Starting phenix.real_space_refine on Mon Mar 25 14:28:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7t_13244/03_2024/7p7t_13244_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7t_13244/03_2024/7p7t_13244.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7t_13244/03_2024/7p7t_13244_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7t_13244/03_2024/7p7t_13244_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7t_13244/03_2024/7p7t_13244_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7t_13244/03_2024/7p7t_13244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7t_13244/03_2024/7p7t_13244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7t_13244/03_2024/7p7t_13244_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7t_13244/03_2024/7p7t_13244_updated.pdb" } resolution = 2.9 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= 0.002 sd= 0.004 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: 8 Type Number sf(0) Gaussians K 138 8.98 5 Zn 4 6.06 5 P 4703 5.49 5 Mg 161 5.21 5 S 156 5.16 5 C 75110 2.51 5 N 27413 2.21 5 O 41395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149080 Number of models: 1 Model: "" Number of chains: 68 Chain: "0" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4347 Classifications: {'peptide': 534} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 517} Chain: "1" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 491 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "2" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 428 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "3" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 647 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "4" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 406 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "5" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 410 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "6" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 522 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "8" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 305 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "A" Number of atoms: 62268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2901, 62268 Classifications: {'RNA': 2901} Modifications used: {'rna2p_pur': 299, 'rna2p_pyr': 153, 'rna3p_pur': 1386, 'rna3p_pyr': 1063} Link IDs: {'rna2p': 451, 'rna3p': 2449} Chain breaks: 2 Chain: "B" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2439 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 45} Link IDs: {'rna2p': 12, 'rna3p': 101} Chain: "C" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1546 Classifications: {'RNA': 72} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p': 5, 'rna3p_pur': 32, 'rna3p_pyr': 28} Link IDs: {'rna2p': 7, 'rna3p': 64} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1624 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 65} Chain: "F" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1693 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "G" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2106 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 16, 'TRANS': 257} Chain: "H" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1572 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "I" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1572 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain: "J" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1392 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "K" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1335 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain: "M" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1146 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 7, 'TRANS': 139} Chain: "N" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 923 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1096 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "P" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1070 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "Q" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "R" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 908 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "S" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "T" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'TRANS': 117} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 97} Chain: "V" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "W" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "Y" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "Z" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "a" Number of atoms: 32595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1521, 32595 Classifications: {'RNA': 1521} Modifications used: {'rna2p_pur': 113, 'rna2p_pyr': 88, 'rna3p_pur': 740, 'rna3p_pyr': 580} Link IDs: {'rna2p': 201, 'rna3p': 1319} Chain breaks: 2 Chain: "b" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 287 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain breaks: 1 Chain: "c" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1773 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 8, 'TRANS': 213} Chain: "d" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1618 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain: "e" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1611 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain: "f" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1204 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "g" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 786 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "h" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1218 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "i" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "j" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "k" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 773 Classifications: {'peptide': 96} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 89} Chain: "l" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 854 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "m" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1051 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain: "n" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 902 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "o" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "p" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 716 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "q" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 692 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "r" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "s" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 511 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 663 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "u" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 608 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "0" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 209 Unusual residues: {' K': 92, ' MG': 117} Classifications: {'undetermined': 209} Link IDs: {None: 208} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' MG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' MG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 103 Unusual residues: {' K': 35, ' MG': 39, 'PUT': 1, 'SCM': 1} Classifications: {'undetermined': 76} Link IDs: {None: 75} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6141 SG CYS 4 30 64.619 63.677 155.123 1.00 91.74 S ATOM 6161 SG CYS 4 33 65.460 60.394 152.960 1.00 93.63 S ATOM 6239 SG CYS 4 43 65.950 63.808 151.403 1.00 90.46 S ATOM 6257 SG CYS 4 46 62.875 62.781 151.876 1.00 88.71 S ATOM 6391 SG CYS 5 9 196.604 111.200 98.217 1.00 89.58 S ATOM 6410 SG CYS 5 12 195.068 108.148 96.617 1.00 92.83 S ATOM 6623 SG CYS 5 36 196.257 107.793 99.852 1.00 89.40 S ATOM 7710 SG CYS 8 11 136.612 143.100 191.029 1.00 94.52 S ATOM 7735 SG CYS 8 14 136.235 139.559 189.736 1.00 90.84 S ATOM 7841 SG CYS 8 27 133.440 141.354 191.900 1.00 93.26 S ATOM A0YCS SG CYS o 24 159.215 228.668 129.121 1.00 97.23 S ATOM A0YDI SG CYS o 27 156.583 226.140 130.102 1.00 95.67 S ATOM A0YGM SG CYS o 40 157.924 226.037 126.578 1.00 97.74 S ATOM A0YHB SG CYS o 43 155.740 228.783 127.513 1.00 97.79 S Time building chain proxies: 58.98, per 1000 atoms: 0.40 Number of scatterers: 149080 At special positions: 0 Unit cell: (249.28, 280.44, 239.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 K 138 19.00 S 156 16.00 P 4703 15.00 Mg 161 11.99 O 41395 8.00 N 27413 7.00 C 75110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 69.62 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 46 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 43 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 30 " pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 12 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 9 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 36 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 33 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " pdb=" ZN o 102 " pdb="ZN ZN o 102 " - pdb=" SG CYS o 43 " pdb="ZN ZN o 102 " - pdb=" SG CYS o 40 " pdb="ZN ZN o 102 " - pdb=" SG CYS o 27 " pdb="ZN ZN o 102 " - pdb=" SG CYS o 24 " Number of angles added : 15 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11218 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: 192 helices and 82 sheets defined 39.5% alpha, 19.7% beta 1603 base pairs and 2478 stacking pairs defined. Time for finding SS restraints: 83.13 Creating SS restraints... Processing helix chain '0' and resid 38 through 48 removed outlier: 3.640A pdb=" N PHE 0 43 " --> pdb=" O LYS 0 39 " (cutoff:3.500A) Processing helix chain '0' and resid 79 through 89 removed outlier: 3.810A pdb=" N GLY 0 87 " --> pdb=" O PHE 0 83 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG 0 88 " --> pdb=" O LEU 0 84 " (cutoff:3.500A) Proline residue: 0 89 - end of helix Processing helix chain '0' and resid 90 through 108 removed outlier: 4.689A pdb=" N ASP 0 108 " --> pdb=" O LEU 0 104 " (cutoff:3.500A) Processing helix chain '0' and resid 111 through 130 removed outlier: 3.617A pdb=" N ASP 0 130 " --> pdb=" O LEU 0 126 " (cutoff:3.500A) Processing helix chain '0' and resid 132 through 144 removed outlier: 3.614A pdb=" N SER 0 136 " --> pdb=" O TYR 0 132 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU 0 138 " --> pdb=" O ALA 0 134 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL 0 142 " --> pdb=" O LEU 0 138 " (cutoff:3.500A) Processing helix chain '0' and resid 148 through 155 removed outlier: 3.747A pdb=" N PHE 0 152 " --> pdb=" O ASP 0 148 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP 0 153 " --> pdb=" O PHE 0 149 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN 0 154 " --> pdb=" O ASP 0 150 " (cutoff:3.500A) Proline residue: 0 155 - end of helix No H-bonds generated for 'chain '0' and resid 148 through 155' Processing helix chain '0' and resid 160 through 176 removed outlier: 3.865A pdb=" N LYS 0 176 " --> pdb=" O VAL 0 172 " (cutoff:3.500A) Processing helix chain '0' and resid 190 through 204 removed outlier: 3.789A pdb=" N PHE 0 196 " --> pdb=" O SER 0 192 " (cutoff:3.500A) Processing helix chain '0' and resid 214 through 222 removed outlier: 3.829A pdb=" N ILE 0 221 " --> pdb=" O PHE 0 217 " (cutoff:3.500A) Processing helix chain '0' and resid 241 through 280 Processing helix chain '0' and resid 284 through 305 Processing helix chain '0' and resid 368 through 378 Processing helix chain '0' and resid 410 through 416 Processing helix chain '0' and resid 421 through 433 Processing helix chain '0' and resid 442 through 447 removed outlier: 3.862A pdb=" N LEU 0 446 " --> pdb=" O LYS 0 442 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N SER 0 447 " --> pdb=" O VAL 0 443 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 442 through 447' Processing helix chain '0' and resid 448 through 463 removed outlier: 3.823A pdb=" N LYS 0 463 " --> pdb=" O VAL 0 459 " (cutoff:3.500A) Processing helix chain '0' and resid 477 through 491 Processing helix chain '0' and resid 501 through 509 Processing helix chain '0' and resid 525 through 534 removed outlier: 4.894A pdb=" N LEU 0 529 " --> pdb=" O SER 0 525 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU 0 530 " --> pdb=" O PRO 0 526 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 10 removed outlier: 5.248A pdb=" N THR 1 10 " --> pdb=" O ILE 1 6 " (cutoff:3.500A) Processing helix chain '1' and resid 11 through 35 removed outlier: 3.836A pdb=" N GLY 1 35 " --> pdb=" O GLN 1 31 " (cutoff:3.500A) Processing helix chain '1' and resid 39 through 60 removed outlier: 4.523A pdb=" N ILE 1 43 " --> pdb=" O ASN 1 39 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS 1 44 " --> pdb=" O THR 1 40 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 Processing helix chain '2' and resid 40 through 51 Processing helix chain '3' and resid 55 through 60 removed outlier: 3.534A pdb=" N THR 3 59 " --> pdb=" O HIS 3 55 " (cutoff:3.500A) Processing helix chain '3' and resid 69 through 79 Processing helix chain '4' and resid 9 through 19 removed outlier: 4.811A pdb=" N HIS 4 19 " --> pdb=" O LYS 4 15 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 27 Proline residue: 5 27 - end of helix Processing helix chain '6' and resid 8 through 16 Processing helix chain '6' and resid 17 through 25 removed outlier: 4.029A pdb=" N THR 6 24 " --> pdb=" O LYS 6 20 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 Processing helix chain '7' and resid 7 through 14 Processing helix chain '7' and resid 32 through 37 removed outlier: 4.157A pdb=" N LYS 7 36 " --> pdb=" O ARG 7 32 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N THR 7 37 " --> pdb=" O PHE 7 33 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 32 through 37' Processing helix chain '7' and resid 38 through 46 removed outlier: 3.960A pdb=" N LYS 7 46 " --> pdb=" O ARG 7 42 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 63 removed outlier: 5.771A pdb=" N GLN 7 60 " --> pdb=" O LYS 7 56 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN 7 61 " --> pdb=" O ARG 7 57 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU 7 62 " --> pdb=" O ILE 7 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 16 removed outlier: 4.654A pdb=" N ASP F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 34 Processing helix chain 'F' and resid 81 through 91 Processing helix chain 'F' and resid 98 through 107 removed outlier: 4.382A pdb=" N ALA F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY F 106 " --> pdb=" O ALA F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 125 removed outlier: 4.277A pdb=" N ALA F 122 " --> pdb=" O PRO F 118 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 132 removed outlier: 4.174A pdb=" N VAL F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 159 removed outlier: 4.192A pdb=" N ALA F 152 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 200 Processing helix chain 'G' and resid 30 through 35 removed outlier: 3.619A pdb=" N LEU G 34 " --> pdb=" O GLU G 30 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLN G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 30 through 35' Processing helix chain 'G' and resid 131 through 136 removed outlier: 3.750A pdb=" N ILE G 135 " --> pdb=" O PRO G 131 " (cutoff:3.500A) Proline residue: G 136 - end of helix No H-bonds generated for 'chain 'G' and resid 131 through 136' Processing helix chain 'G' and resid 207 through 215 removed outlier: 3.751A pdb=" N SER G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 226 removed outlier: 4.072A pdb=" N MET G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ASN G 226 " --> pdb=" O GLY G 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 221 through 226' Processing helix chain 'G' and resid 264 through 271 removed outlier: 4.714A pdb=" N LYS G 268 " --> pdb=" O ALA G 264 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU G 269 " --> pdb=" O LYS G 265 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL G 271 " --> pdb=" O ASP G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 202 removed outlier: 3.851A pdb=" N GLU G 201 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 62 removed outlier: 3.644A pdb=" N SER H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASN H 62 " --> pdb=" O GLU H 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 57 through 62' Processing helix chain 'H' and resid 63 through 