Starting phenix.real_space_refine on Sun Feb 25 22:43:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7s_13243/02_2024/7p7s_13243_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7s_13243/02_2024/7p7s_13243.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7s_13243/02_2024/7p7s_13243_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7s_13243/02_2024/7p7s_13243_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7s_13243/02_2024/7p7s_13243_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7s_13243/02_2024/7p7s_13243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7s_13243/02_2024/7p7s_13243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7s_13243/02_2024/7p7s_13243_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7s_13243/02_2024/7p7s_13243_updated.pdb" } resolution = 3.0 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 152 8.98 5 Zn 4 6.06 5 P 4631 5.49 5 Mg 189 5.21 5 S 155 5.16 5 C 74417 2.51 5 N 27138 2.21 5 O 40887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 147573 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: "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': 112, 'rna2p_pyr': 88, 'rna3p_pur': 741, 'rna3p_pyr': 580} Link IDs: {'rna2p': 200, 'rna3p': 1320} Chain breaks: 2 Chain: "b" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 285 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} 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: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 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: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 242 Unusual residues: {' K': 102, ' MG': 140} Classifications: {'undetermined': 242} Link IDs: {None: 241} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 111 Unusual residues: {' K': 38, ' MG': 44, 'PUT': 1, 'SCM': 1} Classifications: {'undetermined': 84} Link IDs: {None: 83} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6141 SG CYS 4 30 69.470 63.560 155.028 1.00 84.77 S ATOM 6161 SG CYS 4 33 70.270 60.518 152.851 1.00 85.16 S ATOM 6239 SG CYS 4 43 71.169 63.994 151.661 1.00 82.14 S ATOM 6257 SG CYS 4 46 67.577 62.891 151.789 1.00 82.17 S ATOM 6391 SG CYS 5 9 201.343 111.393 98.158 1.00 83.43 S ATOM 6410 SG CYS 5 12 199.838 108.258 96.426 1.00 84.37 S ATOM 6623 SG CYS 5 36 201.150 107.567 99.895 1.00 80.22 S ATOM 7710 SG CYS 8 11 141.835 142.571 191.549 1.00 86.91 S ATOM 7735 SG CYS 8 14 141.235 139.097 189.999 1.00 81.33 S ATOM 7841 SG CYS 8 27 138.612 140.742 192.292 1.00 85.73 S ATOM A0X5S SG CYS o 24 163.675 229.369 128.299 1.00112.38 S ATOM A0X6I SG CYS o 27 161.008 226.980 129.362 1.00114.30 S ATOM A0X9M SG CYS o 40 162.407 226.747 125.802 1.00114.03 S ATOM A0XAB SG CYS o 43 160.143 229.566 126.790 1.00112.24 S Time building chain proxies: 58.10, per 1000 atoms: 0.39 Number of scatterers: 147573 At special positions: 0 Unit cell: (253.38, 280.44, 238.62, 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 152 19.00 S 155 16.00 P 4631 15.00 Mg 189 11.99 O 40887 8.00 N 27138 7.00 C 74417 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: 70.03 Conformation dependent library (CDL) restraints added in 8.5 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 36 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 12 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 9 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 33 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " pdb=" ZN o 102 " pdb="ZN ZN o 102 " - pdb=" SG CYS o 27 " pdb="ZN ZN o 102 " - pdb=" SG CYS o 43 " pdb="ZN ZN o 102 " - pdb=" SG CYS o 24 " pdb="ZN ZN o 102 " - pdb=" SG CYS o 40 " 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: 190 helices and 83 sheets defined 39.3% alpha, 19.9% beta 1555 base pairs and 2406 stacking pairs defined. Time for finding SS restraints: 90.03 Creating SS restraints... Processing helix chain '0' and resid 38 through 48 removed outlier: 3.654A pdb=" N PHE 0 43 " --> pdb=" O LYS 0 39 " (cutoff:3.500A) Processing helix chain '0' and resid 79 through 89 removed outlier: 3.789A pdb=" N GLY 0 87 " --> pdb=" O PHE 0 83 " (cutoff:3.500A) removed outlier: 4.318A 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: 4.612A pdb=" N ASP 0 108 " --> pdb=" O LEU 0 104 " (cutoff:3.500A) Processing helix chain '0' and resid 111 through 130 removed outlier: 3.570A pdb=" N ASP 0 130 " --> pdb=" O LEU 0 126 " (cutoff:3.500A) Processing helix chain '0' and resid 132 through 144 removed outlier: 3.583A pdb=" N SER 0 136 " --> pdb=" O TYR 0 132 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU 0 138 " --> pdb=" O ALA 0 134 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL 0 142 " --> pdb=" O LEU 0 138 " (cutoff:3.500A) Processing helix chain '0' and resid 148 through 155 removed outlier: 3.780A pdb=" N PHE 0 152 " --> pdb=" O ASP 0 148 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP 0 153 " --> pdb=" O PHE 0 149 " (cutoff:3.500A) removed outlier: 3.775A 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: 3.881A pdb=" N LYS 0 176 " --> pdb=" O VAL 0 172 " (cutoff:3.500A) Processing helix chain '0' and resid 190 through 204 removed outlier: 3.757A pdb=" N PHE 0 196 " --> pdb=" O SER 0 192 " (cutoff:3.500A) Processing helix chain '0' and resid 214 through 222 removed outlier: 3.808A 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 435 through 441 removed outlier: 4.763A pdb=" N VAL 0 439 " --> pdb=" O TYR 0 435 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN 0 440 " --> pdb=" O ASP 0 436 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS 0 441 " --> pdb=" O ASP 0 437 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 435 through 441' Processing helix chain '0' and resid 442 through 447 removed outlier: 3.846A pdb=" N LEU 0 446 " --> pdb=" O LYS 0 442 " (cutoff:3.500A) removed outlier: 5.860A 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: 3.816A 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: 4.926A pdb=" N LEU 0 529 " --> pdb=" O SER 0 525 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU 0 530 " --> pdb=" O PRO 0 526 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 10 removed outlier: 5.109A pdb=" N THR 1 10 " --> pdb=" O ILE 1 6 " (cutoff:3.500A) Processing helix chain '1' and resid 11 through 35 removed outlier: 3.819A pdb=" N GLY 1 35 " --> pdb=" O GLN 1 31 " (cutoff:3.500A) Processing helix chain '1' and resid 39 through 60 removed outlier: 4.435A pdb=" N ILE 1 43 " --> pdb=" O ASN 1 39 " (cutoff:3.500A) removed outlier: 4.209A 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: 3.556A 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: 4.798A 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: 4.011A pdb=" N THR 6 24 " --> pdb=" O LYS 6 20 " (cutoff:3.500A) removed outlier: 5.481A 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: 4.112A pdb=" N LYS 7 36 " --> pdb=" O ARG 7 32 " (cutoff:3.500A) removed outlier: 5.062A 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: 4.050A pdb=" N LYS 7 46 " --> pdb=" O ARG 7 42 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 63 removed outlier: 5.722A pdb=" N GLN 7 60 " --> pdb=" O LYS 7 56 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLN 7 61 " --> pdb=" O ARG 7 57 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU 7 62 " --> pdb=" O ILE 7 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 16 removed outlier: 4.541A 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 97 through 105 removed outlier: 4.323A pdb=" N ALA F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 129 removed outlier: 4.718A pdb=" N LYS F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU F 127 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 159 removed outlier: 4.661A 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 131 through 136 removed outlier: 3.691A 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: 3.593A pdb=" N SER G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 226 removed outlier: 3.914A pdb=" N MET G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) removed outlier: 5.460A 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 266 through 271 removed outlier: 5.437A pdb=" N VAL G 271 " --> pdb=" O ASP G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 202 removed outlier: 4.045A pdb=" N GLU G 201 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 62 removed outlier: 3.596A pdb=" N SER H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 5.087A 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 71 removed outlier: 4.102A pdb=" N LYS H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.872A pdb=" N TYR H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 5.003A 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 98 through 103 removed outlier: 4.878A pdb=" N PHE H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLN H 103 " --> pdb=" O VAL H 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 98 through 103' 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: 3.713A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 removed outlier: 5.922A 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 169 removed outlier: 4.336A pdb=" N ASN I 169 " --> pdb=" O LEU I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 190 removed outlier: 5.114A 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: 4.317A 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 40 through 46 removed outlier: 5.239A pdb=" N VAL J 44 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 4.452A 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: 3.539A pdb=" N SER J 107 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 4.566A 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: 4.672A pdb=" N ILE J 137 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 5.688A 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 'K' and resid 3 through 8 removed outlier: 5.326A 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: 4.119A 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: 3.593A 