time/residue: 1.1182 time to fit residues: 1883.7919 Evaluate side-chains 972 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 935 time to evaluate : 6.878 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.8434 time to fit residues: 67.6361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1100 random chunks: chunk 655 optimal weight: 0.6980 chunk 423 optimal weight: 20.0000 chunk 633 optimal weight: 0.9990 chunk 319 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 674 optimal weight: 0.6980 chunk 722 optimal weight: 0.8980 chunk 524 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 833 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 121 HIS ** CA 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 105 GLN ** CN 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 68 HIS LB 109 HIS LB 183 GLN LF 110 GLN LN 57 GLN ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 77 ASN Cc 30 HIS Ce 88 GLN Cf 412 ASN Cg 183 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 124589 Z= 0.158 Angle : 0.533 14.082 180082 Z= 0.272 Chirality : 0.035 0.583 22168 Planarity : 0.005 0.092 14231 Dihedral : 14.378 178.964 38299 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 0.82 % Allowed : 25.44 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.57 (0.09), residues: 8678 helix: 1.54 (0.09), residues: 3550 sheet: 0.09 (0.15), residues: 1230 loop : -0.57 (0.10), residues: 3898 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 954 time to evaluate : 6.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 21 residues processed: 990 average time/residue: 1.1407 time to fit residues: 1912.0896 Evaluate side-chains 946 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 925 time to evaluate : 6.942 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.8597 time to fit residues: 42.8688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1100 random chunks: chunk 964 optimal weight: 30.0000 chunk 1015 optimal weight: 50.0000 chunk 926 optimal weight: 30.0000 chunk 987 optimal weight: 10.0000 chunk 594 optimal weight: 0.6980 chunk 430 optimal weight: 20.0000 chunk 775 optimal weight: 2.9990 chunk 303 optimal weight: 0.0060 chunk 892 optimal weight: 0.6980 chunk 934 optimal weight: 50.0000 chunk 984 optimal weight: 50.0000 overall best weight: 2.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 105 GLN ** CJ 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 186 HIS ** CU 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 68 HIS LB 164 HIS LB 183 GLN LF 110 GLN ** LQ 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 88 HIS LY 18 HIS ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 37 GLN ** Lh 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 77 ASN Cc 30 HIS Cd 260 GLN ** Cd 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 88 GLN Cg 183 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 124589 Z= 0.301 Angle : 0.597 12.307 180082 Z= 0.304 Chirality : 0.039 0.587 22168 Planarity : 0.005 0.093 14231 Dihedral : 14.451 179.115 38299 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.06 % Rotamer: Outliers : 0.50 % Allowed : 25.74 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.50 (0.09), residues: 8678 helix: 1.46 (0.09), residues: 3551 sheet: 0.08 (0.15), residues: 1204 loop : -0.60 (0.10), residues: 3923 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 949 time to evaluate : 6.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 966 average time/residue: 1.1135 time to fit residues: 1808.8329 Evaluate side-chains 934 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 920 time to evaluate : 6.917 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.9558 time to fit residues: 32.7378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1100 random chunks: chunk 648 optimal weight: 5.9990 chunk 1044 optimal weight: 30.0000 chunk 637 optimal weight: 0.4980 chunk 495 optimal weight: 6.9990 chunk 726 optimal weight: 3.9990 chunk 1095 optimal weight: 6.9990 chunk 1008 optimal weight: 20.0000 chunk 872 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 674 optimal weight: 0.9980 chunk 535 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 68 HIS LB 109 HIS LB 183 GLN ** LF 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 110 GLN ** LQ 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 88 HIS ** LS 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 77 ASN Lh 118 GLN ** Cc 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 260 GLN ** Cd 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 412 ASN Cg 183 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 124589 Z= 0.214 Angle : 0.558 14.276 180082 Z= 0.285 Chirality : 0.037 0.583 22168 Planarity : 0.005 0.092 14231 Dihedral : 14.402 178.862 38299 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 0.27 % Allowed : 25.94 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.58 (0.09), residues: 8678 helix: 1.53 (0.09), residues: 3547 sheet: 0.11 (0.15), residues: 1185 loop : -0.55 (0.10), residues: 3946 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17356 Ramachandran restraints generated. 8678 Oldfield, 0 Emsley, 8678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 946 time to evaluate : 6.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 958 average time/residue: 1.1139 time to fit residues: 1797.1874 Evaluate side-chains 932 residues out of total 7555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 923 time to evaluate : 6.958 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.8043 time to fit residues: 22.6657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1100 random chunks: chunk 693 optimal weight: 8.9990 chunk 929 optimal weight: 10.0000 chunk 267 optimal weight: 0.7980 chunk 804 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 242 optimal weight: 2.9990 chunk 874 optimal weight: 8.9990 chunk 365 optimal weight: 1.9990 chunk 897 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 160 optimal weight: 50.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 170 ASN ** CJ 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 216 ASN CU 246 GLN CU 287 GLN LB 68 HIS ** LF 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 110 GLN LN 57 GLN ** LQ 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 77 ASN ** Cd 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 88 GLN Cg 183 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.204033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.155082 restraints weight = 153065.223| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.05 r_work: 0.3136 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 124589 Z= 0.207 Angle : 0.555 14.296 180082 Z= 0.283 Chirality : 0.037 0.577 22168 Planarity : 0.005 0.091 14231 Dihedral : 14.365 178.449 38299 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.85 % Favored : 96.08 % Rotamer: Outliers : 0.27 % Allowed : 26.06 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.60 (0.09), residues: 8678 helix: 1.55 (0.09), residues: 3559 sheet: 0.10 (0.15), residues: 1200 loop : -0.54 (0.10), residues: 3919 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34152.96 seconds wall clock time: 593 minutes 30.21 seconds (35610.21 seconds total)