72 removed outlier: 4.073A pdb=" N LYS H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ALA H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.926A pdb=" N TYR H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLU H 92 " --> pdb=" O LEU H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 92' Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'I' and resid 29 through 45 removed outlier: 3.766A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 removed outlier: 6.225A pdb=" N ARG I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 121 Processing helix chain 'I' and resid 135 through 147 Processing helix chain 'I' and resid 160 through 168 Processing helix chain 'I' and resid 182 through 190 removed outlier: 5.227A pdb=" N ASN I 190 " --> pdb=" O VAL I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 206 Processing helix chain 'J' and resid 2 through 21 removed outlier: 4.311A pdb=" N THR J 13 " --> pdb=" O ILE J 9 " (cutoff:3.500A) Proline residue: J 14 - end of helix Processing helix chain 'J' and resid 41 through 46 removed outlier: 4.663A pdb=" N SER J 45 " --> pdb=" O GLY J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 62 Processing helix chain 'J' and resid 93 through 111 removed outlier: 3.774A pdb=" N SER J 107 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU J 108 " --> pdb=" O VAL J 104 " (cutoff:3.500A) Proline residue: J 109 - end of helix Processing helix chain 'J' and resid 162 through 174 Processing helix chain 'J' and resid 134 through 139 removed outlier: 4.626A pdb=" N ILE J 137 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHE J 138 " --> pdb=" O GLN J 135 " (cutoff:3.500A) Proline residue: J 139 - end of helix No H-bonds generated for 'chain 'J' and resid 134 through 139' Processing helix chain 'J' and resid 142 through 147 removed outlier: 4.566A pdb=" N LEU J 145 " --> pdb=" O ASP J 142 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL J 146 " --> pdb=" O TYR J 143 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP J 147 " --> pdb=" O ASP J 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 142 through 147' Processing helix chain 'K' and resid 3 through 8 removed outlier: 5.520A pdb=" N VAL K 8 " --> pdb=" O ILE K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 81 Processing helix chain 'K' and resid 137 through 153 removed outlier: 4.129A pdb=" N ARG K 152 " --> pdb=" O ILE K 148 " (cutoff:3.500A) Proline residue: K 153 - end of helix Processing helix chain 'M' and resid 25 through 39 Processing helix chain 'M' and resid 89 through 97 Processing helix chain 'M' and resid 98 through 111 removed outlier: 3.530A pdb=" N MET M 109 " --> pdb=" O SER M 105 " (cutoff:3.500A) Proline residue: M 111 - end of helix Processing helix chain 'M' and resid 113 through 123 removed outlier: 3.758A pdb=" N LYS M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 73 removed outlier: 4.134A pdb=" N LYS M 73 " --> pdb=" O LYS M 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 68 through 73' Processing helix chain 'N' and resid 104 through 110 removed outlier: 4.619A pdb=" N GLU N 108 " --> pdb=" O ARG N 104 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN N 109 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 118 Processing helix chain 'O' and resid 56 through 62 Proline residue: O 62 - end of helix Processing helix chain 'O' and resid 78 through 85 removed outlier: 4.057A pdb=" N ARG O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE O 85 " --> pdb=" O THR O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 129 through 140 removed outlier: 3.632A pdb=" N GLY O 140 " --> pdb=" O ILE O 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 59 Processing helix chain 'P' and resid 110 through 126 Proline residue: P 126 - end of helix Processing helix chain 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 34 through 54 removed outlier: 4.587A pdb=" N SER Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 66 removed outlier: 3.839A pdb=" N PHE Q 65 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 98 removed outlier: 5.280A pdb=" N GLY Q 94 " --> pdb=" O PHE Q 90 " (cutoff:3.500A) Proline residue: Q 95 - end of helix Processing helix chain 'R' and resid 6 through 20 removed outlier: 3.801A pdb=" N ARG R 17 " --> pdb=" O LYS R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 87 Processing helix chain 'R' and resid 102 through 115 Processing helix chain 'S' and resid 2 through 14 removed outlier: 4.312A pdb=" N GLU S 11 " --> pdb=" O GLU S 7 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLN S 12 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG S 14 " --> pdb=" O GLN S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 104 removed outlier: 4.513A pdb=" N ARG S 101 " --> pdb=" O LEU S 97 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA S 102 " --> pdb=" O TYR S 98 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU S 103 " --> pdb=" O TYR S 99 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N HIS S 104 " --> pdb=" O LEU S 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 97 through 104' Processing helix chain 'T' and resid 8 through 22 Processing helix chain 'T' and resid 25 through 31 removed outlier: 4.442A pdb=" N HIS T 29 " --> pdb=" O TYR T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 37 Processing helix chain 'T' and resid 39 through 73 removed outlier: 3.771A pdb=" N ARG T 51 " --> pdb=" O PHE T 47 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG T 55 " --> pdb=" O ARG T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 87 Processing helix chain 'T' and resid 91 through 101 Processing helix chain 'T' and resid 102 through 119 Processing helix chain 'V' and resid 18 through 30 removed outlier: 3.721A pdb=" N VAL V 25 " --> pdb=" O LYS V 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 44 Processing helix chain 'V' and resid 46 through 65 removed outlier: 4.378A pdb=" N GLY V 50 " --> pdb=" O ASN V 46 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE V 51 " --> pdb=" O LYS V 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 7 removed outlier: 3.864A pdb=" N ILE W 7 " --> pdb=" O LEU W 3 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 23 Processing helix chain 'W' and resid 34 through 46 Processing helix chain 'X' and resid 64 through 69 removed outlier: 4.360A pdb=" N VAL X 68 " --> pdb=" O HIS X 64 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N MET X 69 " --> pdb=" O VAL X 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 64 through 69' Processing helix chain 'Z' and resid 50 through 57 removed outlier: 4.099A pdb=" N SER Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLY Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 13 Processing helix chain 'c' and resid 24 through 29 removed outlier: 4.139A pdb=" N LYS c 28 " --> pdb=" O ASN c 24 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS c 29 " --> pdb=" O PRO c 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 24 through 29' Processing helix chain 'c' and resid 42 through 64 removed outlier: 3.523A pdb=" N GLY c 64 " --> pdb=" O VAL c 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 88 removed outlier: 5.140A pdb=" N GLU c 78 " --> pdb=" O LYS c 74 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA c 79 " --> pdb=" O GLN c 75 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 124 removed outlier: 3.697A pdb=" N LYS c 109 " --> pdb=" O ASP c 105 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG c 110 " --> pdb=" O THR c 106 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU c 121 " --> pdb=" O ILE c 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 148 Processing helix chain 'c' and resid 165 through 170 Processing helix chain 'c' and resid 171 through 180 Processing helix chain 'c' and resid 192 through 197 removed outlier: 4.663A pdb=" N ILE c 196 " --> pdb=" O ASP c 192 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP c 197 " --> pdb=" O PRO c 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 192 through 197' Processing helix chain 'c' and resid 206 through 225 Processing helix chain 'd' and resid 6 through 12 removed outlier: 3.584A pdb=" N ARG d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 47 Processing helix chain 'd' and resid 71 through 77 Processing helix chain 'd' and resid 80 through 95 Processing helix chain 'd' and resid 107 through 112 removed outlier: 4.369A pdb=" N ASP d 111 " --> pdb=" O LYS d 107 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ALA d 112 " --> pdb=" O PRO d 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 107 through 112' Processing helix chain 'd' and resid 113 through 126 Processing helix chain 'd' and resid 128 through 144 Processing helix chain 'e' and resid 7 through 16 removed outlier: 4.083A pdb=" N VAL e 11 " --> pdb=" O PRO e 7 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 29 removed outlier: 4.204A pdb=" N ARG e 28 " --> pdb=" O LYS e 24 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ARG e 29 " --> pdb=" O GLU e 25 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 62 Processing helix chain 'e' and resid 64 through 79 removed outlier: 5.266A pdb=" N LYS e 79 " --> pdb=" O ALA e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 95 removed outlier: 5.799A pdb=" N LEU e 95 " --> pdb=" O LEU e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 96 through 103 Processing helix chain 'e' and resid 107 through 118 Processing helix chain 'e' and resid 143 through 148 removed outlier: 4.664A pdb=" N ASN e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 159 Processing helix chain 'e' and resid 182 through 187 removed outlier: 4.663A pdb=" N TYR e 187 " --> pdb=" O ARG e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 201 removed outlier: 3.729A pdb=" N VAL e 195 " --> pdb=" O ASP e 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 55 through 71 Processing helix chain 'f' and resid 109 through 119 Processing helix chain 'f' and resid 132 through 148 removed outlier: 5.604A pdb=" N LYS f 148 " --> pdb=" O LEU f 144 " (cutoff:3.500A) Processing helix chain 'f' and resid 149 through 158 Processing helix chain 'f' and resid 160 through 165 Processing helix chain 'g' and resid 18 through 37 Processing helix chain 'g' and resid 75 through 88 removed outlier: 5.352A pdb=" N ASP g 88 " --> pdb=" O ALA g 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 20 through 31 Processing helix chain 'h' and resid 35 through 54 Processing helix chain 'h' and resid 57 through 70 Processing helix chain 'h' and resid 92 through 111 Processing helix chain 'h' and resid 115 through 130 Processing helix chain 'h' and resid 132 through 153 removed outlier: 4.946A pdb=" N ALA h 150 " --> pdb=" O ASP h 146 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE h 151 " --> pdb=" O ALA h 147 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA h 152 " --> pdb=" O ASN h 148 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N HIS h 153 " --> pdb=" O ARG h 149 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 21 Processing helix chain 'i' and resid 30 through 44 Processing helix chain 'i' and resid 114 through 122 Processing helix chain 'j' and resid 34 through 40 Proline residue: j 40 - end of helix Processing helix chain 'j' and resid 41 through 56 Proline residue: j 51 - end of helix Processing helix chain 'j' and resid 71 through 92 Proline residue: j 92 - end of helix Processing helix chain 'j' and resid 93 through 102 removed outlier: 4.529A pdb=" N ALA j 97 " --> pdb=" O ASP j 93 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 33 Processing helix chain 'k' and resid 80 through 91 removed outlier: 3.869A pdb=" N VAL k 84 " --> pdb=" O THR k 80 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP k 85 " --> pdb=" O PRO k 81 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP k 91 " --> pdb=" O LEU k 87 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 51 Processing helix chain 'l' and resid 54 through 60 removed outlier: 4.667A pdb=" N SER l 58 " --> pdb=" O GLY l 54 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR l 59 " --> pdb=" O SER l 55 " (cutoff:3.500A) Proline residue: l 60 - end of helix No H-bonds generated for 'chain 'l' and resid 54 through 60' Processing helix chain 'l' and resid 61 through 78 Processing helix chain 'l' and resid 92 through 104 Processing helix chain 'm' and resid 3 through 11 Proline residue: m 11 - end of helix Processing helix chain 'm' and resid 21 through 26 removed outlier: 4.122A pdb=" N ASN m 25 " --> pdb=" O SER m 21 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS m 26 " --> pdb=" O PRO m 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 21 through 26' Processing helix chain 'm' and resid 126 through 131 removed outlier: 4.577A pdb=" N TYR m 130 " --> pdb=" O SER m 126 " (cutoff:3.500A) Processing helix chain 'n' and resid 14 through 23 removed outlier: 3.917A pdb=" N ILE n 22 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR n 23 " --> pdb=" O LEU n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 26 through 38 Processing helix chain 'n' and resid 44 through 49 removed outlier: 5.501A pdb=" N THR n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 50 through 64 removed outlier: 4.299A pdb=" N LYS n 64 " --> pdb=" O ILE n 60 " (cutoff:3.500A) Processing helix chain 'n' and resid 66 through 84 Processing helix chain 'n' and resid 85 through 94 Processing helix chain 'n' and resid 106 through 111 Processing helix chain 'o' and resid 2 through 13 Proline residue: o 13 - end of helix Processing helix chain 'o' and resid 40 through 51 Processing helix chain 'p' and resid 4 through 16 Processing helix chain 'p' and resid 24 through 47 Processing helix chain 'p' and resid 49 through 74 Processing helix chain 'p' and resid 75 through 86 Processing helix chain 'q' and resid 52 through 63 Processing helix chain 'q' and resid 67 through 78 Processing helix chain 'q' and resid 79 through 88 Processing helix chain 's' and resid 15 through 21 Processing helix chain 's' and resid 29 through 38 removed outlier: 4.044A pdb=" N ARG s 35 " --> pdb=" O GLU s 31 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE s 36 " --> pdb=" O LEU s 32 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N SER s 38 " --> pdb=" O LYS s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 45 through 50 Processing helix chain 's' and resid 52 through 70 Processing helix chain 't' and resid 12 through 24 removed outlier: 4.383A pdb=" N GLY t 24 " --> pdb=" O GLU t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 41 through 46 removed outlier: 5.419A pdb=" N GLY t 46 " --> pdb=" O PRO t 42 " (cutoff:3.500A) Processing helix chain 't' and resid 63 through 68 removed outlier: 6.287A pdb=" N GLY t 68 " --> pdb=" O GLU t 64 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 76 removed outlier: 4.060A pdb=" N PHE t 74 " --> pdb=" O LYS t 70 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA t 75 " --> pdb=" O LEU t 71 " (cutoff:3.500A) Proline residue: t 76 - end of helix No H-bonds generated for 'chain 't' and resid 70 through 76' Processing helix chain 'u' and resid 4 through 42 Processing helix chain 'u' and resid 45 through 64 removed outlier: 4.376A pdb=" N LYS u 63 " --> pdb=" O MET u 59 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY u 64 " --> pdb=" O ALA u 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 67 through 82 Processing sheet with id= 1, first strand: chain '0' and resid 20 through 23 removed outlier: 3.576A pdb=" N MET 0 1 " --> pdb=" O LEU 0 23 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '0' and resid 63 through 68 removed outlier: 4.399A pdb=" N SER 0 207 " --> pdb=" O GLU 0 178 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS 0 224 " --> pdb=" O LYS 0 28 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS 0 234 " --> pdb=" O ASP 0 229 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '0' and resid 350 through 353 removed outlier: 4.661A pdb=" N LEU 0 330 " --> pdb=" O ILE 0 353 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '0' and resid 358 through 363 removed outlier: 3.557A pdb=" N ASN 0 520 " --> pdb=" O ILE 0 515 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '0' and resid 394 through 399 Processing sheet with id= 6, first strand: chain '2' and resid 32 through 38 removed outlier: 4.119A pdb=" N SER 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU 2 53 " --> pdb=" O LYS 2 9 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '3' and resid 21 through 25 removed outlier: 