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 124 removed outlier: 3.676A pdb=" N LYS M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASN M 124 " --> pdb=" O PHE M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 110 removed outlier: 4.497A pdb=" N GLU N 108 " --> pdb=" O ARG N 104 " (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: 4.049A pdb=" N ARG O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) removed outlier: 4.728A 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: 3.549A 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: 4.627A pdb=" N SER Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 66 removed outlier: 3.933A pdb=" N PHE Q 65 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 98 removed outlier: 5.147A 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 22 removed outlier: 3.733A pdb=" N ARG R 17 " --> pdb=" O LYS R 13 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS R 21 " --> pdb=" O ARG R 17 " (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: 4.231A pdb=" N GLU S 11 " --> pdb=" O GLU S 7 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN S 12 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG S 14 " --> pdb=" O GLN S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 104 removed outlier: 4.467A pdb=" N ARG S 101 " --> pdb=" O LEU S 97 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA S 102 " --> pdb=" O TYR S 98 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU S 103 " --> pdb=" O TYR S 99 " (cutoff:3.500A) removed outlier: 5.112A 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: 4.348A 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: 3.769A pdb=" N ARG T 51 " --> pdb=" O PHE T 47 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 3.669A 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: 3.787A 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: 4.306A pdb=" N GLY V 50 " --> pdb=" O ASN V 46 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE V 51 " --> pdb=" O LYS V 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 8 removed outlier: 3.956A pdb=" N ILE W 7 " --> pdb=" O LEU W 3 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LYS W 8 " --> pdb=" O LEU W 4 " (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: 4.377A pdb=" N VAL X 68 " --> pdb=" O HIS X 64 " (cutoff:3.500A) removed outlier: 5.476A 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: 4.040A pdb=" N SER Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) removed outlier: 4.655A 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 32 removed outlier: 3.861A pdb=" N LYS c 28 " --> pdb=" O ASN c 24 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS c 29 " --> pdb=" O PRO c 25 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N PHE c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 64 Processing helix chain 'c' and resid 76 through 88 Processing helix chain 'c' and resid 103 through 124 removed outlier: 3.622A pdb=" N LYS c 109 " --> pdb=" O ASP c 105 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG c 110 " --> pdb=" O THR c 106 " (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: 4.747A pdb=" N ILE c 196 " --> pdb=" O ASP c 192 " (cutoff:3.500A) removed outlier: 5.338A 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: 3.734A 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: 4.059A pdb=" N ASP d 111 " --> pdb=" O LYS d 107 " (cutoff:3.500A) removed outlier: 5.582A 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: 4.139A pdb=" N VAL e 11 " --> pdb=" O PRO e 7 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 28 removed outlier: 4.276A pdb=" N ARG e 28 " --> pdb=" O LYS e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 62 Processing helix chain 'e' and resid 64 through 79 removed outlier: 5.412A pdb=" N LYS e 79 " --> pdb=" O ALA e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 94 Processing helix chain 'e' and resid 95 through 103 Processing helix chain 'e' and resid 107 through 118 Processing helix chain 'e' and resid 143 through 148 removed outlier: 4.631A 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: 4.771A pdb=" N TYR e 187 " --> pdb=" O ARG e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 201 removed outlier: 3.706A 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: 5.510A 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: 5.219A pdb=" N ASP g 88 " --> pdb=" O ALA g 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 20 through 31 removed outlier: 3.594A pdb=" N THR h 24 " --> pdb=" O SER h 20 " (cutoff:3.500A) 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 112 removed outlier: 5.618A pdb=" N GLY h 112 " --> pdb=" O ALA h 108 " (cutoff:3.500A) Processing helix chain 'h' and resid 115 through 130 Processing helix chain 'h' and resid 132 through 153 removed outlier: 4.896A pdb=" N ALA h 150 " --> pdb=" O ASP h 146 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE h 151 " --> pdb=" O ALA h 147 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA h 152 " --> pdb=" O ASN h 148 " (cutoff:3.500A) removed outlier: 5.073A 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 39 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: 4.806A 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: 3.860A pdb=" N VAL k 84 " --> pdb=" O THR k 80 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP k 85 " --> pdb=" O PRO k 81 " (cutoff:3.500A) removed outlier: 5.437A 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: 4.283A pdb=" N SER l 58 " --> pdb=" O GLY l 54 " (cutoff:3.500A) removed outlier: 3.734A 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 27 removed outlier: 4.080A pdb=" N ASN m 25 " --> pdb=" O SER m 21 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS m 26 " --> pdb=" O PRO m 22 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLY m 27 " --> pdb=" O ALA m 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 21 through 27' Processing helix chain 'm' and resid 126 through 131 removed outlier: 4.568A pdb=" N TYR m 130 " --> pdb=" O SER m 126 " (cutoff:3.500A) Processing helix chain 'n' and resid 14 through 23 removed outlier: 3.915A pdb=" N ILE n 22 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 5.400A 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: 5.431A pdb=" N THR n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 50 through 64 removed outlier: 4.290A pdb=" N LYS n 64 " --> pdb=" O ILE n 60 " (cutoff:3.500A) Processing helix chain 'n' and resid 66 through 83 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: 3.865A pdb=" N ARG s 35 " --> pdb=" O GLU s 31 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE s 36 " --> pdb=" O LEU s 32 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE s 37 " --> pdb=" O LEU s 33 " (cutoff:3.500A) removed outlier: 5.837A 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: 4.600A pdb=" N GLY t 24 " --> pdb=" O GLU t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 41 through 46 removed outlier: 5.700A pdb=" N GLY t 46 " --> pdb=" O PRO t 42 " (cutoff:3.500A) Processing helix chain 't' and resid 63 through 68 removed outlier: 5.973A pdb=" N GLY t 68 " --> pdb=" O GLU t 64 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 76 removed outlier: 3.993A pdb=" N PHE t 74 " --> pdb=" O LYS t 70 " (cutoff:3.500A) removed outlier: 3.687A 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: 4.467A pdb=" N LYS u 63 " --> pdb=" O MET u 59 " (cutoff:3.500A) removed outlier: 3.803A 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: 3.542A 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: 4.420A pdb=" N SER 0 207 " --> pdb=" O GLU 0 178 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS 0 224 " --> pdb=" O LYS 0 28 " (cutoff:3.500A) removed outlier: 3.830A 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: 4.534A 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 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: 3.973A pdb=" N SER 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) removed outlier: 7.419A 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: 3.868A pdb=" N PHE 3 21 " --> pdb=" O ASP 3 16 " (cutoff:3.500A) removed outlier: 3.624A 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 30 No H-bonds generated for sheet with id= 8 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: 5.800A 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: 5.825A 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: 6.248A pdb=" N HIS 8 33 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N CYS 8 27 " --> pdb=" O HIS 8 33 " (cutoff:3.500A) removed outlier: 5.161A 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: 5.739A 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 96 Processing sheet with id= 15, first strand: chain 'F' and resid 169 through 175 removed outlier: 5.569A pdb=" N GLY F 169 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL F 42 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN F 211 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 4.530A 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: 6.453A pdb=" N ALA G 2 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N MET G 16 " --> pdb=" O TYR G 6 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 33 through 36 No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'G' and resid 80 through 83 removed outlier: 6.719A pdb=" N LEU G 93 " --> pdb=" O LYS G 79 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N MET G 114 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N GLY G 127 " --> pdb=" O ARG G 115 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL G 117 " --> pdb=" O GLY G 127 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 138 through 142 removed outlier: 4.074A pdb=" N THR G 139 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 90 through 96 removed outlier: 5.353A pdb=" N ASN G 90 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL G 100 " --> pdb=" O TYR G 96 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.374A pdb=" N LYS H 3 