3.981A pdb=" N PHE 3 21 " --> pdb=" O ASP 3 16 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET 3 15 " --> pdb=" O LEU 3 46 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '4' and resid 26 through 29 removed outlier: 7.224A pdb=" N GLY 4 26 " --> pdb=" O SER 4 39 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '5' and resid 3 through 8 Processing sheet with id= 10, first strand: chain '5' and resid 30 through 34 removed outlier: 5.694A pdb=" N LEU 5 30 " --> pdb=" O GLU 5 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '7' and resid 22 through 25 removed outlier: 5.832A pdb=" N LEU 7 22 " --> pdb=" O VAL 7 50 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '8' and resid 1 through 5 removed outlier: 6.217A pdb=" N HIS 8 33 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N CYS 8 27 " --> pdb=" O HIS 8 33 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 59 through 64 removed outlier: 5.762A pdb=" N ILE F 59 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 93 through 97 Processing sheet with id= 15, first strand: chain 'F' and resid 169 through 175 removed outlier: 5.786A pdb=" N GLY F 169 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL F 42 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN F 211 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE F 212 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 2 through 6 removed outlier: 6.591A pdb=" N ALA G 2 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N MET G 16 " --> pdb=" O TYR G 6 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 80 through 83 removed outlier: 6.693A pdb=" N LEU G 93 " --> pdb=" O LYS G 79 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N MET G 114 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLY G 127 " --> pdb=" O ARG G 115 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL G 117 " --> pdb=" O GLY G 127 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 138 through 142 removed outlier: 4.099A pdb=" N THR G 139 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 91 through 96 removed outlier: 3.873A pdb=" N VAL G 100 " --> pdb=" O TYR G 96 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.323A pdb=" N LYS H 3 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU H 199 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR H 113 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP H 167 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 11 through 17 removed outlier: 4.077A pdb=" N GLU H 21 " --> pdb=" O THR H 17 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 79 through 84 removed outlier: 6.612A pdb=" N GLN H 50 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS H 95 " --> pdb=" O VAL H 35 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 106 through 109 removed outlier: 4.266A pdb=" N ASP H 106 " --> pdb=" O VAL H 176 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 2 through 7 removed outlier: 3.904A pdb=" N LEU I 6 " --> pdb=" O GLY I 15 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY I 15 " --> pdb=" O LEU I 6 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 122 through 125 Processing sheet with id= 26, first strand: chain 'J' and resid 65 through 69 removed outlier: 4.443A pdb=" N GLY J 86 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE J 85 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL J 40 " --> pdb=" O ILE J 85 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLY J 39 " --> pdb=" O GLY J 151 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY J 151 " --> pdb=" O GLY J 39 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 16 through 19 Processing sheet with id= 28, first strand: chain 'K' and resid 41 through 45 Processing sheet with id= 29, first strand: chain 'K' and resid 94 through 99 removed outlier: 6.590A pdb=" N ASN K 101 " --> pdb=" O ALA K 117 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'K' and resid 121 through 125 removed outlier: 6.261A pdb=" N ILE K 132 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N THR K 129 " --> pdb=" O LEU K 89 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'M' and resid 16 through 19 Processing sheet with id= 32, first strand: chain 'M' and resid 75 through 79 removed outlier: 7.401A pdb=" N GLY M 84 " --> pdb=" O SER M 79 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'N' and resid 18 through 21 removed outlier: 4.587A pdb=" N SER N 6 " --> pdb=" O THR N 21 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASN N 82 " --> pdb=" O ARG N 7 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE N 86 " --> pdb=" O ALA N 11 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS N 59 " --> pdb=" O ILE N 87 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP N 37 " --> pdb=" O ILE N 62 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'N' and resid 68 through 71 removed outlier: 3.928A pdb=" N SER N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'N' and resid 63 through 66 removed outlier: 3.837A pdb=" N LYS N 66 " --> pdb=" O GLU N 81 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU N 81 " --> pdb=" O LYS N 66 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'P' and resid 63 through 67 removed outlier: 7.276A pdb=" N MET P 103 " --> pdb=" O LYS P 67 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE P 104 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU P 31 " --> pdb=" O ARG P 134 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS P 128 " --> pdb=" O THR P 37 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'P' and resid 72 through 75 removed outlier: 6.785A pdb=" N LYS P 72 " --> pdb=" O TRP P 93 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP P 93 " --> pdb=" O LYS P 72 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR P 74 " --> pdb=" O GLU P 91 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'Q' and resid 72 through 75 Processing sheet with id= 39, first strand: chain 'R' and resid 54 through 57 Processing sheet with id= 40, first strand: chain 'S' and resid 38 through 45 removed outlier: 6.641A pdb=" N THR S 25 " --> pdb=" O VAL S 87 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN S 83 " --> pdb=" O HIS S 29 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S' and resid 49 through 52 removed outlier: 3.709A pdb=" N LYS S 49 " --> pdb=" O THR S 60 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 11 through 15 Processing sheet with id= 43, first strand: chain 'U' and resid 18 through 23 removed outlier: 4.260A pdb=" N GLN U 18 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS U 94 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU U 59 " --> pdb=" O GLU U 98 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU U 31 " --> pdb=" O VAL U 62 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'U' and resid 64 through 67 Processing sheet with id= 45, first strand: chain 'U' and resid 70 through 76 Processing sheet with id= 46, first strand: chain 'V' and resid 6 through 13 removed outlier: 9.433A pdb=" N THR V 6 " --> pdb=" O GLU V 114 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL V 111 " --> pdb=" O SER V 77 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 78 through 84 removed outlier: 4.918A pdb=" N THR V 105 " --> pdb=" O GLY V 84 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 85 through 93 removed outlier: 3.738A pdb=" N THR V 105 " --> pdb=" O PRO V 85 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER V 97 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'W' and resid 8 through 11 removed outlier: 5.090A pdb=" N THR W 26 " --> pdb=" O VAL W 11 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG W 76 " --> pdb=" O VAL W 29 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS W 73 " --> pdb=" O PRO W 60 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS W 61 " --> pdb=" O THR W 72 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'X' and resid 9 through 12 removed outlier: 4.232A pdb=" N LYS X 19 " --> pdb=" O VAL X 11 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'X' and resid 25 through 28 removed outlier: 3.665A pdb=" N ALA X 25 " --> pdb=" O ILE X 34 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'X' and resid 39 through 45 removed outlier: 5.461A pdb=" N ASN X 39 " --> pdb=" O ALA X 61 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'X' and resid 80 through 83 removed outlier: 7.037A pdb=" N LYS X 80 " --> pdb=" O LYS X 95 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG X 92 " --> pdb=" O LEU X 101 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU X 99 " --> pdb=" O SER X 94 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Y' and resid 46 through 49 removed outlier: 4.218A pdb=" N GLN Y 49 " --> pdb=" O ASP Y 66 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP Y 66 " --> pdb=" O GLN Y 49 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Y' and resid 75 through 80 Processing sheet with id= 56, first strand: chain 'Z' and resid 12 through 19 removed outlier: 4.352A pdb=" N ASN Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'c' and resid 15 through 18 removed outlier: 5.804A pdb=" N HIS c 15 " --> pdb=" O ILE c 41 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR c 39 " --> pdb=" O GLY c 17 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'c' and resid 89 through 93 Processing sheet with id= 59, first strand: chain 'd' and resid 53 through 58 removed outlier: 4.096A pdb=" N THR d 53 " --> pdb=" O HIS d 68 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'd' and resid 163 through 168 removed outlier: 4.573A pdb=" N ASP d 180 " --> pdb=" O ARG d 203 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'e' and resid 165 through 170 removed outlier: 7.890A pdb=" N PHE e 165 " --> pdb=" O THR e 178 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'f' and resid 12 through 15 Processing sheet with id= 63, first strand: chain 'f' and resid 83 through 88 removed outlier: 7.741A pdb=" N HIS f 83 " --> pdb=" O PRO f 98 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG f 93 " --> pdb=" O LEU f 128 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA f 99 " --> pdb=" O ASP f 122 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASP f 122 " --> pdb=" O ALA f 99 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'f' and resid 33 through 40 Processing sheet with id= 65, first strand: chain 'g' and resid 38 through 41 removed outlier: 6.830A pdb=" N ASN g 67 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N GLU g 60 " --> pdb=" O PRO g 15 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS g 6 " --> pdb=" O VAL g 98 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG g 92 " --> pdb=" O ILE g 12 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'g' and resid 42 through 45 Processing sheet with id= 67, first strand: chain 'g' and resid 46 through 50 Processing sheet with id= 68, first strand: chain 'h' and resid 72 through 79 removed outlier: 6.402A pdb=" N VAL h 72 " --> pdb=" O VAL h 91 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'i' and resid 23 through 28 removed outlier: 6.601A pdb=" N GLU i 23 " --> pdb=" O LEU i 64 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'i' and resid 76 through 79 removed outlier: 4.715A pdb=" N ASN i 76 " --> pdb=" O TRP i 132 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE i 105 " --> pdb=" O ILE i 128 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'j' and resid 5 through 11 Processing sheet with id= 72, first strand: chain 'k' and resid 39 through 42 removed outlier: 4.599A pdb=" N LYS k 71 " --> pdb=" O LEU k 42 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG k 7 " --> pdb=" O LYS k 101 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'k' and resid 44 through 52 Processing sheet with id= 74, first strand: chain 'l' and resid 42 through 45 removed outlier: 3.567A pdb=" N ASN l 29 " --> pdb=" O THR l 26 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL l 84 " --> pdb=" O THR l 108 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'l' and resid 83 through 88 removed outlier: 5.954A pdb=" N GLY l 88 " --> pdb=" O VAL l 113 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'm' and resid 27 through 30 Processing sheet with id= 77, first strand: chain 'm' and resid 42 through 45 removed outlier: 5.069A pdb=" N LEU m 94 " --> pdb=" O VAL m 111 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'm' and resid 49 through 54 removed outlier: 5.407A pdb=" N LYS m 64 " --> pdb=" O ILE m 80 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE m 74 " --> pdb=" O LEU m 70 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'q' and resid 5 through 11 Processing sheet with id= 80, first strand: chain 'r' and resid 9 through 14 removed outlier: 5.430A pdb=" N LYS r 9 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS r 63 " --> pdb=" O LEU r 79 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'r' and resid 22 through 33 No H-bonds generated for sheet with id= 81 Processing sheet with id= 82, first strand: chain 't' and resid 30 through 33 removed outlier: 4.401A pdb=" N PHE t 47 " --> pdb=" O ILE t 62 " (cutoff:3.500A) 2173 hydrogen bonds defined for protein. 6396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4002 hydrogen bonds 6328 hydrogen bond angles 0 basepair planarities 1603 basepair parallelities 2478 stacking parallelities Total time for adding SS restraints: 258.80 Time building geometry restraints manager: 74.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.10: 3 1.10 - 1.28: 12375 1.28 - 1.45: 78873 1.45 - 1.63: 69987 1.63 - 1.81: 303 Bond restraints: 161541 Sorted by residual: bond pdb=" C5 SCM a1615 " pdb=" O1B SCM a1615 " ideal model delta sigma weight residual 1.524 0.923 0.601 2.00e-02 2.50e+03 9.04e+02 bond pdb=" C6 SCM a1615 " pdb=" O1 SCM a1615 " ideal model delta sigma weight residual 0.917 1.431 -0.514 2.00e-02 2.50e+03 6.59e+02 bond pdb=" C12 SCM a1615 " pdb=" O2B SCM a1615 " ideal model delta sigma weight residual 1.506 1.009 0.497 2.00e-02 2.50e+03 6.18e+02 bond pdb=" C3 SCM a1615 " pdb=" C4 SCM a1615 " ideal model delta sigma weight residual 1.054 1.536 -0.482 2.00e-02 2.50e+03 5.81e+02 bond pdb=" C4 SCM a1615 " pdb=" C5 SCM a1615 " ideal model delta sigma weight residual 1.493 1.095 0.398 2.00e-02 2.50e+03 3.97e+02 ... (remaining 161536 not shown) Histogram of bond angle deviations from ideal: 82.33 - 97.53: 1 97.53 - 112.74: 118804 112.74 - 127.95: 114613 127.95 - 143.15: 7963 143.15 - 158.36: 1 Bond angle restraints: 241382 Sorted by residual: angle pdb=" C5 T6A C 37 " pdb=" C6 T6A C 37 " pdb=" N6 T6A C 37 " ideal model delta sigma weight residual 122.16 158.36 -36.20 3.00e+00 1.11e-01 1.46e+02 angle pdb=" N6 T6A C 37 " pdb=" C6 T6A C 37 " pdb=" N1 T6A C 37 " ideal model delta sigma weight residual 117.83 82.33 35.50 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C1' ATP 0 601 " pdb=" N9 ATP 0 601 " pdb=" C8 ATP 0 601 " ideal model delta sigma weight residual 92.72 114.45 -21.73 3.00e+00 1.11e-01 5.25e+01 angle pdb=" C1' ATP 0 602 " pdb=" N9 ATP 0 602 " pdb=" C8 ATP 0 602 " ideal model delta sigma weight residual 92.72 114.29 -21.57 3.00e+00 1.11e-01 5.17e+01 angle pdb=" O3' C A1927 " pdb=" C3' C A1927 " pdb=" C2' C A1927 " ideal model delta sigma weight residual 113.70 119.29 -5.59 1.50e+00 4.44e-01 1.39e+01 ... (remaining 241377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 91319 35.95 - 71.90: 10575 71.90 - 107.84: 1223 107.84 - 143.79: 28 143.79 - 179.74: 35 Dihedral angle restraints: 103180 sinusoidal: 85744 harmonic: 17436 Sorted by residual: dihedral pdb=" C4' G a 9 " pdb=" C3' G a 9 " pdb=" C2' G a 9 " pdb=" C1' G a 9 " ideal model delta sinusoidal sigma weight residual -35.00 35.32 -70.32 1 8.00e+00 1.56e-02 9.95e+01 dihedral pdb=" C4' A a 845 " pdb=" C3' A a 845 " pdb=" C2' A a 845 " pdb=" C1' A a 845 " ideal model delta sinusoidal sigma weight residual -35.00 33.33 -68.33 1 8.00e+00 1.56e-02 9.46e+01 dihedral pdb=" C5' G a 9 " pdb=" C4' G a 9 " pdb=" C3' G a 9 " pdb=" O3' G a 9 " ideal model delta sinusoidal sigma weight residual 147.00 80.43 66.57 1 8.00e+00 1.56e-02 9.04e+01 ... (remaining 103177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.688: 30824 0.688 - 1.375: 1 1.375 - 2.063: 0 2.063 - 2.750: 0 2.750 - 3.438: 2 Chirality restraints: 30827 Sorted by residual: chirality pdb=" C5 SCM a1615 " pdb=" C4 SCM a1615 " pdb=" C6 SCM a1615 " pdb=" O1B SCM a1615 " both_signs ideal model delta sigma weight residual False 2.40 -1.04 3.44 2.00e-01 2.50e+01 2.95e+02 chirality pdb=" C6 SCM a1615 " pdb=" C5 SCM a1615 " pdb=" O1 SCM a1615 " pdb=" O2B SCM a1615 " both_signs ideal model delta sigma weight residual False 1.09 -2.21 3.30 2.00e-01 2.50e+01 2.73e+02 chirality pdb=" C12 SCM a1615 " pdb=" C11 SCM a1615 " pdb=" C7 SCM a1615 " pdb=" O2B SCM a1615 " both_signs ideal model delta sigma weight residual False 2.37 1.68 0.69 2.00e-01 2.50e+01 1.19e+01 ... (remaining 30824 not shown) Planarity restraints: 13100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU C 54 " -0.037 2.00e-02 2.50e+03 5.77e-01 7.48e+03 pdb=" C4' 5MU C 54 " -0.437 2.00e-02 2.50e+03 pdb=" O4' 5MU C 54 " -0.632 2.00e-02 2.50e+03 pdb=" C3' 5MU C 54 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 5MU C 54 " 0.581 2.00e-02 2.50e+03 pdb=" C2' 5MU C 54 " 0.202 2.00e-02 2.50e+03 pdb=" O2' 5MU C 54 " -0.918 2.00e-02 2.50e+03 pdb=" C1' 5MU C 54 " -0.231 2.00e-02 2.50e+03 pdb=" N1 5MU C 54 " 0.879 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP 0 601 " 0.369 2.00e-02 2.50e+03 4.05e-01 3.70e+03 pdb=" C2' ATP 0 601 " -0.551 2.00e-02 2.50e+03 pdb=" C3' ATP 0 601 " -0.362 2.00e-02 2.50e+03 pdb=" C4' ATP 0 601 " 0.338 2.00e-02 2.50e+03 pdb=" C5' ATP 0 601 " -0.511 2.00e-02 2.50e+03 pdb=" N9 ATP 0 601 " -0.158 2.00e-02 2.50e+03 pdb=" O2' ATP 0 601 " -0.112 2.00e-02 2.50e+03 pdb=" O3' ATP 0 601 " 0.558 2.00e-02 2.50e+03 pdb=" O4' ATP 0 601 " 0.430 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP 0 602 " 0.339 2.00e-02 2.50e+03 3.36e-01 2.54e+03 pdb=" C2' ATP 0 602 " -0.487 2.00e-02 2.50e+03 pdb=" C3' ATP 0 602 " -0.446 2.00e-02 2.50e+03 pdb=" C4' ATP 0 602 " 0.359 2.00e-02 2.50e+03 pdb=" C5' ATP 0 602 " -0.296 2.00e-02 2.50e+03 pdb=" N9 ATP 0 602 " -0.220 2.00e-02 2.50e+03 pdb=" O2' ATP 0 602 " 0.168 2.00e-02 2.50e+03 pdb=" O3' ATP 0 602 " 0.300 2.00e-02 2.50e+03 pdb=" O4' ATP 0 602 " 0.283 2.00e-02 2.50e+03 ... (remaining 13097 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.37: 705 2.37 - 3.06: 93715 3.06 - 3.76: 347926 3.76 - 4.45: 529258 4.45 - 5.14: 706742 Nonbonded interactions: 1678346 Sorted by model distance: nonbonded pdb=" O5' A a 529 " pdb="MG MG a1663 " model vdw 1.679 2.170 nonbonded pdb=" O4' A a 529 " pdb="MG MG a1663 " model vdw 1.771 2.170 nonbonded pdb=" O2' G A 295 " pdb=" O5' G A 296 " model vdw 1.852 2.440 nonbonded pdb=" O2' A A1828 " pdb=" O5' A A1829 " model vdw 1.858 2.440 nonbonded pdb=" OP1 A A1793 " pdb="MG MG A3161 " model vdw 1.864 2.170 ... (remaining 1678341 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: 7.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 20.920 Check model and map are aligned: 1.690 Set scattering table: 1.010 Process input model: 607.280 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.330 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:14.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 655.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 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 0.601 161541 Z= 0.282 Angle : 0.403 36.200 241382 Z= 0.222 Chirality : 0.040 3.438 30827 Planarity : 0.007 0.577 13100 Dihedral : 22.610 179.741 91962 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 0.66 % Allowed : 5.69 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.11), residues: 6001 helix: 2.08 (0.11), residues: 2076 sheet: -0.15 (0.15), residues: 1182 loop : -0.10 (0.12), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 108 HIS 0.005 0.001 HIS K 111 PHE 0.009 0.001 PHE t 10 TYR 0.011 0.001 TYR c 90 ARG 0.012 0.000 ARG 0 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1159 time to evaluate : 6.687 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: 0 77 LYS cc_start: 0.9085 (mttt) cc_final: 0.8687 (mtmm) REVERT: 0 151 LEU cc_start: 0.9067 (mp) cc_final: 0.8642 (tt) REVERT: 0 216 ASP cc_start: 0.9073 (m-30) cc_final: 0.8834 (p0) REVERT: 0 342 HIS cc_start: 0.8333 (m-70) cc_final: 0.7964 (m90) REVERT: 0 422 ASP cc_start: 0.8533 (m-30) cc_final: 0.8185 (t0) REVERT: 1 11 THR cc_start: 0.9015 (m) cc_final: 0.8800 (t) REVERT: 2 9 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8331 (mtpt) REVERT: 3 12 VAL cc_start: 0.7162 (p) cc_final: 0.6518 (m) REVERT: 3 24 LEU cc_start: 0.6943 (tp) cc_final: 0.6377 (pt) REVERT: 3 43 TYR cc_start: 0.7863 (m-80) cc_final: 0.7505 (m-80) REVERT: 8 20 LYS cc_start: 0.9091 (mmmm) cc_final: 0.8850 (mtmt) REVERT: F 60 ARG cc_start: 0.7838 (ttt180) cc_final: 0.7615 (ttm110) REVERT: F 78 PHE cc_start: 0.7465 (m-80) cc_final: 0.6498 (m-80) REVERT: F 82 GLU cc_start: 0.7043 (tp30) cc_final: 0.6828 (tp30) REVERT: F 83 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7841 (mtmt) REVERT: F 110 ASP cc_start: 0.5007 (OUTLIER) cc_final: 0.4766 (m-30) REVERT: H 91 TYR cc_start: 0.8917 (m-80) cc_final: 0.8615 (m-80) REVERT: H 106 ASP cc_start: 0.7981 (m-30) cc_final: 0.7728 (m-30) REVERT: H 146 MET cc_start: 0.9321 (mmm) cc_final: 0.8968 (mmm) REVERT: J 67 ILE cc_start: 0.9283 (mt) cc_final: 0.8987 (tp) REVERT: J 123 ASP cc_start: 0.8472 (p0) cc_final: 0.8136 (p0) REVERT: J 125 ARG cc_start: 0.8624 (mmt-90) cc_final: 0.8184 (mpp80) REVERT: J 130 LEU cc_start: 0.8222 (tp) cc_final: 0.7929 (pp) REVERT: M 77 ARG cc_start: 0.8015 (ptp90) cc_final: 0.7662 (ptt-90) REVERT: Q 47 MET cc_start: 0.9082 (mmp) cc_final: 0.8806 (mmt) REVERT: R 33 ILE cc_start: 0.9287 (mm) cc_final: 0.9052 (tp) REVERT: R 81 GLU cc_start: 0.9024 (pt0) cc_final: 0.8811 (pt0) REVERT: Y 84 ASP cc_start: 0.8401 (p0) cc_final: 0.7951 (p0) REVERT: Y 85 LYS cc_start: 0.8929 (mttt) cc_final: 0.8709 (mttp) REVERT: Z 11 LYS cc_start: 0.9175 (pttm) cc_final: 0.8911 (ptpt) REVERT: c 108 GLN cc_start: 0.9052 (mm110) cc_final: 0.8797 (mm110) REVERT: c 217 MET cc_start: 0.9261 (mmp) cc_final: 0.8796 (mmp) REVERT: d 138 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8212 (tp-100) REVERT: f 41 ASP cc_start: 0.7189 (t0) cc_final: 0.6443 (t0) REVERT: g 10 MET cc_start: 0.8798 (ttp) cc_final: 0.8429 (ttp) REVERT: g 34 LYS cc_start: 0.9169 (mttm) cc_final: 0.8959 (mtmm) REVERT: g 46 TRP cc_start: 0.7969 (t60) cc_final: 0.7545 (t60) REVERT: g 58 PHE cc_start: 0.8159 (m-80) cc_final: 0.7772 (m-80) REVERT: g 72 SER cc_start: 0.8442 (p) cc_final: 0.8144 (t) REVERT: h 49 ILE cc_start: 0.9232 (mt) cc_final: 0.8974 (mm) REVERT: h 53 SER cc_start: 0.8714 (m) cc_final: 0.8420 (t) REVERT: h 136 LYS cc_start: 0.9344 (tttm) cc_final: 0.8900 (tttm) REVERT: h 140 ASP cc_start: 0.8651 (m-30) cc_final: 0.8360 (m-30) REVERT: h 143 LYS cc_start: 0.8982 (ttpp) cc_final: 0.8759 (mtmm) REVERT: i 61 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.8031 (mtp-110) REVERT: j 43 ASP cc_start: 0.8051 (p0) cc_final: 0.7545 (p0) REVERT: j 112 GLU cc_start: 0.8078 (tt0) cc_final: 0.7791 (tt0) REVERT: k 20 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8564 (mm110) REVERT: k 23 ASP cc_start: 0.8704 (m-30) cc_final: 0.8390 (p0) REVERT: k 32 THR cc_start: 0.8600 (p) cc_final: 0.8376 (p) REVERT: k 90 LEU cc_start: 0.8148 (tp) cc_final: 0.7484 (pp) REVERT: m 91 SER cc_start: 0.9130 (t) cc_final: 0.8842 (p) REVERT: n 12 ASP cc_start: 0.8362 (p0) cc_final: 0.7857 (t0) REVERT: n 28 THR cc_start: 0.8992 (m) cc_final: 0.8515 (t) REVERT: n 36 ASN cc_start: 0.9075 (m-40) cc_final: 0.8825 (m110) REVERT: n 41 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7994 (mt-10) REVERT: o 46 GLU cc_start: 0.8654 (tt0) cc_final: 0.8409 (tt0) REVERT: o 57 LYS cc_start: 0.8851 (ptmm) cc_final: 0.8622 (pttm) REVERT: p 84 ARG cc_start: 0.9039 (mtp180) cc_final: 0.8796 (mmm-85) REVERT: r 83 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7994 (mt-10) REVERT: s 32 LEU cc_start: 0.9207 (tp) cc_final: 0.8894 (tp) REVERT: t 22 GLN cc_start: 0.8255 (mt0) cc_final: 0.7555 (tp40) REVERT: t 44 PHE cc_start: 0.9196 (m-10) cc_final: 0.8980 (m-80) REVERT: t 47 PHE cc_start: 0.8194 (m-80) cc_final: 0.7828 (m-80) REVERT: t 60 VAL cc_start: 0.9304 (t) cc_final: 0.9089 (p) REVERT: t 61 TYR cc_start: 0.8445 (t80) cc_final: 0.8155 (t80) REVERT: u 32 ILE cc_start: 0.9251 (mt) cc_final: 0.8912 (mp) REVERT: u 36 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8249 (mt-10) REVERT: u 52 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8481 (mm-30) REVERT: u 68 LYS cc_start: 0.9095 (ttmt) cc_final: 0.8875 (ttmm) outliers start: 34 outliers final: 13 residues processed: 1186 average time/residue: 2.1905 time to fit residues: 3748.6924 Evaluate side-chains 771 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 756 time to evaluate : 6.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 88 ARG Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain F residue 83 LYS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain e residue 31 TYR Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain n residue 60 ILE Chi-restraints excluded: chain u residue 45 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 893 optimal weight: 6.9990 chunk 801 optimal weight: 30.0000 chunk 444 optimal weight: 20.0000 chunk 273 optimal weight: 20.0000 chunk 540 optimal weight: 20.0000 chunk 428 optimal weight: 20.0000 chunk 829 optimal weight: 20.0000 chunk 320 optimal weight: 20.0000 chunk 504 optimal weight: 20.0000 chunk 617 optimal weight: 20.0000 chunk 960 optimal weight: 9.9990 overall best weight: 15.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 520 ASN 1 20 GLN 2 18 ASN ** 3 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 32 ASN F 58 GLN F 226 GLN G 35 GLN G 142 HIS G 163 GLN J 27 GLN ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 161 ASN K 97 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN T 52 GLN c 8 GLN e 86 ASN ** e 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN ** l 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 GLN m 109 HIS n 27 ASN p 5 GLN p 46 HIS q 88 ASN u 3 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 161541 Z= 0.502 Angle : 0.691 26.142 241382 Z= 0.352 Chirality : 0.044 1.705 30827 Planarity : 0.005 0.133 13100 Dihedral : 23.228 179.693 79753 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.91 % Allowed : 13.80 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.11), residues: 6001 helix: 1.79 (0.11), residues: 2090 sheet: -0.07 (0.15), residues: 1156 loop : -0.23 (0.12), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 0 121 HIS 0.008 0.001 HIS e 36 PHE 0.021 0.002 PHE 0 152 TYR 0.018 0.002 TYR e 61 ARG 0.015 0.001 ARG s 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 753 time to evaluate : 6.773 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: 0 145 MET cc_start: 0.7416 (tmm) cc_final: 0.6731 (tmm) REVERT: 0 151 LEU cc_start: 0.9094 (mp) cc_final: 0.8687 (tt) REVERT: 0 342 HIS cc_start: 0.8510 (m-70) cc_final: 0.8166 (m90) REVERT: 0 346 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7670 (p90) REVERT: 1 4 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7656 (pmtt) REVERT: 1 17 LYS cc_start: 0.9305 (tppp) cc_final: 0.8844 (tttt) REVERT: 1 45 GLU cc_start: 0.8433 (tt0) cc_final: 0.8182 (tt0) REVERT: 2 30 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8863 (mmpt) REVERT: 2 55 ASP cc_start: 0.8391 (m-30) cc_final: 0.8151 (m-30) REVERT: 3 12 VAL cc_start: 0.7274 (p) cc_final: 0.6641 (m) REVERT: 3 41 ASN cc_start: 0.7923 (t0) cc_final: 0.7707 (t0) REVERT: 8 20 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8885 (mtmt) REVERT: F 78 PHE cc_start: 0.7283 (m-80) cc_final: 0.7025 (m-80) REVERT: F 83 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8001 (mtmt) REVERT: F 110 ASP cc_start: 0.4893 (OUTLIER) cc_final: 0.4397 (t0) REVERT: J 26 MET cc_start: 0.8742 (tpp) cc_final: 0.8471 (mmm) REVERT: J 78 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.9065 (mtp85) REVERT: J 130 LEU cc_start: 0.8247 (tp) cc_final: 0.8045 (pp) REVERT: J 158 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8575 (t) REVERT: K 35 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6557 (ttp80) REVERT: M 139 GLU cc_start: 0.8399 (pm20) cc_final: 0.8073 (pm20) REVERT: N 31 LYS cc_start: 0.8528 (mtmp) cc_final: 0.8270 (mttp) REVERT: U 59 GLU cc_start: 0.7972 (mp0) cc_final: 0.7426 (mp0) REVERT: W 22 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7918 (tm-30) REVERT: X 45 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8173 (mp10) REVERT: Y 84 ASP cc_start: 0.8462 (p0) cc_final: 0.8070 (p0) REVERT: Y 85 LYS cc_start: 0.8962 (mttt) cc_final: 0.8738 (mttm) REVERT: Z 11 LYS cc_start: 0.9227 (pttm) cc_final: 0.8932 (ptpt) REVERT: c 28 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9127 (ttmm) REVERT: c 57 MET cc_start: 0.8979 (mmt) cc_final: 0.8240 (mmm) REVERT: c 108 GLN cc_start: 0.9055 (mm110) cc_final: 0.8800 (mm110) REVERT: c 217 MET cc_start: 0.9223 (mmp) cc_final: 0.8795 (mmp) REVERT: d 138 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8230 (tp40) REVERT: f 43 ASN cc_start: 0.7910 (p0) cc_final: 0.7348 (p0) REVERT: g 10 MET cc_start: 0.8746 (ttp) cc_final: 0.8432 (ttm) REVERT: g 34 LYS cc_start: 0.9178 (mttm) cc_final: 0.8963 (mtmm) REVERT: g 46 TRP cc_start: 0.8089 (t60) cc_final: 0.7582 (t60) REVERT: g 72 SER cc_start: 0.8292 (p) cc_final: 0.7877 (t) REVERT: h 74 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: h 122 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8615 (mmtm) REVERT: h 140 ASP cc_start: 0.8621 (m-30) cc_final: 0.8354 (m-30) REVERT: j 112 GLU cc_start: 0.8188 (tt0) cc_final: 0.7894 (tt0) REVERT: k 20 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8624 (mm110) REVERT: k 23 ASP cc_start: 0.8857 (m-30) cc_final: 0.8606 (p0) REVERT: k 67 MET cc_start: 0.8725 (ttm) cc_final: 0.7752 (ttp) REVERT: l 106 GLU cc_start: 0.8201 (tp30) cc_final: 0.7981 (tm-30) REVERT: l 125 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.8923 (ptmm) REVERT: l 126 ARG cc_start: 0.7923 (mmt180) cc_final: 0.7102 (mmt180) REVERT: n 12 ASP cc_start: 0.8576 (p0) cc_final: 0.7770 (t0) REVERT: n 31 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8656 (mmmm) REVERT: n 36 ASN cc_start: 0.9093 (m-40) cc_final: 0.8736 (m110) REVERT: o 46 GLU cc_start: 0.8593 (tt0) cc_final: 0.8341 (tt0) REVERT: o 57 LYS cc_start: 0.8969 (ptmm) cc_final: 0.8754 (pttm) REVERT: q 32 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8024 (ttt90) REVERT: s 29 ASP cc_start: 0.9021 (t0) cc_final: 0.8815 (t0) REVERT: t 12 ASP cc_start: 0.8230 (m-30) cc_final: 0.7997 (m-30) REVERT: t 22 GLN cc_start: 0.8165 (mt0) cc_final: 0.7219 (tp40) REVERT: t 29 LYS cc_start: 0.8667 (mmpt) cc_final: 0.8263 (mmpt) REVERT: t 47 PHE cc_start: 0.8278 (m-80) cc_final: 0.7919 (m-80) REVERT: t 53 ASP cc_start: 0.8651 (p0) cc_final: 0.8070 (p0) REVERT: t 56 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8174 (pptt) REVERT: t 61 TYR cc_start: 0.8493 (t80) cc_final: 0.8228 (t80) REVERT: u 32 ILE cc_start: 0.9284 (mt) cc_final: 0.8901 (mp) REVERT: u 52 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8442 (mm-30) REVERT: u 68 LYS cc_start: 0.9127 (ttmt) cc_final: 0.8868 (ttmm) outliers start: 201 outliers final: 67 residues processed: 859 average time/residue: 2.0709 time to fit residues: 2603.1521 Evaluate side-chains 767 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 684 time to evaluate : 6.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 0 residue 530 GLU Chi-restraints excluded: chain 1 residue 4 LYS Chi-restraints excluded: chain 2 residue 30 LYS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 17 SER Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 3 residue 71 VAL Chi-restraints excluded: chain 4 residue 21 LYS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain F residue 83 LYS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 35 ARG Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain W residue 21 ASP Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain X residue 45 GLN Chi-restraints excluded: chain X residue 74 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain c residue 28 LYS Chi-restraints excluded: chain c residue 202 SER Chi-restraints excluded: chain c residue 214 THR Chi-restraints excluded: chain d residue 81 SER Chi-restraints excluded: chain e residue 31 TYR Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain g residue 22 LYS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 11 ASP Chi-restraints excluded: chain h residue 50 ILE Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 122 LYS Chi-restraints excluded: chain h residue 131 THR Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain i residue 101 LEU Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 57 THR Chi-restraints excluded: chain l residue 15 ASN Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain l residue 125 LYS Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 31 LYS Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain o residue 50 LYS Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 32 ARG Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 43 SER Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 79 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 533 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 799 optimal weight: 9.9990 chunk 654 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 962 optimal weight: 20.0000 chunk 1039 optimal weight: 30.0000 chunk 857 optimal weight: 9.9990 chunk 954 optimal weight: 5.9990 chunk 328 optimal weight: 10.0000 chunk 772 optimal weight: 10.