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU H 199 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR H 113 " --> pdb=" O LEU H 199 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 11 through 17 removed outlier: 4.095A pdb=" N GLU H 21 " --> pdb=" O THR H 17 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 33 through 36 removed outlier: 6.551A pdb=" N GLN H 50 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 105 through 109 removed outlier: 4.117A pdb=" N ASP H 106 " --> pdb=" O VAL H 176 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 2 through 7 removed outlier: 3.612A pdb=" N LEU I 6 " --> pdb=" O GLY I 15 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY I 15 " --> pdb=" O LEU I 6 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'I' and resid 122 through 125 Processing sheet with id= 27, first strand: chain 'J' and resid 65 through 69 removed outlier: 4.369A pdb=" N GLY J 86 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLY J 39 " --> pdb=" O GLY J 151 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY J 151 " --> pdb=" O GLY J 39 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'K' and resid 16 through 19 Processing sheet with id= 29, first strand: chain 'K' and resid 41 through 45 Processing sheet with id= 30, first strand: chain 'K' and resid 94 through 98 Processing sheet with id= 31, first strand: chain 'K' and resid 121 through 125 removed outlier: 6.227A pdb=" N ILE K 132 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N THR K 129 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG K 163 " --> pdb=" O GLU K 88 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'M' and resid 16 through 19 Processing sheet with id= 33, first strand: chain 'M' and resid 75 through 79 removed outlier: 7.268A pdb=" N GLY M 84 " --> pdb=" O SER M 79 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'N' and resid 18 through 21 removed outlier: 4.723A pdb=" N SER N 6 " --> pdb=" O THR N 21 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASN N 82 " --> pdb=" O ARG N 7 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'N' and resid 66 through 71 removed outlier: 5.290A pdb=" N SER N 67 " --> pdb=" O PHE N 79 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE N 79 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'O' and resid 74 through 77 Processing sheet with id= 37, first strand: chain 'O' and resid 121 through 124 Processing sheet with id= 38, first strand: chain 'P' and resid 63 through 67 removed outlier: 7.247A pdb=" N MET P 103 " --> pdb=" O LYS P 67 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE P 104 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLU P 31 " --> pdb=" O ARG P 134 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS P 128 " --> pdb=" O THR P 37 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'P' and resid 72 through 75 removed outlier: 6.766A pdb=" N LYS P 72 " --> pdb=" O TRP P 93 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP P 93 " --> pdb=" O LYS P 72 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR P 74 " --> pdb=" O GLU P 91 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'Q' and resid 29 through 33 removed outlier: 4.425A pdb=" N MET Q 120 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N TYR Q 104 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Q' and resid 72 through 75 Processing sheet with id= 42, first strand: chain 'R' and resid 54 through 57 Processing sheet with id= 43, first strand: chain 'S' and resid 38 through 45 removed outlier: 6.567A pdb=" N THR S 25 " --> pdb=" O VAL S 87 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN S 83 " --> pdb=" O HIS S 29 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'S' and resid 49 through 52 removed outlier: 3.671A pdb=" N LYS S 49 " --> pdb=" O THR S 60 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'U' and resid 11 through 15 Processing sheet with id= 46, first strand: chain 'U' and resid 18 through 23 removed outlier: 4.306A pdb=" N GLN U 18 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS U 94 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU U 59 " --> pdb=" O GLU U 98 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU U 31 " --> pdb=" O VAL U 62 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'U' and resid 64 through 67 Processing sheet with id= 48, first strand: chain 'U' and resid 70 through 76 Processing sheet with id= 49, first strand: chain 'V' and resid 6 through 13 removed outlier: 9.476A pdb=" N THR V 6 " --> pdb=" O GLU V 114 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR V 105 " --> pdb=" O GLY V 84 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'V' and resid 86 through 93 removed outlier: 3.841A pdb=" N SER V 97 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'W' and resid 24 through 29 removed outlier: 4.263A pdb=" N ARG W 76 " --> pdb=" O VAL W 29 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS W 73 " --> pdb=" O PRO W 60 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'X' and resid 9 through 12 removed outlier: 4.203A pdb=" N LYS X 19 " --> pdb=" O VAL X 11 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'X' and resid 25 through 28 removed outlier: 3.596A pdb=" N ALA X 25 " --> pdb=" O ILE X 34 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'X' and resid 39 through 45 removed outlier: 5.387A pdb=" N ASN X 39 " --> pdb=" O ALA X 61 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'X' and resid 80 through 83 removed outlier: 7.064A pdb=" N LYS X 80 " --> pdb=" O LYS X 95 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG X 92 " --> pdb=" O LEU X 101 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU X 99 " --> pdb=" O SER X 94 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Y' and resid 46 through 49 removed outlier: 4.522A pdb=" N GLN Y 49 " --> pdb=" O ASP Y 66 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP Y 66 " --> pdb=" O GLN Y 49 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Y' and resid 75 through 80 Processing sheet with id= 58, first strand: chain 'Z' and resid 12 through 19 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'c' and resid 15 through 18 removed outlier: 5.941A pdb=" N HIS c 15 " --> pdb=" O ILE c 41 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TYR c 39 " --> pdb=" O GLY c 17 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'c' and resid 89 through 93 Processing sheet with id= 61, first strand: chain 'd' and resid 19 through 22 removed outlier: 5.988A pdb=" N ASP d 19 " --> pdb=" O ILE d 54 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG d 58 " --> pdb=" O LYS d 21 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR d 53 " --> pdb=" O HIS d 68 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'd' and resid 163 through 168 removed outlier: 4.764A pdb=" N ASP d 180 " --> pdb=" O ARG d 203 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'e' and resid 137 through 141 removed outlier: 5.307A pdb=" N GLN e 138 " --> pdb=" O PHE e 177 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE e 177 " --> pdb=" O GLN e 138 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE e 165 " --> pdb=" O THR e 178 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'f' and resid 11 through 16 removed outlier: 6.842A pdb=" N LEU f 36 " --> pdb=" O VAL f 16 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'f' and resid 83 through 88 removed outlier: 7.594A pdb=" N HIS f 83 " --> pdb=" O PRO f 98 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG f 93 " --> pdb=" O LEU f 128 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA f 99 " --> pdb=" O ASP f 122 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP f 122 " --> pdb=" O ALA f 99 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'f' and resid 32 through 41 removed outlier: 6.195A pdb=" N HIS f 45 " --> pdb=" O ASP f 41 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'g' and resid 38 through 41 removed outlier: 6.511A pdb=" N ASN g 67 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS g 6 " --> pdb=" O VAL g 98 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG g 92 " --> pdb=" O ILE g 12 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'g' and resid 42 through 45 Processing sheet with id= 69, first strand: chain 'g' and resid 46 through 50 Processing sheet with id= 70, first strand: chain 'h' and resid 72 through 79 removed outlier: 6.413A pdb=" N VAL h 72 " --> pdb=" O VAL h 91 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'i' and resid 23 through 28 removed outlier: 6.706A pdb=" N GLU i 23 " --> pdb=" O LEU i 64 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'i' and resid 76 through 79 removed outlier: 4.562A pdb=" N ASN i 76 " --> pdb=" O TRP i 132 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE i 105 " --> pdb=" O ILE i 128 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'j' and resid 5 through 11 Processing sheet with id= 74, first strand: chain 'k' and resid 39 through 42 removed outlier: 4.579A pdb=" N LYS k 71 " --> pdb=" O LEU k 42 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG k 7 " --> pdb=" O LYS k 101 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'k' and resid 44 through 52 Processing sheet with id= 76, first strand: chain 'l' and resid 42 through 45 removed outlier: 7.437A pdb=" N VAL l 84 " --> pdb=" O THR l 108 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'l' and resid 83 through 88 removed outlier: 5.447A pdb=" N GLY l 88 " --> pdb=" O VAL l 113 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'm' and resid 42 through 45 removed outlier: 5.016A pdb=" N LEU m 94 " --> pdb=" O VAL m 111 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'm' and resid 49 through 54 removed outlier: 5.327A pdb=" N LYS m 64 " --> pdb=" O ILE m 80 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'q' and resid 5 through 11 Processing sheet with id= 81, first strand: chain 'r' and resid 9 through 14 removed outlier: 5.445A pdb=" N LYS r 9 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS r 63 " --> pdb=" O LEU r 79 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'r' and resid 22 through 34 No H-bonds generated for sheet with id= 82 Processing sheet with id= 83, first strand: chain 't' and resid 30 through 33 removed outlier: 4.530A pdb=" N PHE t 47 " --> pdb=" O ILE t 62 " (cutoff:3.500A) 2157 hydrogen bonds defined for protein. 