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 20 GLN 3 8 ASN F 58 GLN F 105 GLN F 226 GLN I 141 GLN I 145 ASN K 97 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 8 GLN e 97 ASN g 36 ASN h 153 HIS ** l 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 GLN n 27 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 161541 Z= 0.291 Angle : 0.588 23.728 241382 Z= 0.303 Chirality : 0.038 1.902 30827 Planarity : 0.005 0.129 13100 Dihedral : 23.237 179.330 79737 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.40 % Allowed : 15.28 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.11), residues: 6001 helix: 1.89 (0.11), residues: 2090 sheet: -0.06 (0.15), residues: 1156 loop : -0.15 (0.12), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 104 HIS 0.006 0.001 HIS e 36 PHE 0.021 0.002 PHE 3 23 TYR 0.016 0.001 TYR g 7 ARG 0.008 0.001 ARG g 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 763 time to evaluate : 6.787 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: 0 151 LEU cc_start: 0.9048 (mp) cc_final: 0.8680 (tt) REVERT: 0 342 HIS cc_start: 0.8489 (m-70) cc_final: 0.8166 (m90) REVERT: 1 17 LYS cc_start: 0.9292 (tppp) cc_final: 0.8940 (tttt) REVERT: 2 9 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8255 (mtpp) REVERT: 2 30 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8852 (mmpt) REVERT: 3 41 ASN cc_start: 0.7963 (t0) cc_final: 0.7698 (t0) REVERT: 8 20 LYS cc_start: 0.9076 (mmmm) cc_final: 0.8864 (mtmt) REVERT: F 83 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8157 (mtmt) REVERT: F 94 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.6355 (m-80) REVERT: F 110 ASP cc_start: 0.5138 (OUTLIER) cc_final: 0.4589 (t0) REVERT: F 164 ARG cc_start: 0.8882 (ttt90) cc_final: 0.8597 (ttt90) REVERT: H 191 ASN cc_start: 0.9320 (OUTLIER) cc_final: 0.8910 (p0) REVERT: J 26 MET cc_start: 0.8748 (tpp) cc_final: 0.8478 (mmm) REVERT: J 78 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.9054 (mtp85) REVERT: J 125 ARG cc_start: 0.8502 (mmt-90) cc_final: 0.8152 (mpp80) REVERT: J 150 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6336 (mtp180) REVERT: J 158 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8446 (t) REVERT: K 97 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: M 139 GLU cc_start: 0.8345 (pm20) cc_final: 0.8034 (pm20) REVERT: N 31 LYS cc_start: 0.8464 (mtmp) cc_final: 0.8261 (mttp) REVERT: U 59 GLU cc_start: 0.7999 (mp0) cc_final: 0.7507 (mp0) REVERT: W 22 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7893 (tm-30) REVERT: X 45 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: Y 84 ASP cc_start: 0.8418 (p0) cc_final: 0.8029 (p0) REVERT: Y 85 LYS cc_start: 0.8885 (mttt) cc_final: 0.8672 (mttm) REVERT: Z 11 LYS cc_start: 0.9192 (pttm) cc_final: 0.8916 (ptpt) REVERT: c 57 MET cc_start: 0.9012 (mmt) cc_final: 0.8400 (mmm) REVERT: c 108 GLN cc_start: 0.9016 (mm110) cc_final: 0.8715 (mm110) REVERT: c 217 MET cc_start: 0.9214 (mmp) cc_final: 0.8785 (mmp) REVERT: d 138 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8297 (tp40) REVERT: g 10 MET cc_start: 0.8748 (ttp) cc_final: 0.8421 (ttp) REVERT: g 33 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8944 (mt) REVERT: g 34 LYS cc_start: 0.9168 (mttm) cc_final: 0.8923 (mtmm) REVERT: g 46 TRP cc_start: 0.8088 (t60) cc_final: 0.7697 (t60) REVERT: g 72 SER cc_start: 0.8284 (p) cc_final: 0.7835 (t) REVERT: h 24 THR cc_start: 0.8961 (m) cc_final: 0.8751 (p) REVERT: h 74 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: h 122 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8652 (mmmm) REVERT: h 140 ASP cc_start: 0.8612 (m-30) cc_final: 0.8303 (m-30) REVERT: j 104 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8812 (mm) REVERT: j 112 GLU cc_start: 0.8154 (tt0) cc_final: 0.7837 (tt0) REVERT: k 20 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8648 (mm110) REVERT: l 106 GLU cc_start: 0.8245 (tp30) cc_final: 0.8003 (tm-30) REVERT: l 126 ARG cc_start: 0.7925 (mmt180) cc_final: 0.7129 (mmt180) REVERT: n 12 ASP cc_start: 0.8625 (p0) cc_final: 0.7795 (t0) REVERT: n 36 ASN cc_start: 0.9021 (m-40) cc_final: 0.8698 (m110) REVERT: o 35 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8314 (mtt90) REVERT: o 46 GLU cc_start: 0.8578 (tt0) cc_final: 0.8327 (tt0) REVERT: o 57 LYS cc_start: 0.8937 (ptmm) cc_final: 0.8689 (pttm) REVERT: p 5 GLN cc_start: 0.8484 (tt0) cc_final: 0.8277 (mm-40) REVERT: p 7 ARG cc_start: 0.6466 (ptt90) cc_final: 0.6123 (ptt90) REVERT: p 35 ASP cc_start: 0.8643 (m-30) cc_final: 0.8328 (m-30) REVERT: q 32 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7848 (ttt90) REVERT: s 29 ASP cc_start: 0.9019 (t0) cc_final: 0.8704 (t0) REVERT: t 6 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8770 (ptpt) REVERT: t 12 ASP cc_start: 0.8165 (m-30) cc_final: 0.7881 (m-30) REVERT: t 22 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7368 (tp40) REVERT: t 29 LYS cc_start: 0.8740 (mmpt) cc_final: 0.8364 (mmpt) REVERT: t 32 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8649 (ptmm) REVERT: t 47 PHE cc_start: 0.8271 (m-80) cc_final: 0.7937 (m-80) REVERT: t 53 ASP cc_start: 0.8711 (p0) cc_final: 0.8134 (p0) REVERT: t 55 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8237 (ptt180) REVERT: t 56 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8302 (pptt) REVERT: t 61 TYR cc_start: 0.8541 (t80) cc_final: 0.8165 (t80) REVERT: u 32 ILE cc_start: 0.9228 (mt) cc_final: 0.8857 (mp) REVERT: u 52 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8429 (mm-30) REVERT: u 59 MET cc_start: 0.8881 (mtp) cc_final: 0.8515 (mtp) REVERT: u 68 LYS cc_start: 0.9094 (ttmt) cc_final: 0.8850 (ttmm) outliers start: 175 outliers final: 74 residues processed: 859 average time/residue: 2.0852 time to fit residues: 2634.2199 Evaluate side-chains 784 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 689 time to evaluate : 6.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 1 residue 11 THR Chi-restraints excluded: chain 2 residue 30 LYS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 17 SER Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 71 VAL Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 48 THR Chi-restraints excluded: chain F residue 83 LYS Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain X residue 45 GLN Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 74 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain c residue 202 SER Chi-restraints excluded: chain c residue 214 THR Chi-restraints excluded: chain d residue 81 SER Chi-restraints excluded: chain e residue 31 TYR Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain g residue 22 LYS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 11 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 50 ILE Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 122 LYS Chi-restraints excluded: chain h residue 131 THR Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 104 LEU Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain m residue 20 ASP Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain o residue 35 ARG Chi-restraints excluded: chain o residue 50 LYS Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 32 ARG Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 43 SER Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 58 ASP Chi-restraints excluded: chain u residue 79 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 950 optimal weight: 50.0000 chunk 723 optimal weight: 30.0000 chunk 499 optimal weight: 50.0000 chunk 106 optimal weight: 20.0000 chunk 459 optimal weight: 5.9990 chunk 646 optimal weight: 1.9990 chunk 965 optimal weight: 30.0000 chunk 1022 optimal weight: 20.0000 chunk 504 optimal weight: 20.0000 chunk 915 optimal weight: 5.9990 chunk 275 optimal weight: 20.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 487 ASN 1 20 GLN 3 8 ASN F 58 GLN F 226 GLN ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 8 GLN d 61 ASN e 97 ASN e 113 GLN g 36 ASN h 153 HIS ** l 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 GLN n 50 ASN p 5 GLN s 21 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 161541 Z= 0.362 Angle : 0.616 23.559 241382 Z= 0.316 Chirality : 0.040 1.919 30827 Planarity : 0.005 0.129 13100 Dihedral : 23.198 179.173 79735 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 3.60 % Allowed : 16.85 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.11), residues: 6001 helix: 1.77 (0.11), residues: 2084 sheet: -0.07 (0.15), residues: 1142 loop : -0.20 (0.12), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 104 HIS 0.009 0.001 HIS d 33 PHE 0.027 0.002 PHE 3 23 TYR 0.020 0.002 TYR F 21 ARG 0.009 0.001 ARG i 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 722 time to evaluate : 6.813 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: 0 26 PHE cc_start: 0.8050 (m-80) cc_final: 0.7687 (m-80) REVERT: 0 151 LEU cc_start: 0.9097 (mp) cc_final: 0.8763 (tt) REVERT: 0 342 HIS cc_start: 0.8541 (m-70) cc_final: 0.8183 (m90) REVERT: 1 17 LYS cc_start: 0.9318 (tppp) cc_final: 0.9037 (tttt) REVERT: 1 45 GLU cc_start: 0.8433 (tt0) cc_final: 0.8219 (tt0) REVERT: 2 30 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8849 (mmpt) REVERT: 3 41 ASN cc_start: 0.7913 (t0) cc_final: 0.7580 (t0) REVERT: 8 20 LYS cc_start: 0.9079 (mmmm) cc_final: 0.8877 (mtmt) REVERT: F 94 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.6298 (m-80) REVERT: F 110 ASP cc_start: 0.5468 (OUTLIER) cc_final: 0.4828 (t0) REVERT: H 191 ASN cc_start: 0.9326 (OUTLIER) cc_final: 0.8926 (p0) REVERT: J 78 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.9056 (mtp85) REVERT: J 125 ARG cc_start: 0.8525 (mmt-90) cc_final: 0.8119 (mpp80) REVERT: J 158 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8454 (t) REVERT: K 40 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8511 (m-30) REVERT: K 97 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8310 (pm20) REVERT: M 139 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: R 60 ASP cc_start: 0.7957 (p0) cc_final: 0.7573 (p0) REVERT: S 38 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: U 31 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7907 (mm-30) REVERT: U 59 GLU cc_start: 0.8035 (mp0) cc_final: 0.7520 (mp0) REVERT: W 22 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7842 (tm-30) REVERT: W 88 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: X 45 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8209 (mp10) REVERT: Y 84 ASP cc_start: 0.8427 (p0) cc_final: 0.8055 (p0) REVERT: Y 85 LYS cc_start: 0.8889 (mttt) cc_final: 0.8685 (mttm) REVERT: Z 11 LYS cc_start: 0.9224 (pttm) cc_final: 0.8933 (ptpt) REVERT: c 57 MET cc_start: 0.9013 (mmt) cc_final: 0.8457 (mmm) REVERT: c 217 MET cc_start: 0.9217 (mmp) cc_final: 0.8768 (mmp) REVERT: d 138 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8328 (tp40) REVERT: g 31 THR cc_start: 0.9141 (p) cc_final: 0.8853 (p) REVERT: g 33 LEU cc_start: 0.9222 (mp) cc_final: 0.8921 (mt) REVERT: g 34 LYS cc_start: 0.9185 (mttm) cc_final: 0.8949 (mtmm) REVERT: g 48 LYS cc_start: 0.9013 (tppp) cc_final: 0.8810 (tppp) REVERT: g 72 SER cc_start: 0.8345 (p) cc_final: 0.7924 (t) REVERT: g 97 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8491 (ttmm) REVERT: h 24 THR cc_start: 0.8971 (m) cc_final: 0.8756 (p) REVERT: h 74 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: h 122 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8660 (mmtm) REVERT: h 140 ASP cc_start: 0.8631 (m-30) cc_final: 0.8310 (m-30) REVERT: j 112 GLU cc_start: 0.8165 (tt0) cc_final: 0.7834 (tt0) REVERT: l 125 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.8966 (ptmm) REVERT: l 126 ARG cc_start: 0.7972 (mmt180) cc_final: 0.7189 (mmt180) REVERT: n 32 LYS cc_start: 0.9075 (mtmt) cc_final: 0.8509 (mmtt) REVERT: n 36 ASN cc_start: 0.9019 (m-40) cc_final: 0.8656 (m110) REVERT: o 35 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8313 (mtt90) REVERT: o 46 GLU cc_start: 0.8547 (tt0) cc_final: 0.8319 (tt0) REVERT: o 57 LYS cc_start: 0.8919 (ptmm) cc_final: 0.8670 (pttm) REVERT: p 19 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8399 (tp30) REVERT: q 32 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7862 (ttt90) REVERT: s 29 ASP cc_start: 0.9001 (t0) cc_final: 0.8712 (t0) REVERT: t 12 ASP cc_start: 0.8208 (m-30) cc_final: 0.7886 (m-30) REVERT: t 22 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7351 (tp40) REVERT: t 29 LYS cc_start: 0.8748 (mmpt) cc_final: 0.8324 (mmpt) REVERT: t 32 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8744 (ptmm) REVERT: t 47 PHE cc_start: 0.8266 (m-80) cc_final: 0.8052 (m-80) REVERT: t 53 ASP cc_start: 0.8687 (p0) cc_final: 0.8135 (p0) REVERT: t 55 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8100 (ptt180) REVERT: t 56 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8251 (pptt) REVERT: t 61 TYR cc_start: 0.8431 (t80) cc_final: 0.8098 (t80) REVERT: t 66 MET cc_start: 0.8444 (mtt) cc_final: 0.8234 (ptp) REVERT: u 32 ILE cc_start: 0.9152 (mt) cc_final: 0.8489 (mp) REVERT: u 34 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8995 (ttmt) REVERT: u 36 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: u 52 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8420 (mm-30) REVERT: u 59 MET cc_start: 0.8893 (mtp) cc_final: 0.8556 (mtp) REVERT: u 68 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8860 (ttmm) outliers start: 185 outliers final: 89 residues processed: 821 average time/residue: 2.0583 time to fit residues: 2490.0896 Evaluate side-chains 798 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 687 time to evaluate : 6.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 0 residue 362 VAL Chi-restraints excluded: chain 0 residue 513 MET Chi-restraints excluded: chain 1 residue 11 THR Chi-restraints excluded: chain 2 residue 30 LYS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 71 VAL Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 139 ASN Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 139 GLU Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain S residue 38 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain W residue 21 ASP Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 45 GLN Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 74 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain c residue 202 SER Chi-restraints excluded: chain c residue 214 THR Chi-restraints excluded: chain d residue 81 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 31 TYR Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain g residue 22 LYS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain h residue 11 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 50 ILE Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 122 LYS Chi-restraints excluded: chain h residue 131 THR Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 125 LYS Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain o residue 35 ARG Chi-restraints excluded: chain o residue 50 LYS Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 32 ARG Chi-restraints excluded: chain q residue 35 GLU Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain s residue 51 THR Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 43 SER Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 58 ASP Chi-restraints excluded: chain u residue 79 SER Chi-restraints excluded: chain u residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 851 optimal weight: 20.0000 chunk 580 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 761 optimal weight: 20.0000 chunk 421 optimal weight: 50.0000 chunk 872 optimal weight: 20.0000 chunk 706 optimal weight: 20.0000 chunk 1 optimal weight: 0.5980 chunk 522 optimal weight: 30.0000 chunk 917 optimal weight: 40.0000 chunk 258 optimal weight: 10.0000 overall best weight: 10.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 8 ASN F 49 ASN F 58 GLN F 226 GLN J 172 GLN ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 8 GLN d 122 GLN ** j 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN ** l 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 GLN n 50 ASN s 21 HIS u 3 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 161541 Z= 0.337 Angle : 0.605 23.547 241382 Z= 0.311 Chirality : 0.039 1.920 30827 Planarity : 0.005 0.127 13100 Dihedral : 23.204 178.980 79731 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.72 % Favored : 97.27 % Rotamer: Outliers : 3.75 % Allowed : 17.75 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.11), residues: 6001 helix: 1.72 (0.11), residues: 2092 sheet: -0.06 (0.15), residues: 1148 loop : -0.22 (0.12), residues: 2761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 104 HIS 0.005 0.001 HIS e 36 PHE 0.030 0.002 PHE 3 23 TYR 0.017 0.002 TYR p 15 ARG 0.010 0.001 ARG g 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 722 time to evaluate : 6.633 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: 0 26 PHE cc_start: 0.8031 (m-80) cc_final: 0.7689 (m-80) REVERT: 0 93 MET cc_start: 0.8903 (mtm) cc_final: 0.8531 (ttp) REVERT: 0 151 LEU cc_start: 0.9113 (mp) cc_final: 0.8757 (tt) REVERT: 0 342 HIS cc_start: 0.8536 (m-70) cc_final: 0.8166 (m90) REVERT: 1 5 GLU cc_start: 0.8394 (mp0) cc_final: 0.8084 (mp0) REVERT: 1 45 GLU cc_start: 0.8417 (tt0) cc_final: 0.8179 (tt0) REVERT: 2 30 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8849 (mmpt) REVERT: 3 41 ASN cc_start: 0.7879 (t0) cc_final: 0.7525 (t0) REVERT: 8 20 LYS cc_start: 0.9076 (mmmm) cc_final: 0.8873 (mtmt) REVERT: 8 24 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8931 (mtp) REVERT: F 60 ARG cc_start: 0.6420 (ttp-170) cc_final: 0.6197 (ttm110) REVERT: F 78 PHE cc_start: 0.7599 (m-10) cc_final: 0.7367 (m-80) REVERT: F 93 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6853 (t70) REVERT: F 94 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.5495 (m-80) REVERT: F 104 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7072 (mt) REVERT: F 110 ASP cc_start: 0.5516 (OUTLIER) cc_final: 0.4881 (t0) REVERT: G 66 ASP cc_start: 0.8680 (t0) cc_final: 0.8420 (t0) REVERT: J 26 MET cc_start: 0.8726 (tpp) cc_final: 0.8189 (mtp) REVERT: J 78 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.9064 (mtp85) REVERT: J 125 ARG cc_start: 0.8480 (mmt-90) cc_final: 0.8064 (mpp80) REVERT: J 158 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8443 (t) REVERT: J 172 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: K 40 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8550 (m-30) REVERT: M 139 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: U 31 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7928 (mm-30) REVERT: U 59 GLU cc_start: 0.8038 (mp0) cc_final: 0.7504 (mp0) REVERT: W 22 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7836 (tm-30) REVERT: W 88 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7862 (mm-30) REVERT: X 45 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: Y 84 ASP cc_start: 0.8406 (p0) cc_final: 0.8035 (p0) REVERT: Y 85 LYS cc_start: 0.8883 (mttt) cc_final: 0.8682 (mttm) REVERT: Z 11 LYS cc_start: 0.9219 (pttm) cc_final: 0.8936 (ptpt) REVERT: c 57 MET cc_start: 0.9006 (mmt) cc_final: 0.8500 (mmm) REVERT: c 217 MET cc_start: 0.9218 (mmp) cc_final: 0.8791 (mmp) REVERT: d 138 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8261 (tp40) REVERT: g 33 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8853 (mt) REVERT: g 34 LYS cc_start: 0.9177 (mttm) cc_final: 0.8943 (mtmm) REVERT: g 72 SER cc_start: 0.8306 (p) cc_final: 0.7866 (t) REVERT: g 97 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8407 (ttmm) REVERT: h 74 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: h 122 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8690 (mmmm) REVERT: h 140 ASP cc_start: 0.8640 (m-30) cc_final: 0.8317 (m-30) REVERT: j 100 ARG cc_start: 0.8646 (tmm160) cc_final: 0.8412 (tmm160) REVERT: j 112 GLU cc_start: 0.8151 (tt0) cc_final: 0.7815 (tt0) REVERT: l 125 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.8969 (ptmm) REVERT: l 126 ARG cc_start: 0.7972 (mmt180) cc_final: 0.7165 (mmt180) REVERT: n 32 LYS cc_start: 0.9083 (mtmt) cc_final: 0.8495 (mmtt) REVERT: n 36 ASN cc_start: 0.9030 (m-40) cc_final: 0.8691 (m110) REVERT: n 41 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8034 (mm-30) REVERT: n 49 THR cc_start: 0.8865 (t) cc_final: 0.8643 (p) REVERT: n 61 ASP cc_start: 0.8606 (p0) cc_final: 0.8232 (p0) REVERT: o 46 GLU cc_start: 0.8599 (tt0) cc_final: 0.8367 (tt0) REVERT: o 57 LYS cc_start: 0.8903 (ptmm) cc_final: 0.8655 (pttm) REVERT: p 19 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8186 (tm-30) REVERT: p 84 ARG cc_start: 0.9087 (mtp180) cc_final: 0.8873 (ttt180) REVERT: q 32 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7849 (ttt90) REVERT: s 21 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.8025 (t-170) REVERT: s 29 ASP cc_start: 0.8987 (t0) cc_final: 0.8696 (t0) REVERT: t 6 LYS cc_start: 0.9063 (ptpt) cc_final: 0.8801 (ptpt) REVERT: t 12 ASP cc_start: 0.8188 (m-30) cc_final: 0.7846 (m-30) REVERT: t 22 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7390 (tp40) REVERT: t 29 LYS cc_start: 0.8744 (mmpt) cc_final: 0.8346 (mmpt) REVERT: t 32 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8729 (ptmm) REVERT: t 53 ASP cc_start: 0.8672 (p0) cc_final: 0.8134 (p0) REVERT: t 55 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8124 (ptt180) REVERT: t 56 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8298 (pptt) REVERT: u 34 LYS cc_start: 0.9238 (ttmm) cc_final: 0.8982 (ttmt) REVERT: u 59 MET cc_start: 0.8901 (mtp) cc_final: 0.8583 (mtp) REVERT: u 68 LYS cc_start: 0.9114 (ttmt) cc_final: 0.8854 (ttmm) outliers start: 193 outliers final: 98 residues processed: 823 average time/residue: 2.0639 time to fit residues: 2502.2892 Evaluate side-chains 806 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 685 time to evaluate : 6.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 0 residue 362 VAL Chi-restraints excluded: chain 0 residue 530 GLU Chi-restraints excluded: chain 1 residue 11 THR Chi-restraints excluded: chain 2 residue 30 LYS Chi-restraints excluded: chain 3 residue 8 ASN Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 71 VAL Chi-restraints excluded: chain 4 residue 36 MET Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 8 residue 24 MET Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 172 GLN Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 139 GLU Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain W residue 21 ASP Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 45 GLN Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain c residue 202 SER Chi-restraints excluded: chain c residue 214 THR Chi-restraints excluded: chain d residue 81 SER Chi-restraints excluded: chain e residue 31 TYR Chi-restraints excluded: chain e residue 171 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 22 LYS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 11 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 50 ILE Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 122 LYS Chi-restraints excluded: chain h residue 131 THR Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain l residue 125 LYS Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 12 ASP Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 34 LEU Chi-restraints excluded: chain n residue 42 ASP Chi-restraints excluded: chain o residue 35 ARG Chi-restraints excluded: chain o residue 50 LYS Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 32 ARG Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain s residue 21 HIS Chi-restraints excluded: chain s residue 51 THR Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 43 SER Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 58 ASP Chi-restraints excluded: chain u residue 79 SER Chi-restraints excluded: chain u residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 344 optimal weight: 10.0000 chunk 920 optimal weight: 8.9990 chunk 202 optimal weight: 50.0000 chunk 600 optimal weight: 7.9990 chunk 252 optimal weight: 20.0000 chunk 1023 optimal weight: 9.9990 chunk 849 optimal weight: 20.0000 chunk 473 optimal weight: 0.0060 chunk 85 optimal weight: 0.0470 chunk 338 optimal weight: 10.0000 chunk 537 optimal weight: 10.0000 overall best weight: 5.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 49 ASN F 58 GLN F 226 GLN J 172 GLN K 71 ASN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 8 GLN ** j 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 ASN ** s 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 3 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 161541 Z= 0.205 Angle : 0.563 23.559 241382 Z= 0.289 Chirality : 0.036 1.915 30827 Planarity : 0.004 0.124 13100 Dihedral : 23.212 178.449 79731 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.68 % Favored : 97.30 % Rotamer: Outliers : 3.15 % Allowed : 18.97 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.11), residues: 6001 helix: 1.80 (0.11), residues: 2090 sheet: -0.02 (0.15), residues: 1172 loop : -0.15 (0.12), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 0 121 HIS 0.037 0.001 HIS s 21 PHE 0.034 0.001 PHE 3 23 TYR 0.024 0.001 TYR 0 200 ARG 0.013 0.000 ARG k 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 746 time to evaluate : 6.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 26 PHE cc_start: 0.8033 (m-80) cc_final: 0.7686 (m-80) REVERT: 0 93 MET cc_start: 0.8940 (mtm) cc_final: 0.8631 (ttp) REVERT: 0 151 LEU cc_start: 0.9068 (mp) cc_final: 0.8689 (tt) REVERT: 0 200 TYR cc_start: 0.8899 (t80) cc_final: 0.8698 (t80) REVERT: 0 342 HIS cc_start: 0.8476 (m-70) cc_final: 0.8117 (m90) REVERT: 1 4 LYS cc_start: 0.8064 (ptpp) cc_final: 0.7605 (pmtt) REVERT: 1 5 GLU cc_start: 0.8235 (mp0) cc_final: 0.7522 (mp0) REVERT: 1 17 LYS cc_start: 0.9311 (tppp) cc_final: 0.9084 (tptm) REVERT: 1 45 GLU cc_start: 0.8389 (tt0) cc_final: 0.8176 (tt0) REVERT: 2 30 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8818 (mmpt) REVERT: 3 10 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8846 (mm110) REVERT: 3 41 ASN cc_start: 0.7927 (t0) cc_final: 0.7568 (t0) REVERT: 8 20 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8859 (mtmt) REVERT: F 34 ASN cc_start: 0.6625 (OUTLIER) cc_final: 0.6109 (t0) REVERT: F 93 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6776 (t70) REVERT: F 94 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.5328 (m-80) REVERT: F 104 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.6914 (mt) REVERT: F 110 ASP cc_start: 0.5604 (OUTLIER) cc_final: 0.4964 (t0) REVERT: F 120 MET cc_start: 0.2886 (ptp) cc_final: 0.2579 (tmm) REVERT: F 137 MET cc_start: 0.7122 (mmm) cc_final: 0.6844 (mmm) REVERT: G 66 ASP cc_start: 0.8671 (t0) cc_final: 0.8389 (t0) REVERT: J 26 MET cc_start: 0.8650 (tpp) cc_final: 0.8198 (mtp) REVERT: J 78 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.9031 (mtp85) REVERT: J 125 ARG cc_start: 0.8465 (mmt-90) cc_final: 0.8061 (mpp80) REVERT: J 158 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8425 (t) REVERT: J 172 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8509 (mt0) REVERT: M 139 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7958 (pm20) REVERT: R 78 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8988 (tt) REVERT: R 81 GLU cc_start: 0.9028 (pt0) cc_final: 0.8814 (pt0) REVERT: U 59 GLU cc_start: 0.7991 (mp0) cc_final: 0.7493 (mp0) REVERT: W 22 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7772 (tm-30) REVERT: X 45 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8178 (mp10) REVERT: Y 84 ASP cc_start: 0.8358 (p0) cc_final: 0.7968 (p0) REVERT: Z 11 LYS cc_start: 0.9190 (pttm) cc_final: 0.8934 (ptpt) REVERT: c 57 MET cc_start: 0.8988 (mmt) cc_final: 0.8472 (mmt) REVERT: c 217 MET cc_start: 0.9207 (mmp) cc_final: 0.8798 (mmp) REVERT: d 138 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8294 (tp40) REVERT: g 6 LYS cc_start: 0.8490 (mtpm) cc_final: 0.8248 (mtmt) REVERT: g 10 MET cc_start: 0.8752 (ttm) cc_final: 0.8463 (mtt) REVERT: g 28 ARG cc_start: 0.9098 (ptm-80) cc_final: 0.8726 (ptm160) REVERT: g 33 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8858 (mt) REVERT: g 34 LYS cc_start: 0.9155 (mttm) cc_final: 0.8921 (mtmm) REVERT: g 72 SER cc_start: 0.8255 (p) cc_final: 0.7803 (t) REVERT: g 97 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8466 (ttmm) REVERT: h 74 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: h 140 ASP cc_start: 0.8604 (m-30) cc_final: 0.8249 (m-30) REVERT: j 100 ARG cc_start: 0.8615 (tmm160) cc_final: 0.8376 (tmm160) REVERT: j 112 GLU cc_start: 0.8116 (tt0) cc_final: 0.7777 (tt0) REVERT: l 126 ARG cc_start: 0.7930 (mmt180) cc_final: 0.7155 (mmt180) REVERT: n 32 LYS cc_start: 0.9059 (mtmt) cc_final: 0.8439 (mmtt) REVERT: n 36 ASN cc_start: 0.9054 (m-40) cc_final: 0.8723 (m110) REVERT: n 52 GLN cc_start: 0.9203 (mt0) cc_final: 0.8999 (mt0) REVERT: o 35 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8493 (mtt90) REVERT: o 46 GLU cc_start: 0.8561 (tt0) cc_final: 0.8317 (tt0) REVERT: o 57 LYS cc_start: 0.8866 (ptmm) cc_final: 0.8626 (pttm) REVERT: p 19 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8199 (tm-30) REVERT: p 81 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9266 (tt) REVERT: q 32 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7786 (ttt90) REVERT: s 29 ASP cc_start: 0.8982 (t0) cc_final: 0.8715 (t0) REVERT: t 12 ASP cc_start: 0.8178 (m-30) cc_final: 0.7833 (m-30) REVERT: t 22 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7287 (tp40) REVERT: t 29 LYS cc_start: 0.8708 (mmpt) cc_final: 0.8356 (mmpt) REVERT: t 55 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8182 (ptt180) REVERT: t 61 TYR cc_start: 0.8437 (t80) cc_final: 0.8123 (t80) REVERT: u 34 LYS cc_start: 0.9253 (ttmm) cc_final: 0.8937 (ttmt) REVERT: u 52 GLU cc_start: 0.8801 (tp30) cc_final: 0.8279 (mm-30) REVERT: u 59 MET cc_start: 0.8896 (mtp) cc_final: 0.8576 (mtp) REVERT: u 68 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8850 (ttmm) outliers start: 162 outliers final: 81 residues processed: 841 average time/residue: 2.0397 time to fit residues: 2532.4154 Evaluate side-chains 790 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 690 time to evaluate : 6.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 141 LEU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 317 MET Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 0 residue 530 GLU Chi-restraints excluded: chain 1 residue 11 THR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 30 LYS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 71 VAL Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 172 GLN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 139 GLU Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain W residue 21 ASP Chi-restraints excluded: chain X residue 45 GLN Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain c residue 202 SER Chi-restraints excluded: chain c residue 214 THR Chi-restraints excluded: chain d residue 81 SER Chi-restraints excluded: chain e residue 171 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 11 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 131 THR Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 12 ASP Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 34 LEU Chi-restraints excluded: chain n residue 42 ASP Chi-restraints excluded: chain o residue 35 ARG Chi-restraints excluded: chain o residue 50 LYS Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain p residue 81 LEU Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 32 ARG Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain s residue 51 THR Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 43 SER Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 58 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 986 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 583 optimal weight: 10.0000 chunk 747 optimal weight: 30.0000 chunk 579 optimal weight: 20.0000 chunk 861 optimal weight: 20.0000 chunk 571 optimal weight: 20.0000 chunk 1019 optimal weight: 5.9990 chunk 638 optimal weight: 20.0000 chunk 621 optimal weight: 10.0000 chunk 470 optimal weight: 9.9990 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 8 ASN 3 10 GLN F 49 ASN F 58 GLN F 226 GLN c 8 GLN g 36 ASN ** l 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 ASN ** o 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 21 HIS u 3 ASN u 21 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 161541 Z= 0.288 Angle : 0.585 23.476 241382 Z= 0.300 Chirality : 0.038 1.920 30827 Planarity : 0.004 0.125 13100 Dihedral : 23.152 178.085 79729 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.75 % Favored : 97.23 % Rotamer: Outliers : 3.17 % Allowed : 19.51 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.11), residues: 6001 helix: 1.77 (0.11), residues: 2089 sheet: -0.01 (0.15), residues: 1170 loop : -0.16 (0.12), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 104 HIS 0.004 0.001 HIS o 16 PHE 0.038 0.002 PHE 3 23 TYR 0.032 0.002 TYR 0 99 ARG 0.012 0.000 ARG g 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 702 time to evaluate : 6.