6363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3899 hydrogen bonds 6196 hydrogen bond angles 0 basepair planarities 1555 basepair parallelities 2406 stacking parallelities Total time for adding SS restraints: 264.92 Time building geometry restraints manager: 74.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 14409 1.31 - 1.43: 69981 1.43 - 1.56: 65882 1.56 - 1.68: 9255 1.68 - 1.81: 288 Bond restraints: 159815 Sorted by residual: bond pdb=" C6 SCM a1675 " pdb=" O1 SCM a1675 " ideal model delta sigma weight residual 0.917 1.443 -0.526 2.00e-02 2.50e+03 6.92e+02 bond pdb=" C2' ATP 0 601 " pdb=" C3' ATP 0 601 " ideal model delta sigma weight residual 1.531 1.237 0.294 1.20e-02 6.94e+03 5.99e+02 bond pdb=" C2' ATP 0 602 " pdb=" C3' ATP 0 602 " ideal model delta sigma weight residual 1.531 1.239 0.292 1.20e-02 6.94e+03 5.92e+02 bond pdb=" C3 SCM a1675 " pdb=" C4 SCM a1675 " ideal model delta sigma weight residual 1.054 1.472 -0.418 2.00e-02 2.50e+03 4.37e+02 bond pdb=" C6 SCM a1675 " pdb=" O2B SCM a1675 " ideal model delta sigma weight residual 1.165 1.455 -0.290 2.00e-02 2.50e+03 2.11e+02 ... (remaining 159810 not shown) Histogram of bond angle deviations from ideal: 99.95 - 107.40: 31038 107.40 - 114.85: 101658 114.85 - 122.31: 74424 122.31 - 129.76: 28741 129.76 - 137.21: 2842 Bond angle restraints: 238703 Sorted by residual: angle pdb=" PB ATP 0 601 " pdb=" O3B ATP 0 601 " pdb=" PG ATP 0 601 " ideal model delta sigma weight residual 139.87 123.37 16.50 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PB ATP 0 602 " pdb=" O3B ATP 0 602 " pdb=" PG ATP 0 602 " ideal model delta sigma weight residual 139.87 124.58 15.29 1.00e+00 1.00e+00 2.34e+02 angle pdb=" PA ATP 0 601 " pdb=" O3A ATP 0 601 " pdb=" PB ATP 0 601 " ideal model delta sigma weight residual 136.83 123.44 13.39 1.00e+00 1.00e+00 1.79e+02 angle pdb=" PA ATP 0 602 " pdb=" O3A ATP 0 602 " pdb=" PB ATP 0 602 " ideal model delta sigma weight residual 136.83 123.83 13.00 1.00e+00 1.00e+00 1.69e+02 angle pdb=" N1 ATP 0 602 " pdb=" C2 ATP 0 602 " pdb=" N3 ATP 0 602 " ideal model delta sigma weight residual 128.69 119.94 8.75 1.00e+00 1.00e+00 7.66e+01 ... (remaining 238698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 90324 35.71 - 71.41: 10504 71.41 - 107.12: 1199 107.12 - 142.83: 30 142.83 - 178.53: 35 Dihedral angle restraints: 102092 sinusoidal: 84656 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 35.83 -70.83 1 8.00e+00 1.56e-02 1.01e+02 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 33.16 -68.16 1 8.00e+00 1.56e-02 9.42e+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 80.97 66.03 1 8.00e+00 1.56e-02 8.91e+01 ... (remaining 102089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.967: 30480 0.967 - 1.933: 0 1.933 - 2.900: 0 2.900 - 3.867: 1 3.867 - 4.834: 1 Chirality restraints: 30482 Sorted by residual: chirality pdb=" C5 SCM a1675 " pdb=" C4 SCM a1675 " pdb=" C6 SCM a1675 " pdb=" O1B SCM a1675 " both_signs ideal model delta sigma weight residual False 2.40 -2.44 4.83 2.00e-01 2.50e+01 5.84e+02 chirality pdb=" C6 SCM a1675 " pdb=" C5 SCM a1675 " pdb=" O1 SCM a1675 " pdb=" O2B SCM a1675 " both_signs ideal model delta sigma weight residual False 1.09 -2.35 3.44 2.00e-01 2.50e+01 2.96e+02 chirality pdb=" C7 SCM a1675 " pdb=" C12 SCM a1675 " pdb=" C8 SCM a1675 " pdb=" O1B SCM a1675 " both_signs ideal model delta sigma weight residual False -1.93 -2.40 0.47 2.00e-01 2.50e+01 5.47e+00 ... (remaining 30479 not shown) Planarity restraints: 13023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A1804 " 0.011 2.00e-02 2.50e+03 1.75e-02 8.40e+00 pdb=" N9 A A1804 " -0.044 2.00e-02 2.50e+03 pdb=" C8 A A1804 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A A1804 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A1804 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A A1804 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A A1804 " -0.002 2.00e-02 2.50e+03 pdb=" N1 A A1804 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A A1804 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A A1804 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A A1804 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 875 " -0.012 2.00e-02 2.50e+03 1.63e-02 7.92e+00 pdb=" N9 G A 875 " 0.042 2.00e-02 2.50e+03 pdb=" C8 G A 875 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A 875 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G A 875 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G A 875 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 875 " 0.001 2.00e-02 2.50e+03 pdb=" N1 G A 875 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 875 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G A 875 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A 875 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G A 875 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A2022 " 0.021 2.00e-02 2.50e+03 1.43e-02 6.13e+00 pdb=" N9 G A2022 " -0.041 2.00e-02 2.50e+03 pdb=" C8 G A2022 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A2022 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G A2022 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A2022 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G A2022 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G A2022 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A2022 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A2022 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A2022 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G A2022 " 0.017 2.00e-02 2.50e+03 ... (remaining 13020 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.45: 1148 2.45 - 3.13: 114178 3.13 - 3.80: 353580 3.80 - 4.47: 520195 4.47 - 5.14: 682604 Nonbonded interactions: 1671705 Sorted by model distance: nonbonded pdb=" OP1 A A1065 " pdb="MG MG A3073 " model vdw 1.782 2.170 nonbonded pdb=" O4 U a1008 " pdb="MG MG a1666 " model vdw 1.799 2.170 nonbonded pdb=" OP1 C A1380 " pdb="MG MG A3227 " model vdw 1.802 2.170 nonbonded pdb=" OP2 U A 119 " pdb="MG MG A3098 " model vdw 1.803 2.170 nonbonded pdb=" OP1 G a 971 " pdb="MG MG a1637 " model vdw 1.806 2.170 ... (remaining 1671700 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.850 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: 0.150 Extract box with map and model: 21.040 Check model and map are aligned: 1.690 Set scattering table: 1.050 Process input model: 622.470 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.410 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: 0.040 Load rotamer database and sin/cos tables:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 665.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 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 0.526 159815 Z= 0.335 Angle : 0.474 16.496 238703 Z= 0.271 Chirality : 0.048 4.834 30482 Planarity : 0.004 0.043 13023 Dihedral : 22.608 178.533 90874 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.58 % Favored : 97.40 % Rotamer: Outliers : 0.78 % Allowed : 5.87 % Favored : 93.35 % 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: 1.91 (0.11), residues: 2063 sheet: -0.13 (0.15), residues: 1154 loop : -0.19 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP c 104 HIS 0.005 0.001 HIS K 111 PHE 0.011 0.001 PHE 3 74 TYR 0.013 0.001 TYR c 90 ARG 0.013 0.001 ARG 6 3 *********************** 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 1035 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 995 time to evaluate : 6.082 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: 0 121 TRP cc_start: 0.8913 (m100) cc_final: 0.8418 (m100) REVERT: 0 334 ASN cc_start: 0.8961 (m-40) cc_final: 0.8541 (t0) REVERT: 1 9 LEU cc_start: 0.9429 (mt) cc_final: 0.9187 (mt) REVERT: 2 5 LYS cc_start: 0.9543 (ttpp) cc_final: 0.8913 (ttmt) REVERT: 3 17 SER cc_start: 0.7399 (t) cc_final: 0.6812 (m) REVERT: 3 34 THR cc_start: 0.8543 (t) cc_final: 0.8191 (t) REVERT: 4 52 LYS cc_start: 0.8792 (mtmm) cc_final: 0.8583 (mtmm) REVERT: F 58 GLN cc_start: 0.7466 (pt0) cc_final: 0.7247 (pp30) REVERT: F 83 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8518 (mmmt) REVERT: F 94 PHE cc_start: 0.6874 (m-80) cc_final: 0.6634 (m-80) REVERT: I 149 ASP cc_start: 0.8927 (p0) cc_final: 0.8684 (p0) REVERT: J 78 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.7739 (ttp80) REVERT: J 156 ILE cc_start: 0.9680 (mp) cc_final: 0.9328 (pp) REVERT: J 167 ARG cc_start: 0.8902 (ttm-80) cc_final: 0.8694 (ttm110) REVERT: K 104 THR cc_start: 0.9033 (m) cc_final: 0.8763 (p) REVERT: N 42 THR cc_start: 0.9238 (m) cc_final: 0.8990 (t) REVERT: N 110 ASN cc_start: 0.8888 (t0) cc_final: 0.8577 (t0) REVERT: Q 79 SER cc_start: 0.7809 (t) cc_final: 0.7444 (m) REVERT: R 1 MET cc_start: 0.7918 (tpp) cc_final: 0.7692 (tpp) REVERT: R 117 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8209 (tm-30) REVERT: V 70 ASP cc_start: 0.7937 (t0) cc_final: 0.7433 (t0) REVERT: W 43 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8219 (mm-30) REVERT: Y 91 TYR cc_start: 0.8922 (m-80) cc_final: 0.8696 (m-80) REVERT: Z 36 VAL cc_start: 0.9289 (t) cc_final: 0.9079 (m) REVERT: c 57 MET cc_start: 0.8936 (mmm) cc_final: 0.8535 (mmt) REVERT: c 108 GLN cc_start: 0.8608 (mm110) cc_final: 0.8358 (mm110) REVERT: e 25 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: e 31 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: e 113 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: f 30 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7701 (ttm110) REVERT: h 142 HIS cc_start: 0.8571 (m170) cc_final: 0.8099 (m90) REVERT: j 46 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8712 (tm-30) REVERT: k 75 ASP cc_start: 0.7923 (m-30) cc_final: 0.7356 (m-30) REVERT: l 68 GLU cc_start: 0.9259 (tt0) cc_final: 0.8619 (tm-30) REVERT: l 76 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8456 (tm-30) REVERT: l 77 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7815 (m-70) REVERT: p 9 ASN cc_start: 0.9073 (m-40) cc_final: 0.8572 (m-40) REVERT: p 38 GLN cc_start: 0.9340 (tt0) cc_final: 0.9131 (mt0) REVERT: p 76 GLN cc_start: 0.8836 (mm110) cc_final: 0.8528 (mp10) REVERT: q 77 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8183 (mp0) REVERT: s 30 THR cc_start: 0.8381 (m) cc_final: 0.8145 (t) REVERT: s 54 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7865 (tttt) REVERT: t 38 SER cc_start: 0.7317 (m) cc_final: 0.6956 (t) REVERT: t 39 THR cc_start: 0.7802 (m) cc_final: 0.7448 (p) REVERT: t 62 ILE cc_start: 0.9209 (mm) cc_final: 0.9005 (mm) REVERT: u 34 LYS cc_start: 0.9132 (mtmm) cc_final: 0.8921 (mtpm) REVERT: u 47 ASP cc_start: 0.8917 (m-30) cc_final: 0.8693 (t70) REVERT: u 51 ASN cc_start: 0.8713 (m-40) cc_final: 0.8463 (m-40) REVERT: u 66 ILE cc_start: 0.9242 (pt) cc_final: 0.9036 (pp) outliers start: 40 outliers final: 11 residues processed: 1026 average time/residue: 2.1942 time to fit residues: 3229.9925 Evaluate side-chains 706 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 688 time to evaluate : 6.