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 26 PHE cc_start: 0.8040 (m-80) cc_final: 0.7704 (m-80) REVERT: 0 78 MET cc_start: 0.8637 (tmt) cc_final: 0.8360 (tmt) REVERT: 0 93 MET cc_start: 0.8951 (mtm) cc_final: 0.8635 (ttp) REVERT: 0 151 LEU cc_start: 0.9081 (mp) cc_final: 0.8703 (tt) REVERT: 0 342 HIS cc_start: 0.8456 (m-70) cc_final: 0.8078 (m90) REVERT: 1 4 LYS cc_start: 0.8128 (ptpp) cc_final: 0.7627 (pmtt) REVERT: 1 5 GLU cc_start: 0.8242 (mp0) cc_final: 0.7436 (mp0) REVERT: 1 45 GLU cc_start: 0.8398 (tt0) cc_final: 0.8160 (tt0) REVERT: 2 30 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8816 (mmpt) REVERT: 3 39 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.6709 (p0) REVERT: 3 41 ASN cc_start: 0.7940 (t0) cc_final: 0.7693 (t0) REVERT: F 34 ASN cc_start: 0.6582 (OUTLIER) cc_final: 0.6079 (t0) REVERT: F 93 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6861 (t70) REVERT: F 94 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.5284 (m-80) REVERT: F 110 ASP cc_start: 0.5644 (OUTLIER) cc_final: 0.4926 (t0) REVERT: F 120 MET cc_start: 0.2961 (ptp) cc_final: 0.2537 (tmm) REVERT: F 137 MET cc_start: 0.7165 (mmm) cc_final: 0.6845 (mmm) REVERT: J 26 MET cc_start: 0.8684 (tpp) cc_final: 0.8235 (mtp) REVERT: J 38 MET cc_start: 0.8234 (mtm) cc_final: 0.7967 (mtp) REVERT: J 78 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.9004 (mtp85) REVERT: J 83 MET cc_start: 0.8452 (mtt) cc_final: 0.8179 (mtt) REVERT: J 125 ARG cc_start: 0.8433 (mmt-90) cc_final: 0.8040 (mpp80) REVERT: J 158 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8462 (t) REVERT: M 139 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7935 (pm20) REVERT: R 81 GLU cc_start: 0.9017 (pt0) cc_final: 0.8785 (pt0) REVERT: U 59 GLU cc_start: 0.8002 (mp0) cc_final: 0.7499 (mp0) REVERT: W 22 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7852 (tm-30) REVERT: W 88 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: X 45 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: Y 84 ASP cc_start: 0.8390 (p0) cc_final: 0.7996 (p0) REVERT: Z 11 LYS cc_start: 0.9220 (pttm) cc_final: 0.8948 (ptpt) REVERT: c 57 MET cc_start: 0.8988 (mmt) cc_final: 0.8342 (mmm) REVERT: c 217 MET cc_start: 0.9213 (mmp) cc_final: 0.8690 (mmp) REVERT: d 138 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8297 (tp40) REVERT: g 6 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8212 (mtmt) REVERT: g 28 ARG cc_start: 0.9067 (ptm-80) cc_final: 0.8772 (ptm160) REVERT: g 33 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8864 (mt) REVERT: g 34 LYS cc_start: 0.9165 (mttm) cc_final: 0.8917 (mtmm) REVERT: g 72 SER cc_start: 0.8289 (p) cc_final: 0.7858 (t) REVERT: g 97 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8500 (ttmm) REVERT: h 74 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: h 140 ASP cc_start: 0.8579 (m-30) cc_final: 0.8249 (m-30) REVERT: l 125 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9010 (ptmm) REVERT: l 126 ARG cc_start: 0.7951 (mmt180) cc_final: 0.7143 (mmt180) REVERT: n 32 LYS cc_start: 0.9058 (mtmt) cc_final: 0.8701 (mtpt) REVERT: n 36 ASN cc_start: 0.9049 (m-40) cc_final: 0.8721 (m110) REVERT: o 46 GLU cc_start: 0.8561 (tt0) cc_final: 0.8329 (tt0) REVERT: o 57 LYS cc_start: 0.8882 (ptmm) cc_final: 0.8631 (pttm) REVERT: p 19 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8187 (tm-30) REVERT: p 81 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9283 (tt) REVERT: q 32 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7812 (ttt90) REVERT: s 21 HIS cc_start: 0.8386 (OUTLIER) cc_final: 0.8087 (t-170) REVERT: s 29 ASP cc_start: 0.8998 (t0) cc_final: 0.8710 (t0) REVERT: t 6 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8780 (pttt) REVERT: t 12 ASP cc_start: 0.8183 (m-30) cc_final: 0.7860 (m-30) REVERT: t 22 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7316 (tp40) REVERT: t 29 LYS cc_start: 0.8710 (mmpt) cc_final: 0.8345 (mmpt) REVERT: t 32 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8715 (ptmm) REVERT: t 53 ASP cc_start: 0.8713 (p0) cc_final: 0.8211 (p0) REVERT: t 55 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8111 (ptt180) REVERT: t 56 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8318 (pptt) REVERT: u 34 LYS cc_start: 0.9247 (ttmm) cc_final: 0.8997 (ttmt) REVERT: u 52 GLU cc_start: 0.8813 (tp30) cc_final: 0.8289 (mm-30) REVERT: u 59 MET cc_start: 0.8908 (mtp) cc_final: 0.8585 (mtp) REVERT: u 68 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8855 (ttmm) REVERT: u 81 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8982 (tt) outliers start: 163 outliers final: 95 residues processed: 797 average time/residue: 2.0567 time to fit residues: 2427.4772 Evaluate side-chains 802 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 683 time to evaluate : 6.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 141 LEU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 281 SER Chi-restraints excluded: chain 0 residue 317 MET Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 1 residue 11 THR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 30 LYS Chi-restraints excluded: chain 3 residue 8 ASN Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 17 SER Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 3 residue 39 ASP Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 71 VAL Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 139 GLU Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain W residue 21 ASP Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 45 GLN Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 74 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain c residue 202 SER Chi-restraints excluded: chain c residue 214 THR Chi-restraints excluded: chain d residue 81 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 171 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 11 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 131 THR Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain l residue 125 LYS Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 12 ASP Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 34 LEU Chi-restraints excluded: chain n residue 42 ASP Chi-restraints excluded: chain o residue 35 ARG Chi-restraints excluded: chain o residue 50 LYS Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain p residue 81 LEU Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 32 ARG Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain r residue 62 VAL Chi-restraints excluded: chain s residue 21 HIS Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 43 SER Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 58 ASP Chi-restraints excluded: chain u residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 630 optimal weight: 0.0970 chunk 407 optimal weight: 30.0000 chunk 609 optimal weight: 20.0000 chunk 307 optimal weight: 50.0000 chunk 200 optimal weight: 40.0000 chunk 197 optimal weight: 20.0000 chunk 648 optimal weight: 10.0000 chunk 694 optimal weight: 30.0000 chunk 504 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 801 optimal weight: 30.0000 overall best weight: 11.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN F 226 GLN ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 8 GLN d 64 ASN ** j 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN ** l 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 ASN ** o 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 21 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 161541 Z= 0.383 Angle : 0.633 23.408 241382 Z= 0.325 Chirality : 0.040 1.922 30827 Planarity : 0.005 0.127 13100 Dihedral : 23.164 178.387 79729 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.10 % Favored : 96.88 % Rotamer: Outliers : 3.36 % Allowed : 19.65 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.11), residues: 6001 helix: 1.64 (0.11), residues: 2089 sheet: -0.09 (0.15), residues: 1178 loop : -0.22 (0.12), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 0 121 HIS 0.039 0.001 HIS s 21 PHE 0.034 0.002 PHE 3 23 TYR 0.028 0.002 TYR 0 200 ARG 0.013 0.001 ARG g 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 698 time to evaluate : 6.749 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: 0 26 PHE cc_start: 0.8034 (m-80) cc_final: 0.7703 (m-80) REVERT: 0 78 MET cc_start: 0.8735 (tmt) cc_final: 0.8532 (tmt) REVERT: 0 93 MET cc_start: 0.8945 (mtm) cc_final: 0.8635 (ttp) REVERT: 0 151 LEU cc_start: 0.9103 (mp) cc_final: 0.8729 (tt) REVERT: 0 342 HIS cc_start: 0.8480 (m-70) cc_final: 0.8093 (m-70) REVERT: 0 532 TYR cc_start: 0.6756 (t80) cc_final: 0.6468 (t80) REVERT: 1 4 LYS cc_start: 0.8142 (ptpp) cc_final: 0.7884 (pmtt) REVERT: 1 17 LYS cc_start: 0.8634 (tptm) cc_final: 0.8351 (tppp) REVERT: 1 45 GLU cc_start: 0.8416 (tt0) cc_final: 0.8160 (tt0) REVERT: 2 30 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8825 (mmpt) REVERT: 3 39 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.6716 (p0) REVERT: 3 41 ASN cc_start: 0.7831 (t0) cc_final: 0.7599 (t0) REVERT: 8 24 MET cc_start: 0.9153 (mtp) cc_final: 0.8862 (mtp) REVERT: F 34 ASN cc_start: 0.6708 (OUTLIER) cc_final: 0.6160 (t0) REVERT: F 93 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6862 (t70) REVERT: F 94 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.5345 (m-80) REVERT: F 109 PHE cc_start: 0.4174 (OUTLIER) cc_final: 0.3949 (m-80) REVERT: F 110 ASP cc_start: 0.5506 (OUTLIER) cc_final: 0.5296 (m-30) REVERT: F 120 MET cc_start: 0.3389 (ptp) cc_final: 0.2975 (tmm) REVERT: F 137 MET cc_start: 0.7380 (mmm) cc_final: 0.7008 (mmm) REVERT: J 26 MET cc_start: 0.8742 (tpp) cc_final: 0.8248 (mtp) REVERT: J 38 MET cc_start: 0.8225 (mtm) cc_final: 0.7990 (mtp) REVERT: J 78 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.9060 (mtp85) REVERT: J 125 ARG cc_start: 0.8497 (mmt-90) cc_final: 0.8077 (mpp80) REVERT: M 139 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: R 81 GLU cc_start: 0.9030 (pt0) cc_final: 0.8782 (pt0) REVERT: U 31 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7867 (mp0) REVERT: U 59 GLU cc_start: 0.8030 (mp0) cc_final: 0.7510 (mp0) REVERT: W 22 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7784 (tm-30) REVERT: W 88 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: X 45 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8176 (mp10) REVERT: Y 84 ASP cc_start: 0.8419 (p0) cc_final: 0.8070 (p0) REVERT: Z 11 LYS cc_start: 0.9229 (pttm) cc_final: 0.8951 (ptpt) REVERT: c 57 MET cc_start: 0.8991 (mmt) cc_final: 0.8470 (mmt) REVERT: c 217 MET cc_start: 0.9223 (mmp) cc_final: 0.8740 (mmp) REVERT: d 138 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8259 (tp40) REVERT: g 6 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8149 (mtmt) REVERT: g 33 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8890 (mt) REVERT: g 34 LYS cc_start: 0.9172 (mttm) cc_final: 0.8923 (mtmm) REVERT: g 72 SER cc_start: 0.8339 (p) cc_final: 0.7910 (t) REVERT: g 97 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8432 (ttmm) REVERT: h 24 THR cc_start: 0.9104 (m) cc_final: 0.8750 (p) REVERT: h 74 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: h 122 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8714 (mmtm) REVERT: h 140 ASP cc_start: 0.8591 (m-30) cc_final: 0.8264 (m-30) REVERT: l 125 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.8969 (ptmm) REVERT: l 126 ARG cc_start: 0.7993 (mmt180) cc_final: 0.7183 (mmt180) REVERT: n 32 LYS cc_start: 0.9067 (mtmt) cc_final: 0.8711 (mtpt) REVERT: n 36 ASN cc_start: 0.9082 (m-40) cc_final: 0.8757 (m110) REVERT: o 46 GLU cc_start: 0.8552 (tt0) cc_final: 0.8314 (tt0) REVERT: o 57 LYS cc_start: 0.8888 (ptmm) cc_final: 0.8639 (pttm) REVERT: p 19 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8224 (tm-30) REVERT: q 32 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7869 (ttt90) REVERT: s 29 ASP cc_start: 0.9023 (t0) cc_final: 0.8783 (t0) REVERT: s 39 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8634 (pm20) REVERT: t 6 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8794 (pttt) REVERT: t 12 ASP cc_start: 0.8215 (m-30) cc_final: 0.7838 (m-30) REVERT: t 22 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7354 (tp40) REVERT: t 29 LYS cc_start: 0.8688 (mmpt) cc_final: 0.8297 (mmpt) REVERT: t 32 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8709 (ptmm) REVERT: t 53 ASP cc_start: 0.8710 (p0) cc_final: 0.8213 (p0) REVERT: t 55 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8004 (ptt180) REVERT: t 56 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8282 (pptt) REVERT: u 59 MET cc_start: 0.8902 (mtp) cc_final: 0.8604 (mtp) REVERT: u 68 LYS cc_start: 0.9132 (ttmt) cc_final: 0.8868 (ttmm) outliers start: 173 outliers final: 96 residues processed: 799 average time/residue: 2.0814 time to fit residues: 2461.2555 Evaluate side-chains 798 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 680 time to evaluate : 6.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 141 LEU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 281 SER Chi-restraints excluded: chain 0 residue 335 VAL Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 1 residue 11 THR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 30 LYS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 3 residue 39 ASP Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 139 GLU Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain W residue 21 ASP Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 45 GLN Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 74 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain c residue 202 SER Chi-restraints excluded: chain c residue 214 THR Chi-restraints excluded: chain d residue 81 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 171 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 11 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 122 LYS Chi-restraints excluded: chain h residue 131 THR Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 35 ASP Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain l residue 125 LYS Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 12 ASP Chi-restraints excluded: chain n residue 34 LEU Chi-restraints excluded: chain o residue 35 ARG Chi-restraints excluded: chain o residue 50 LYS Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 32 ARG Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain r residue 62 VAL Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 43 SER Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 58 ASP Chi-restraints excluded: chain u residue 79 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 927 optimal weight: 20.0000 chunk 976 optimal weight: 7.9990 chunk 891 optimal weight: 20.0000 chunk 950 optimal weight: 30.0000 chunk 571 optimal weight: 20.0000 chunk 413 optimal weight: 6.9990 chunk 746 optimal weight: 30.0000 chunk 291 optimal weight: 10.0000 chunk 858 optimal weight: 10.0000 chunk 898 optimal weight: 7.9990 chunk 946 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 8 ASN F 49 ASN F 58 GLN F 226 GLN ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 8 GLN l 15 ASN ** l 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 ASN s 21 HIS u 3 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 161541 Z= 0.295 Angle : 0.608 23.378 241382 Z= 0.312 Chirality : 0.038 1.920 30827 Planarity : 0.005 0.126 13100 Dihedral : 23.202 178.496 79729 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.05 % Favored : 96.93 % Rotamer: Outliers : 2.86 % Allowed : 20.31 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.11), residues: 6001 helix: 1.65 (0.11), residues: 2091 sheet: -0.12 (0.15), residues: 1176 loop : -0.24 (0.12), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 104 HIS 0.005 0.001 HIS o 16 PHE 0.033 0.002 PHE 3 23 TYR 0.035 0.002 TYR 0 99 ARG 0.014 0.000 ARG g 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 701 time to evaluate : 6.840 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: 0 26 PHE cc_start: 0.8033 (m-80) cc_final: 0.7701 (m-80) REVERT: 0 78 MET cc_start: 0.8693 (tmt) cc_final: 0.8487 (tmt) REVERT: 0 93 MET cc_start: 0.8943 (mtm) cc_final: 0.8648 (ttp) REVERT: 0 151 LEU cc_start: 0.9085 (mp) cc_final: 0.8708 (tt) REVERT: 0 342 HIS cc_start: 0.8471 (m-70) cc_final: 0.8145 (m90) REVERT: 0 532 TYR cc_start: 0.6748 (t80) cc_final: 0.6461 (t80) REVERT: 1 4 LYS cc_start: 0.8152 (ptpp) cc_final: 0.7905 (pmtt) REVERT: 1 17 LYS cc_start: 0.8631 (tptm) cc_final: 0.8345 (tppp) REVERT: 1 45 GLU cc_start: 0.8409 (tt0) cc_final: 0.8166 (tt0) REVERT: 2 30 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8825 (mmpt) REVERT: 2 55 ASP cc_start: 0.8253 (m-30) cc_final: 0.7884 (m-30) REVERT: 3 39 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.6691 (p0) REVERT: 3 41 ASN cc_start: 0.7906 (t0) cc_final: 0.7681 (t0) REVERT: 8 24 MET cc_start: 0.9156 (mtp) cc_final: 0.8876 (mtp) REVERT: F 34 ASN cc_start: 0.6665 (OUTLIER) cc_final: 0.6145 (t0) REVERT: F 60 ARG cc_start: 0.7099 (mtp85) cc_final: 0.6764 (mtp-110) REVERT: F 93 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6871 (t70) REVERT: F 94 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.5306 (m-80) REVERT: F 110 ASP cc_start: 0.5507 (OUTLIER) cc_final: 0.5294 (m-30) REVERT: F 120 MET cc_start: 0.3381 (ptp) cc_final: 0.2911 (tmm) REVERT: F 137 MET cc_start: 0.7375 (mmm) cc_final: 0.7009 (mmm) REVERT: H 191 ASN cc_start: 0.9358 (OUTLIER) cc_final: 0.8960 (p0) REVERT: J 26 MET cc_start: 0.8684 (tpp) cc_final: 0.8219 (mtp) REVERT: J 38 MET cc_start: 0.8205 (mtm) cc_final: 0.7956 (mtp) REVERT: J 78 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.9056 (mtp85) REVERT: J 125 ARG cc_start: 0.8474 (mmt-90) cc_final: 0.8059 (mpp80) REVERT: M 139 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: N 31 LYS cc_start: 0.8798 (tptt) cc_final: 0.8486 (tttp) REVERT: N 59 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8557 (mmtp) REVERT: R 81 GLU cc_start: 0.9056 (pt0) cc_final: 0.8840 (pt0) REVERT: U 59 GLU cc_start: 0.8019 (mp0) cc_final: 0.7480 (mp0) REVERT: W 22 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7790 (tm-30) REVERT: W 88 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7865 (mm-30) REVERT: X 45 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8143 (mp10) REVERT: Y 84 ASP cc_start: 0.8400 (p0) cc_final: 0.8057 (p0) REVERT: Z 11 LYS cc_start: 0.9226 (pttm) cc_final: 0.8974 (ptpt) REVERT: c 57 MET cc_start: 0.8976 (mmt) cc_final: 0.8435 (mmt) REVERT: c 217 MET cc_start: 0.9187 (mmp) cc_final: 0.8737 (mmp) REVERT: d 138 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8255 (tp40) REVERT: g 6 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8172 (mtmt) REVERT: g 28 ARG cc_start: 0.9055 (ppp80) cc_final: 0.8742 (ppp80) REVERT: g 33 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8885 (mt) REVERT: g 34 LYS cc_start: 0.9169 (mttm) cc_final: 0.8924 (mtmm) REVERT: g 72 SER cc_start: 0.8352 (p) cc_final: 0.7925 (t) REVERT: g 97 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8428 (ttmm) REVERT: h 24 THR cc_start: 0.9110 (m) cc_final: 0.8767 (p) REVERT: h 74 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: h 140 ASP cc_start: 0.8585 (m-30) cc_final: 0.8255 (m-30) REVERT: l 125 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.8991 (ptmm) REVERT: l 126 ARG cc_start: 0.7971 (mmt180) cc_final: 0.7173 (mmt180) REVERT: n 32 LYS cc_start: 0.9060 (mtmt) cc_final: 0.8699 (mtpt) REVERT: n 36 ASN cc_start: 0.9089 (m-40) cc_final: 0.8758 (m110) REVERT: o 46 GLU cc_start: 0.8556 (tt0) cc_final: 0.8319 (tt0) REVERT: o 57 LYS cc_start: 0.8872 (ptmm) cc_final: 0.8634 (pttm) REVERT: p 19 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8224 (tm-30) REVERT: q 32 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7824 (ttt90) REVERT: s 21 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.8016 (t-170) REVERT: s 29 ASP cc_start: 0.9002 (t0) cc_final: 0.8793 (t0) REVERT: s 39 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8612 (pm20) REVERT: t 6 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8782 (pttt) REVERT: t 12 ASP cc_start: 0.8208 (m-30) cc_final: 0.7817 (m-30) REVERT: t 22 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7335 (tp40) REVERT: t 29 LYS cc_start: 0.8627 (mmpt) cc_final: 0.8239 (mmpt) REVERT: t 32 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8696 (ptmm) REVERT: t 41 PHE cc_start: 0.8606 (m-80) cc_final: 0.8309 (m-10) REVERT: t 53 ASP cc_start: 0.8712 (p0) cc_final: 0.8215 (p0) REVERT: t 55 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8026 (ptt180) REVERT: t 56 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8306 (pptt) REVERT: u 59 MET cc_start: 0.8908 (mtp) cc_final: 0.8604 (mtp) REVERT: u 68 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8882 (ttmm) outliers start: 147 outliers final: 96 residues processed: 787 average time/residue: 2.0368 time to fit residues: 2365.4256 Evaluate side-chains 801 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 682 time to evaluate : 6.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 141 LEU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 281 SER Chi-restraints excluded: chain 0 residue 335 VAL Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 1 residue 11 THR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 30 LYS Chi-restraints excluded: chain 3 residue 8 ASN Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 3 residue 39 ASP Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 111 PHE Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 139 GLU Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain P residue 5 LYS Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain W residue 21 ASP Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 45 GLN Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain c residue 202 SER Chi-restraints excluded: chain c residue 214 THR Chi-restraints excluded: chain d residue 81 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 171 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 11 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 131 THR Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 35 ASP Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain l residue 15 ASN Chi-restraints excluded: chain l residue 125 LYS Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 12 ASP Chi-restraints excluded: chain n residue 34 LEU Chi-restraints excluded: chain n residue 42 ASP Chi-restraints excluded: chain o residue 35 ARG Chi-restraints excluded: chain o residue 50 LYS Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 32 ARG Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain s residue 21 HIS Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 43 SER Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 58 ASP Chi-restraints excluded: chain u residue 79 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 624 optimal weight: 10.0000 chunk 1004 optimal weight: 30.0000 chunk 613 optimal weight: 3.9990 chunk 476 optimal weight: 8.9990 chunk 698 optimal weight: 30.0000 chunk 1054 optimal weight: 30.0000 chunk 970 optimal weight: 10.0000 chunk 839 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 648 optimal weight: 20.0000 chunk 514 optimal weight: 40.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 8 ASN 3 10 GLN F 58 GLN F 226 GLN ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 8 GLN ** j 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN ** l 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 ASN s 21 HIS u 3 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 161541 Z= 0.264 Angle : 0.597 23.379 241382 Z= 0.306 Chirality : 0.037 1.919 30827 Planarity : 0.004 0.125 13100 Dihedral : 23.195 178.375 79729 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.05 % Favored : 96.93 % Rotamer: Outliers : 2.64 % Allowed : 20.54 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 6001 helix: 1.67 (0.11), residues: 2093 sheet: -0.11 (0.15), residues: 1182 loop : -0.24 (0.12), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 108 HIS 0.012 0.001 HIS s 21 PHE 0.042 0.002 PHE 3 23 TYR 0.029 0.002 TYR p 78 ARG 0.014 0.000 ARG g 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12002 Ramachandran restraints generated. 6001 Oldfield, 0 Emsley, 6001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 701 time to evaluate : 6.896 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: 0 26 PHE cc_start: 0.8038 (m-80) cc_final: 0.7707 (m-80) REVERT: 0 93 MET cc_start: 0.8943 (mtm) cc_final: 0.8658 (ttp) REVERT: 0 151 LEU cc_start: 0.9080 (mp) cc_final: 0.8702 (tt) REVERT: 0 342 HIS cc_start: 0.8454 (m-70) cc_final: 0.8096 (m90) REVERT: 0 532 TYR cc_start: 0.6733 (t80) cc_final: 0.6440 (t80) REVERT: 1 4 LYS cc_start: 0.8183 (ptpp) cc_final: 0.7970 (pmtt) REVERT: 1 17 LYS cc_start: 0.8632 (tptm) cc_final: 0.8344 (tppp) REVERT: 1 45 GLU cc_start: 0.8391 (tt0) cc_final: 0.8152 (tt0) REVERT: 2 30 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8819 (mmpt) REVERT: 3 39 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.6692 (p0) REVERT: 3 41 ASN cc_start: 0.7884 (t0) cc_final: 0.7653 (t0) REVERT: 8 15 LYS cc_start: 0.9367 (ptpt) cc_final: 0.9122 (pttt) REVERT: 8 24 MET cc_start: 0.9118 (mtp) cc_final: 0.8855 (mtp) REVERT: F 34 ASN cc_start: 0.6756 (OUTLIER) cc_final: 0.6250 (t0) REVERT: F 60 ARG cc_start: 0.6989 (mtp85) cc_final: 0.6784 (mtp-110) REVERT: F 94 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.6243 (m-80) REVERT: F 120 MET cc_start: 0.3521 (ptp) cc_final: 0.3119 (tmm) REVERT: F 137 MET cc_start: 0.7353 (mmm) cc_final: 0.6932 (mmm) REVERT: H 191 ASN cc_start: 0.9363 (OUTLIER) cc_final: 0.8967 (p0) REVERT: J 26 MET cc_start: 0.8679 (tpp) cc_final: 0.8261 (mtp) REVERT: J 38 MET cc_start: 0.8185 (mtm) cc_final: 0.7941 (mtp) REVERT: J 78 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.9037 (mtp85) REVERT: J 83 MET cc_start: 0.8498 (mtt) cc_final: 0.8238 (mtt) REVERT: J 125 ARG cc_start: 0.8469 (mmt-90) cc_final: 0.8055 (mpp80) REVERT: M 139 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: N 59 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8564 (mmtp) REVERT: W 22 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7813 (tm-30) REVERT: W 88 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7867 (mm-30) REVERT: X 45 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: Y 84 ASP cc_start: 0.8388 (p0) cc_final: 0.8035 (p0) REVERT: Z 11 LYS cc_start: 0.9211 (pttm) cc_final: 0.8972 (ptpt) REVERT: c 57 MET cc_start: 0.8967 (mmt) cc_final: 0.8466 (mmt) REVERT: c 217 MET cc_start: 0.9206 (mmp) cc_final: 0.8760 (mmp) REVERT: d 138 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8248 (tp40) REVERT: g 6 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8276 (mtmt) REVERT: g 28 ARG cc_start: 0.9077 (ppp80) cc_final: 0.8841 (ppp80) REVERT: g 33 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8888 (mt) REVERT: g 34 LYS cc_start: 0.9174 (mttm) cc_final: 0.8927 (mtmm) REVERT: g 48 LYS cc_start: 0.8960 (tppp) cc_final: 0.8733 (tppt) REVERT: g 59 ARG cc_start: 0.8716 (mmt180) cc_final: 0.8256 (mmm160) REVERT: g 72 SER cc_start: 0.8330 (p) cc_final: 0.7903 (t) REVERT: g 97 LYS cc_start: 0.8690 (mtpp) cc_final: 0.8420 (ttmm) REVERT: h 24 THR cc_start: 0.9105 (m) cc_final: 0.8759 (p) REVERT: h 74 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: h 140 ASP cc_start: 0.8581 (m-30) cc_final: 0.8249 (m-30) REVERT: l 125 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9020 (ptmm) REVERT: l 126 ARG cc_start: 0.7955 (mmt180) cc_final: 0.7161 (mmt180) REVERT: n 32 LYS cc_start: 0.9059 (mtmt) cc_final: 0.8704 (mtpt) REVERT: n 36 ASN cc_start: 0.9071 (m-40) cc_final: 0.8740 (m110) REVERT: o 46 GLU cc_start: 0.8550 (tt0) cc_final: 0.8316 (tt0) REVERT: o 57 LYS cc_start: 0.8870 (ptmm) cc_final: 0.8633 (pttm) REVERT: p 19 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8210 (tm-30) REVERT: q 32 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7819 (ttt90) REVERT: s 39 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8605 (pm20) REVERT: t 6 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8777 (pttt) REVERT: t 12 ASP cc_start: 0.8216 (m-30) cc_final: 0.7809 (m-30) REVERT: t 22 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7310 (tp40) REVERT: t 29 LYS cc_start: 0.8638 (mmpt) cc_final: 0.8262 (mmpt) REVERT: t 32 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8689 (ptmm) REVERT: t 41 PHE cc_start: 0.8613 (m-80) cc_final: 0.8325 (m-10) REVERT: t 53 ASP cc_start: 0.8718 (p0) cc_final: 0.8233 (p0) REVERT: t 55 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8114 (ptt180) REVERT: t 56 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8326 (pptt) REVERT: u 52 GLU cc_start: 0.8797 (tp30) cc_final: 0.8304 (mm-30) REVERT: u 59 MET cc_start: 0.8902 (mtp) cc_final: 0.8596 (mtp) REVERT: u 68 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8890 (ttmm) outliers start: 136 outliers final: 94 residues processed: 784 average time/residue: 2.1057 time to fit residues: 2440.9420 Evaluate side-chains 796 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 682 time to evaluate : 6.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 141 LEU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 281 SER Chi-restraints excluded: chain 0 residue 335 VAL Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 1 residue 11 THR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 30 LYS Chi-restraints excluded: chain 3 residue 8 ASN Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 3 residue 39 ASP Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 139 ASN Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 167 ASP Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 139 GLU Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain W residue 21 ASP Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 45 GLN Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain c residue 202 SER Chi-restraints excluded: chain c residue 214 THR Chi-restraints excluded: chain d residue 81 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 171 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 11 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 131 THR Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 45 SER Chi-restraints excluded: chain l residue 125 LYS Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 12 ASP Chi-restraints excluded: chain n residue 34 LEU Chi-restraints excluded: chain o residue 35 ARG Chi-restraints excluded: chain o residue 50 LYS Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 32 ARG Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain r residue 62 VAL Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 43 SER Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 5 GLU Chi-restraints excluded: chain u residue 58 ASP Chi-restraints excluded: chain u residue 79 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 666 optimal weight: 8.9990 chunk 894 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 773 optimal weight: 20.0000 chunk 123 optimal weight: 40.0000 chunk 233 optimal weight: 20.0000 chunk 840 optimal weight: 30.0000 chunk 351 optimal weight: 10.0000 chunk 863 optimal weight: 20.0000 chunk 106 optimal weight: 30.0000 chunk 154 optimal weight: 20.0000 overall best weight: 13.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 342 HIS 0 487 ASN 3 8 ASN F 58 GLN F 226 GLN Q 101 GLN c 8 GLN g 36 ASN ** j 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.042923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.031493 restraints weight = 787023.565| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 1.40 r_work: 0.2613 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 161541 Z= 0.450 Angle : 0.669 23.207 241382 Z= 0.342 Chirality : 0.042 1.923 30827 Planarity : 0.005 0.128 13100 Dihedral : 23.161 178.223 79727 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 2.60 % Allowed : 20.84 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.11), residues: 6001 helix: 1.56 (0.11), residues: 2076 sheet: -0.14 (0.15), residues: 1167 loop : -0.33 (0.12), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 108 HIS 0.005 0.001 HIS e 36 PHE 0.035 0.002 PHE 3 23 TYR 0.028 0.002 TYR p 78 ARG 0.015 0.001 ARG g 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40754.89 seconds wall clock time: 712 minutes 11.11 seconds (42731.11 seconds total)