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain F residue 83 LYS Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain T residue 115 ASP Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 31 TYR Chi-restraints excluded: chain e residue 113 GLN Chi-restraints excluded: chain f residue 30 ARG Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain n residue 89 ILE Chi-restraints excluded: chain r residue 42 LYS Chi-restraints excluded: chain s residue 54 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 887 optimal weight: 20.0000 chunk 796 optimal weight: 30.0000 chunk 442 optimal weight: 8.9990 chunk 272 optimal weight: 10.0000 chunk 537 optimal weight: 20.0000 chunk 425 optimal weight: 0.6980 chunk 823 optimal weight: 20.0000 chunk 318 optimal weight: 10.0000 chunk 500 optimal weight: 9.9990 chunk 613 optimal weight: 10.0000 chunk 954 optimal weight: 20.0000 overall best weight: 7.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 352 GLN 1 31 GLN 1 36 GLN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 HIS H 62 ASN I 201 GLN J 135 GLN K 84 GLN K 106 ASN ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 94 HIS d 125 ASN ** e 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 147 GLN e 148 ASN g 16 ASN g 36 ASN g 64 HIS h 64 GLN j 75 GLN k 20 GLN l 64 GLN l 101 GLN ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 88 ASN s 20 ASN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 159815 Z= 0.275 Angle : 0.565 26.415 238703 Z= 0.295 Chirality : 0.037 1.730 30482 Planarity : 0.004 0.050 13023 Dihedral : 23.299 179.123 78677 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer: Outliers : 2.20 % Allowed : 13.35 % Favored : 84.45 % 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: 0.97 (0.11), residues: 6001 helix: 2.04 (0.11), residues: 2085 sheet: -0.05 (0.15), residues: 1178 loop : -0.06 (0.12), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 108 HIS 0.005 0.001 HIS K 111 PHE 0.021 0.002 PHE F 111 TYR 0.035 0.002 TYR o 49 ARG 0.007 0.000 ARG J 3 *********************** 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 866 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 753 time to evaluate : 6.848 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: 0 121 TRP cc_start: 0.8787 (m100) cc_final: 0.8372 (m100) REVERT: 0 334 ASN cc_start: 0.9032 (m-40) cc_final: 0.8818 (p0) REVERT: 1 9 LEU cc_start: 0.9347 (mt) cc_final: 0.9031 (mt) REVERT: 1 23 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7713 (tm-30) REVERT: 4 52 LYS cc_start: 0.8789 (mtmm) cc_final: 0.8544 (mtmm) REVERT: F 60 ARG cc_start: 0.7330 (mtp85) cc_final: 0.7093 (mtp85) REVERT: F 83 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8486 (mmmt) REVERT: F 101 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7778 (m) REVERT: F 147 MET cc_start: 0.7208 (tpt) cc_final: 0.6612 (tpt) REVERT: F 161 VAL cc_start: 0.4145 (OUTLIER) cc_final: 0.3910 (t) REVERT: I 27 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8353 (tp30) REVERT: I 149 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8643 (p0) REVERT: J 78 ARG cc_start: 0.8317 (mtp-110) cc_final: 0.7777 (ttp80) REVERT: J 83 MET cc_start: 0.8862 (mmm) cc_final: 0.8541 (mtp) REVERT: J 112 ARG cc_start: 0.8212 (mmm160) cc_final: 0.7954 (mmm160) REVERT: J 150 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7113 (ttt180) REVERT: J 167 ARG cc_start: 0.8859 (ttm-80) cc_final: 0.8645 (ttm110) REVERT: K 104 THR cc_start: 0.9036 (m) cc_final: 0.8717 (p) REVERT: N 42 THR cc_start: 0.9232 (m) cc_final: 0.9020 (t) REVERT: N 105 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: N 110 ASN cc_start: 0.8907 (t0) cc_final: 0.8636 (t0) REVERT: Q 79 SER cc_start: 0.7684 (t) cc_final: 0.7372 (m) REVERT: R 1 MET cc_start: 0.8110 (tpp) cc_final: 0.7882 (tpp) REVERT: R 31 LEU cc_start: 0.9606 (tp) cc_final: 0.9328 (tt) REVERT: V 70 ASP cc_start: 0.7976 (t0) cc_final: 0.7638 (t70) REVERT: Y 91 TYR cc_start: 0.8872 (m-80) cc_final: 0.8654 (m-80) REVERT: c 57 MET cc_start: 0.8905 (mmm) cc_final: 0.8480 (mmt) REVERT: c 90 TYR cc_start: 0.8057 (m-80) cc_final: 0.7783 (m-80) REVERT: c 108 GLN cc_start: 0.8585 (mm110) cc_final: 0.8214 (mm-40) REVERT: e 31 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.6191 (m-80) REVERT: f 30 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7733 (ttm110) REVERT: h 70 MET cc_start: 0.8173 (mtp) cc_final: 0.7931 (mtm) REVERT: h 142 HIS cc_start: 0.8556 (m170) cc_final: 0.8094 (m90) REVERT: j 46 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8643 (tm-30) REVERT: j 55 THR cc_start: 0.8024 (p) cc_final: 0.7180 (t) REVERT: j 75 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7796 (mt0) REVERT: j 87 LEU cc_start: 0.8693 (tp) cc_final: 0.8464 (tt) REVERT: j 126 GLN cc_start: 0.8063 (tt0) cc_final: 0.7767 (tt0) REVERT: k 27 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8674 (mm-30) REVERT: l 56 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8913 (tppt) REVERT: l 64 GLN cc_start: 0.9209 (tt0) cc_final: 0.8991 (tm-30) REVERT: l 68 GLU cc_start: 0.9116 (tt0) cc_final: 0.8509 (tm-30) REVERT: l 76 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8475 (tm-30) REVERT: l 77 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.7702 (m-70) REVERT: l 101 GLN cc_start: 0.7897 (mt0) cc_final: 0.7583 (mm-40) REVERT: p 76 GLN cc_start: 0.8822 (mm110) cc_final: 0.8529 (mp10) REVERT: q 77 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8202 (mp0) REVERT: s 30 THR cc_start: 0.8469 (m) cc_final: 0.8216 (t) REVERT: t 39 THR cc_start: 0.7882 (m) cc_final: 0.7597 (p) REVERT: t 44 PHE cc_start: 0.8924 (m-80) cc_final: 0.8721 (m-80) REVERT: t 62 ILE cc_start: 0.9198 (mm) cc_final: 0.8845 (mp) REVERT: u 34 LYS cc_start: 0.9175 (mtmm) cc_final: 0.8555 (mtpm) REVERT: u 47 ASP cc_start: 0.8922 (m-30) cc_final: 0.8722 (t70) REVERT: u 51 ASN cc_start: 0.8796 (m-40) cc_final: 0.8494 (m-40) REVERT: u 66 ILE cc_start: 0.9210 (pt) cc_final: 0.8981 (pp) outliers start: 113 outliers final: 44 residues processed: 817 average time/residue: 2.0599 time to fit residues: 2471.8687 Evaluate side-chains 726 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 670 time to evaluate : 6.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 319 ILE Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain F residue 83 LYS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 PHE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain N residue 54 LYS Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain T residue 115 ASP Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 79 THR Chi-restraints excluded: chain c residue 125 THR Chi-restraints excluded: chain d residue 109 ASP Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 31 TYR Chi-restraints excluded: chain e residue 39 ASN Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain f residue 30 ARG Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 78 ASN Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 56 ASN Chi-restraints excluded: chain h residue 144 MET Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain j residue 75 GLN Chi-restraints excluded: chain k residue 52 ILE Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 45 SER Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain u residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 530 optimal weight: 5.9990 chunk 296 optimal weight: 20.0000 chunk 794 optimal weight: 40.0000 chunk 649 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 956 optimal weight: 7.9990 chunk 1032 optimal weight: 50.0000 chunk 851 optimal weight: 30.0000 chunk 948 optimal weight: 9.9990 chunk 325 optimal weight: 20.0000 chunk 767 optimal weight: 30.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 GLN J 21 ASN N 45 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN e 50 GLN ** e 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 113 GLN e 116 ASN e 117 HIS e 138 GLN e 147 GLN ** j 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN l 101 GLN n 76 ASN ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 38 GLN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 3 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 159815 Z= 0.292 Angle : 0.563 23.946 238703 Z= 0.296 Chirality : 0.038 1.905 30482 Planarity : 0.004 0.052 13023 Dihedral : 23.196 178.991 78662 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.47 % Favored : 97.52 % Rotamer: Outliers : 3.15 % Allowed : 13.68 % Favored : 83.17 % 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: 0.94 (0.11), residues: 6001 helix: 1.95 (0.11), residues: 2083 sheet: 0.08 (0.15), residues: 1138 loop : -0.08 (0.12), residues: 2780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 108 HIS 0.005 0.001 HIS p 42 PHE 0.014 0.002 PHE 3 74 TYR 0.031 0.002 TYR o 49 ARG 0.008 0.000 ARG j 45 *********************** 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 886 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 724 time to evaluate : 6.817 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: 0 93 MET cc_start: 0.8482 (mtm) cc_final: 0.8007 (ptm) REVERT: 0 121 TRP cc_start: 0.8665 (m100) cc_final: 0.8339 (m100) REVERT: 0 220 GLN cc_start: 0.8805 (mt0) cc_final: 0.8546 (mt0) REVERT: 4 52 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8470 (mtmm) REVERT: F 60 ARG cc_start: 0.7422 (mtp85) cc_final: 0.7147 (mtp85) REVERT: F 101 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7811 (m) REVERT: F 171 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7034 (pp) REVERT: F 225 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.8010 (p0) REVERT: G 20 ASP cc_start: 0.8572 (p0) cc_final: 0.8356 (p0) REVERT: I 27 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: I 149 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8619 (p0) REVERT: J 78 ARG cc_start: 0.8378 (mtp-110) cc_final: 0.7861 (ttp80) REVERT: J 83 MET cc_start: 0.8916 (mmm) cc_final: 0.8549 (mtp) REVERT: K 99 GLN cc_start: 0.7861 (mp10) cc_final: 0.7635 (mp10) REVERT: K 104 THR cc_start: 0.9050 (m) cc_final: 0.8703 (p) REVERT: N 110 ASN cc_start: 0.8954 (t0) cc_final: 0.8665 (t0) REVERT: Q 79 SER cc_start: 0.7626 (t) cc_final: 0.7345 (m) REVERT: R 1 MET cc_start: 0.8158 (tpp) cc_final: 0.7907 (tpp) REVERT: T 51 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.6809 (mtm-85) REVERT: T 89 ASP cc_start: 0.7835 (t0) cc_final: 0.7229 (t0) REVERT: U 37 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8418 (mt-10) REVERT: V 53 GLU cc_start: 0.8503 (tt0) cc_final: 0.8272 (tm-30) REVERT: V 70 ASP cc_start: 0.8126 (t0) cc_final: 0.7888 (t70) REVERT: X 69 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8618 (ttp) REVERT: Y 91 TYR cc_start: 0.8881 (m-80) cc_final: 0.8639 (m-80) REVERT: c 57 MET cc_start: 0.8876 (mmm) cc_final: 0.8456 (mmt) REVERT: c 90 TYR cc_start: 0.8025 (m-80) cc_final: 0.7649 (m-80) REVERT: c 108 GLN cc_start: 0.8592 (mm110) cc_final: 0.8220 (mm-40) REVERT: f 30 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7699 (ttm110) REVERT: g 30 ASP cc_start: 0.8748 (m-30) cc_final: 0.8442 (m-30) REVERT: g 34 LYS cc_start: 0.8993 (mttp) cc_final: 0.8686 (mptt) REVERT: g 83 LEU cc_start: 0.9389 (mm) cc_final: 0.9159 (mm) REVERT: h 70 MET cc_start: 0.8367 (mtp) cc_final: 0.7785 (mtm) REVERT: h 142 HIS cc_start: 0.8595 (m170) cc_final: 0.8119 (m90) REVERT: j 46 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8532 (tm-30) REVERT: j 55 THR cc_start: 0.7593 (p) cc_final: 0.7017 (t) REVERT: j 87 LEU cc_start: 0.8703 (tp) cc_final: 0.8501 (tt) REVERT: j 126 GLN cc_start: 0.8080 (tt0) cc_final: 0.7770 (tt0) REVERT: k 16 ARG cc_start: 0.8994 (mmm160) cc_final: 0.8775 (mmm160) REVERT: k 24 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8461 (tttt) REVERT: l 56 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8935 (tppt) REVERT: l 64 GLN cc_start: 0.9199 (tt0) cc_final: 0.8825 (tm-30) REVERT: l 68 GLU cc_start: 0.9120 (tt0) cc_final: 0.8526 (tm-30) REVERT: n 36 ASN cc_start: 0.9416 (m110) cc_final: 0.9188 (p0) REVERT: n 107 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7785 (mmp-170) REVERT: q 48 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7891 (mp0) REVERT: q 77 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8195 (mp0) REVERT: r 83 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7703 (tm-30) REVERT: s 30 THR cc_start: 0.8451 (m) cc_final: 0.8212 (t) REVERT: s 34 LYS cc_start: 0.8899 (mtpm) cc_final: 0.8278 (mtmp) REVERT: t 44 PHE cc_start: 0.8890 (m-10) cc_final: 0.8652 (m-80) REVERT: u 51 ASN cc_start: 0.8811 (m-40) cc_final: 0.8504 (m-40) REVERT: u 66 ILE cc_start: 0.9203 (pt) cc_final: 0.8971 (pp) REVERT: u 75 LYS cc_start: 0.9068 (mtpm) cc_final: 0.8862 (mtpt) outliers start: 162 outliers final: 62 residues processed: 809 average time/residue: 2.0241 time to fit residues: 2428.4514 Evaluate side-chains 728 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 655 time to evaluate : 6.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 319 ILE Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 5 residue 47 GLU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 54 LYS Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 69 MET Chi-restraints excluded: chain X residue 79 THR Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain c residue 5 SER Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain d residue 109 ASP Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 39 ASN Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain f residue 30 ARG Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 45 ASP Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 78 ASN Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 56 ASN Chi-restraints excluded: chain h residue 144 MET Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain j residue 37 GLU Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain k residue 52 ILE Chi-restraints excluded: chain k residue 55 THR Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 122 ASP Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain n residue 107 ARG Chi-restraints excluded: chain p residue 80 GLU Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 67 THR Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain t residue 78 ARG Chi-restraints excluded: chain u residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 944 optimal weight: 40.0000 chunk 718 optimal weight: 30.0000 chunk 496 optimal weight: 30.0000 chunk 105 optimal weight: 20.0000 chunk 456 optimal weight: 8.9990 chunk 642 optimal weight: 9.9990 chunk 959 optimal weight: 20.0000 chunk 1015 optimal weight: 20.0000 chunk 501 optimal weight: 6.9990 chunk 909 optimal weight: 30.0000 chunk 273 optimal weight: 20.0000 overall best weight: 13.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 48 HIS ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 GLN K 84 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS c 18 HIS d 125 ASN ** e 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 117 HIS ** j 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN l 101 GLN n 76 ASN p 76 GLN s 56 GLN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 3 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 159815 Z= 0.418 Angle : 0.628 24.114 238703 Z= 0.327 Chirality : 0.041 1.892 30482 Planarity : 0.005 0.055 13023 Dihedral : 23.177 179.739 78649 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.75 % Favored : 97.23 % Rotamer: Outliers : 3.60 % Allowed : 15.53 % Favored : 80.87 % 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: 0.71 (0.11), residues: 6001 helix: 1.72 (0.11), residues: 2081 sheet: -0.00 (0.15), residues: 1173 loop : -0.22 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 0 121 HIS 0.005 0.001 HIS S 77 PHE 0.023 0.002 PHE t 74 TYR 0.025 0.002 TYR o 49 ARG 0.011 0.001 ARG J 167 *********************** 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 875 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 690 time to evaluate : 6.674 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: 0 121 TRP cc_start: 0.8742 (m100) cc_final: 0.8399 (m100) REVERT: 0 220 GLN cc_start: 0.8747 (mt0) cc_final: 0.8495 (mt0) REVERT: 1 58 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8455 (tpt-90) REVERT: 3 3 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7511 (mm-40) REVERT: 5 1 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7924 (tpp) REVERT: F 46 TYR cc_start: 0.8041 (m-80) cc_final: 0.7679 (m-80) REVERT: F 60 ARG cc_start: 0.7232 (mtp85) cc_final: 0.6157 (mtp85) REVERT: F 164 ARG cc_start: 0.8578 (ttt90) cc_final: 0.7612 (ttt90) REVERT: F 189 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6176 (t80) REVERT: F 212 ILE cc_start: 0.7295 (mt) cc_final: 0.7079 (mt) REVERT: F 225 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.8030 (p0) REVERT: I 27 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8350 (tp30) REVERT: I 132 ASP cc_start: 0.8130 (p0) cc_final: 0.7913 (p0) REVERT: I 149 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8624 (p0) REVERT: J 78 ARG cc_start: 0.8408 (mtp-110) cc_final: 0.7833 (ttp80) REVERT: J 83 MET cc_start: 0.8942 (mmm) cc_final: 0.8740 (mmm) REVERT: J 175 MET cc_start: 0.7829 (mmt) cc_final: 0.7439 (mmm) REVERT: K 104 THR cc_start: 0.9062 (m) cc_final: 0.8730 (p) REVERT: N 110 ASN cc_start: 0.8947 (t0) cc_final: 0.8623 (t0) REVERT: Q 79 SER cc_start: 0.7599 (t) cc_final: 0.7276 (m) REVERT: T 51 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.6997 (mtm-85) REVERT: T 89 ASP cc_start: 0.8071 (t0) cc_final: 0.7319 (t0) REVERT: U 37 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8426 (mt-10) REVERT: V 53 GLU cc_start: 0.8523 (tt0) cc_final: 0.8297 (tm-30) REVERT: V 70 ASP cc_start: 0.8161 (t0) cc_final: 0.7911 (t70) REVERT: X 45 GLN cc_start: 0.8486 (tp40) cc_final: 0.8073 (mp10) REVERT: c 57 MET cc_start: 0.8889 (mmm) cc_final: 0.8468 (mmt) REVERT: c 90 TYR cc_start: 0.7986 (m-80) cc_final: 0.7763 (m-80) REVERT: c 108 GLN cc_start: 0.8561 (mm110) cc_final: 0.8244 (mp10) REVERT: e 60 MET cc_start: 0.9021 (tpp) cc_final: 0.8633 (tpp) REVERT: f 30 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7655 (ttm110) REVERT: g 30 ASP cc_start: 0.8718 (m-30) cc_final: 0.8410 (m-30) REVERT: g 34 LYS cc_start: 0.9019 (mttp) cc_final: 0.8736 (mptt) REVERT: g 39 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7864 (pt0) REVERT: h 70 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7951 (mtm) REVERT: h 142 HIS cc_start: 0.8591 (m-70) cc_final: 0.8077 (m90) REVERT: j 46 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8479 (tm-30) REVERT: j 126 GLN cc_start: 0.8085 (tt0) cc_final: 0.7810 (tt0) REVERT: l 64 GLN cc_start: 0.9240 (tt0) cc_final: 0.8986 (tm-30) REVERT: l 68 GLU cc_start: 0.9123 (tt0) cc_final: 0.8498 (tm-30) REVERT: n 66 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8224 (mm-30) REVERT: q 19 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8845 (mmm-85) REVERT: q 58 ASP cc_start: 0.9086 (t70) cc_final: 0.8840 (t0) REVERT: q 77 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8208 (mp0) REVERT: r 83 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7826 (tm-30) REVERT: s 24 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.8195 (t80) REVERT: s 30 THR cc_start: 0.8450 (m) cc_final: 0.8226 (t) REVERT: t 44 PHE cc_start: 0.8987 (m-10) cc_final: 0.8686 (m-80) REVERT: u 34 LYS cc_start: 0.9214 (mtpm) cc_final: 0.8786 (mtmm) REVERT: u 51 ASN cc_start: 0.8805 (m-40) cc_final: 0.8526 (m-40) REVERT: u 66 ILE cc_start: 0.9214 (pt) cc_final: 0.9005 (pp) outliers start: 185 outliers final: 81 residues processed: 794 average time/residue: 2.0107 time to fit residues: 2347.6480 Evaluate side-chains 741 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 646 time to evaluate : 6.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 319 ILE Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 1 residue 58 ARG Chi-restraints excluded: chain 3 residue 3 GLN Chi-restraints excluded: chain 3 residue 45 LEU Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 111 PHE Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 49 ASN Chi-restraints excluded: chain J residue 115 HIS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 54 LYS Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain T residue 115 ASP Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 79 THR Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 39 ASN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain f residue 30 ARG Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 78 ASN Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 56 ASN Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 70 MET Chi-restraints excluded: chain h residue 144 MET Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain j residue 37 GLU Chi-restraints excluded: chain j residue 58 LYS Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 52 ILE Chi-restraints excluded: chain k residue 55 THR Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 80 GLU Chi-restraints excluded: chain q residue 19 ARG Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 67 THR Chi-restraints excluded: chain s residue 22 ILE Chi-restraints excluded: chain s residue 24 TYR Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain t residue 78 ARG Chi-restraints excluded: chain u residue 46 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 846 optimal weight: 20.0000 chunk 576 optimal weight: 10.0000 chunk 14 optimal weight: 50.0000 chunk 756 optimal weight: 30.0000 chunk 419 optimal weight: 9.9990 chunk 866 optimal weight: 5.9990 chunk 702 optimal weight: 20.0000 chunk 1 optimal weight: 0.3980 chunk 518 optimal weight: 3.9990 chunk 911 optimal weight: 40.0000 chunk 256 optimal weight: 10.0000 overall best weight: 6.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 32 ASN F 73 GLN ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 GLN K 84 GLN S 6 GLN U 26 ASN ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS ** e 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 113 GLN e 117 HIS ** j 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 20 GLN l 15 ASN ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 56 GLN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 3 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 159815 Z= 0.212 Angle : 0.542 23.795 238703 Z= 0.284 Chirality : 0.036 1.904 30482 Planarity : 0.004 0.053 13023 Dihedral : 23.190 179.870 78647 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.84 % Allowed : 16.87 % Favored : 80.29 % 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: 0.88 (0.11), residues: 6001 helix: 1.90 (0.11), residues: 2085 sheet: 0.09 (0.15), residues: 1169 loop : -0.16 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 108 HIS 0.005 0.001 HIS l 22 PHE 0.028 0.001 PHE h 62 TYR 0.019 0.001 TYR o 49 ARG 0.011 0.000 ARG 5 24 *********************** 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 846 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 700 time to evaluate : 6.866 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: 0 4 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: 0 121 TRP cc_start: 0.8717 (m100) cc_final: 0.8404 (m100) REVERT: 0 220 GLN cc_start: 0.8791 (mt0) cc_final: 0.8494 (mt0) REVERT: 1 58 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8382 (tpt-90) REVERT: 3 33 GLU cc_start: 0.8384 (pm20) cc_final: 0.7973 (pm20) REVERT: 4 52 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8498 (mtmm) REVERT: 5 1 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7857 (tpp) REVERT: F 137 MET cc_start: 0.8800 (mmt) cc_final: 0.8383 (mmt) REVERT: F 171 ILE cc_start: 0.7747 (mt) cc_final: 0.7278 (pp) REVERT: F 189 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.5979 (t80) REVERT: F 225 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8056 (p0) REVERT: I 132 ASP cc_start: 0.8049 (p0) cc_final: 0.7812 (p0) REVERT: I 149 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8621 (p0) REVERT: I 201 GLN cc_start: 0.8703 (mt0) cc_final: 0.8451 (mt0) REVERT: J 78 ARG cc_start: 0.8365 (mtp-110) cc_final: 0.7745 (ttp80) REVERT: J 83 MET cc_start: 0.8958 (mmm) cc_final: 0.8746 (mmm) REVERT: J 150 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6905 (ttt180) REVERT: J 175 MET cc_start: 0.7778 (mmt) cc_final: 0.7331 (mmm) REVERT: K 104 THR cc_start: 0.9041 (m) cc_final: 0.8705 (p) REVERT: M 80 MET cc_start: 0.8853 (mtp) cc_final: 0.8615 (mtp) REVERT: N 110 ASN cc_start: 0.8914 (t0) cc_final: 0.8590 (t0) REVERT: Q 79 SER cc_start: 0.7563 (t) cc_final: 0.7289 (m) REVERT: R 1 MET cc_start: 0.8073 (tpp) cc_final: 0.7274 (ttm) REVERT: S 71 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7885 (mp0) REVERT: T 51 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.6968 (mtm-85) REVERT: T 89 ASP cc_start: 0.8070 (t0) cc_final: 0.7220 (t0) REVERT: V 53 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8279 (tm-30) REVERT: V 70 ASP cc_start: 0.8159 (t0) cc_final: 0.7912 (t70) REVERT: W 43 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8209 (mm-30) REVERT: X 45 GLN cc_start: 0.8444 (tp40) cc_final: 0.8055 (mp10) REVERT: c 57 MET cc_start: 0.8837 (mmm) cc_final: 0.8464 (mmt) REVERT: c 108 GLN cc_start: 0.8547 (mm110) cc_final: 0.8240 (mp10) REVERT: e 49 MET cc_start: 0.8668 (mmm) cc_final: 0.8437 (mmm) REVERT: e 60 MET cc_start: 0.8916 (tpp) cc_final: 0.8422 (tpp) REVERT: g 4 ASP cc_start: 0.6544 (t0) cc_final: 0.6293 (t0) REVERT: g 30 ASP cc_start: 0.8794 (m-30) cc_final: 0.8501 (m-30) REVERT: g 34 LYS cc_start: 0.8975 (mttp) cc_final: 0.8700 (mptt) REVERT: h 66 MET cc_start: 0.7767 (tpp) cc_final: 0.7467 (tpp) REVERT: h 70 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7880 (mtm) REVERT: h 142 HIS cc_start: 0.8605 (m-70) cc_final: 0.8109 (m90) REVERT: j 46 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8446 (tm-30) REVERT: j 126 GLN cc_start: 0.7933 (tt0) cc_final: 0.7711 (tt0) REVERT: k 24 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7976 (tttm) REVERT: k 66 GLU cc_start: 0.8079 (pt0) cc_final: 0.7788 (pm20) REVERT: l 56 LYS cc_start: 0.9191 (tppt) cc_final: 0.8965 (tppp) REVERT: l 68 GLU cc_start: 0.9088 (tt0) cc_final: 0.8497 (tm-30) REVERT: n 36 ASN cc_start: 0.9402 (m110) cc_final: 0.9068 (p0) REVERT: n 66 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8446 (mm-30) REVERT: p 41 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8309 (mm-30) REVERT: q 48 GLU cc_start: 0.7938 (mp0) cc_final: 0.7635 (mp0) REVERT: q 58 ASP cc_start: 0.9103 (t70) cc_final: 0.8855 (t0) REVERT: q 77 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8156 (mp0) REVERT: r 83 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7878 (tm-30) REVERT: s 30 THR cc_start: 0.8493 (m) cc_final: 0.8175 (t) REVERT: s 34 LYS cc_start: 0.8872 (mtpm) cc_final: 0.8217 (mtmt) REVERT: t 44 PHE cc_start: 0.8933 (m-10) cc_final: 0.8385 (m-80) REVERT: u 34 LYS cc_start: 0.9174 (mtpm) cc_final: 0.8874 (mtpp) REVERT: u 51 ASN cc_start: 0.8756 (m-40) cc_final: 0.8464 (m-40) REVERT: u 66 ILE cc_start: 0.9179 (pt) cc_final: 0.8941 (pp) outliers start: 146 outliers final: 68 residues processed: 782 average time/residue: 2.0489 time to fit residues: 2348.2293 Evaluate side-chains 739 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 659 time to evaluate : 6.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 319 ILE Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 1 residue 58 ARG Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 47 GLU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 49 ASN Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain N residue 54 LYS Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain T residue 115 ASP Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 79 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 48 ASP Chi-restraints excluded: chain d residue 109 ASP Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 39 ASN Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 78 ASN Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 56 ASN Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 70 MET Chi-restraints excluded: chain h residue 144 MET Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain j residue 37 GLU Chi-restraints excluded: chain j residue 56 GLU Chi-restraints excluded: chain j residue 58 LYS Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain k residue 24 LYS Chi-restraints excluded: chain k residue 52 ILE Chi-restraints excluded: chain k residue 55 THR Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain p residue 41 GLU Chi-restraints excluded: chain p residue 80 GLU Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 67 THR Chi-restraints excluded: chain s residue 22 ILE Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain t residue 78 ARG Chi-restraints excluded: chain u residue 47 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 341 optimal weight: 20.0000 chunk 914 optimal weight: 40.0000 chunk 200 optimal weight: 40.0000 chunk 596 optimal weight: 6.9990 chunk 250 optimal weight: 30.0000 chunk 1016 optimal weight: 30.0000 chunk 844 optimal weight: 7.9990 chunk 470 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 336 optimal weight: 20.0000 chunk 533 optimal weight: 20.0000 overall best weight: 12.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 146 GLN F 207 GLN J 21 ASN ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN N 45 GLN ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS d 122 GLN ** e 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 117 HIS ** j 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 20 GLN ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 3 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 159815 Z= 0.405 Angle : 0.618 24.026 238703 Z= 0.322 Chirality : 0.041 1.893 30482 Planarity : 0.004 0.057 13023 Dihedral : 23.131 179.635 78643 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.13 % Allowed : 17.63 % Favored : 79.24 % 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: 1.73 (0.11), residues: 2080 sheet: -0.00 (0.15), residues: 1167 loop : -0.21 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 108 HIS 0.013 0.001 HIS J 115 PHE 0.029 0.002 PHE h 62 TYR 0.024 0.002 TYR F 46 ARG 0.013 0.001 ARG 5 24 *********************** 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 828 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 667 time to evaluate : 6.806 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: 0 121 TRP cc_start: 0.8735 (m100) cc_final: 0.8428 (m100) REVERT: 0 220 GLN cc_start: 0.8802 (mt0) cc_final: 0.8530 (mt0) REVERT: 1 58 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8416 (tpt-90) REVERT: 3 10 GLN cc_start: 0.7787 (pp30) cc_final: 0.7559 (pp30) REVERT: 3 33 GLU cc_start: 0.8482 (pm20) cc_final: 0.8074 (pm20) REVERT: 5 1 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7904 (tpp) REVERT: 8 24 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8437 (mtt) REVERT: F 189 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.5977 (t80) REVERT: G 35 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8489 (mp10) REVERT: I 27 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8314 (tp30) REVERT: I 149 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8598 (p0) REVERT: J 63 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7422 (mt0) REVERT: J 78 ARG cc_start: 0.8402 (mtp-110) cc_final: 0.7746 (ttp80) REVERT: J 83 MET cc_start: 0.8988 (mmm) cc_final: 0.8734 (mmm) REVERT: J 175 MET cc_start: 0.7799 (mmt) cc_final: 0.7346 (mmm) REVERT: K 95 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8134 (ptp90) REVERT: K 104 THR cc_start: 0.9058 (m) cc_final: 0.8721 (p) REVERT: N 110 ASN cc_start: 0.8947 (t0) cc_final: 0.8613 (t0) REVERT: Q 79 SER cc_start: 0.7606 (t) cc_final: 0.7290 (m) REVERT: R 1 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7506 (ttm) REVERT: T 51 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.7011 (mtm-85) REVERT: T 89 ASP cc_start: 0.8163 (t0) cc_final: 0.7365 (t0) REVERT: V 53 GLU cc_start: 0.8525 (tt0) cc_final: 0.8314 (tm-30) REVERT: V 70 ASP cc_start: 0.8196 (t0) cc_final: 0.7958 (t70) REVERT: X 45 GLN cc_start: 0.8494 (tp40) cc_final: 0.8038 (mp10) REVERT: X 69 MET cc_start: 0.8873 (ttp) cc_final: 0.8613 (ttp) REVERT: c 57 MET cc_start: 0.8848 (mmm) cc_final: 0.8462 (mmt) REVERT: c 90 TYR cc_start: 0.8166 (m-80) cc_final: 0.7750 (m-80) REVERT: c 108 GLN cc_start: 0.8563 (mm110) cc_final: 0.8239 (mp10) REVERT: e 60 MET cc_start: 0.8879 (tpp) cc_final: 0.8566 (tpp) REVERT: h 66 MET cc_start: 0.7801 (tpp) cc_final: 0.7545 (tpp) REVERT: h 70 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7927 (mtm) REVERT: h 142 HIS cc_start: 0.8606 (m-70) cc_final: 0.8088 (m90) REVERT: j 46 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8455 (tm-30) REVERT: j 110 MET cc_start: 0.8756 (mmt) cc_final: 0.8516 (mmt) REVERT: j 126 GLN cc_start: 0.8043 (tt0) cc_final: 0.7768 (tt0) REVERT: k 24 LYS cc_start: 0.8376 (tttt) cc_final: 0.8102 (tttm) REVERT: k 66 GLU cc_start: 0.7988 (pt0) cc_final: 0.7647 (pm20) REVERT: l 56 LYS cc_start: 0.9206 (tppt) cc_final: 0.8973 (tppp) REVERT: l 64 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8841 (tm-30) REVERT: l 68 GLU cc_start: 0.9099 (tt0) cc_final: 0.8404 (tm-30) REVERT: l 72 LYS cc_start: 0.8720 (mmpt) cc_final: 0.8373 (mmpt) REVERT: n 36 ASN cc_start: 0.9401 (m110) cc_final: 0.9065 (p0) REVERT: p 41 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8287 (mm-30) REVERT: q 19 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8827 (mmm-85) REVERT: q 58 ASP cc_start: 0.9065 (t70) cc_final: 0.8821 (t0) REVERT: q 77 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8153 (mp0) REVERT: r 83 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7864 (tm-30) REVERT: s 24 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.8137 (t80) REVERT: s 34 LYS cc_start: 0.8847 (mtpm) cc_final: 0.8334 (mtmp) REVERT: t 44 PHE cc_start: 0.9003 (m-10) cc_final: 0.8457 (m-80) REVERT: u 28 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.9176 (tmm) REVERT: u 51 ASN cc_start: 0.8738 (m-40) cc_final: 0.8446 (m-40) REVERT: u 66 ILE cc_start: 0.9222 (pt) cc_final: 0.8992 (pp) outliers start: 161 outliers final: 87 residues processed: 759 average time/residue: 2.0133 time to fit residues: 2241.7075 Evaluate side-chains 744 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 640 time to evaluate : 6.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 216 ASP Chi-restraints excluded: chain 0 residue 319 ILE Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 1 residue 58 ARG Chi-restraints excluded: chain 3 residue 45 LEU Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 47 GLU Chi-restraints excluded: chain 8 residue 24 MET Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 49 ASN Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain J residue 115 HIS Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 40 LYS Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 54 LYS Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain T residue 115 ASP Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 79 THR Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 17 ASP Chi-restraints excluded: chain d residue 48 ASP Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 39 ASN Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 78 ASN Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 56 ASN Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 70 MET Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 37 GLU Chi-restraints excluded: chain j residue 58 LYS Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 52 ILE Chi-restraints excluded: chain k residue 55 THR Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 64 GLN Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 121 ASN Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 41 GLU Chi-restraints excluded: chain p residue 80 GLU Chi-restraints excluded: chain q residue 19 ARG Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 67 THR Chi-restraints excluded: chain s residue 24 TYR Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain u residue 28 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 980 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 579 optimal weight: 7.9990 chunk 742 optimal weight: 20.0000 chunk 575 optimal weight: 10.0000 chunk 856 optimal weight: 40.0000 chunk 567 optimal weight: 8.9990 chunk 1012 optimal weight: 20.0000 chunk 633 optimal weight: 5.9990 chunk 617 optimal weight: 10.0000 chunk 467 optimal weight: 0.9980 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 27 ASN J 21 ASN ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS d 122 GLN ** e 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 113 GLN e 117 HIS f 135 ASN ** j 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 20 GLN ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 3 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 159815 Z= 0.239 Angle : 0.560 23.940 238703 Z= 0.293 Chirality : 0.037 1.902 30482 Planarity : 0.004 0.054 13023 Dihedral : 23.172 179.029 78643 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.74 % Allowed : 18.45 % Favored : 78.81 % 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: 0.79 (0.11), residues: 6001 helix: 1.79 (0.11), residues: 2080 sheet: 0.06 (0.15), residues: 1178 loop : -0.17 (0.12), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 108 HIS 0.010 0.001 HIS J 115 PHE 0.035 0.002 PHE h 62 TYR 0.037 0.002 TYR 0 99 ARG 0.013 0.000 ARG J 3 *********************** 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 816 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 675 time to evaluate : 6.906 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: 0 121 TRP cc_start: 0.8711 (m100) cc_final: 0.8421 (m100) REVERT: 0 139 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7510 (mp) REVERT: 0 220 GLN cc_start: 0.8783 (mt0) cc_final: 0.8485 (mt0) REVERT: 0 369 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8516 (mttp) REVERT: 1 58 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8391 (tpt-90) REVERT: 3 33 GLU cc_start: 0.8455 (pm20) cc_final: 0.8053 (pm20) REVERT: 5 1 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7874 (tpp) REVERT: 8 24 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8382 (mtt) REVERT: F 164 ARG cc_start: 0.8581 (ttt180) cc_final: 0.8330 (mtp180) REVERT: F 189 PHE cc_start: 0.6548 (OUTLIER) cc_final: 0.5926 (t80) REVERT: I 149 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8631 (p0) REVERT: J 78 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.7737 (ttp80) REVERT: J 83 MET cc_start: 0.8975 (mmm) cc_final: 0.8738 (mmm) REVERT: J 150 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7013 (ttt180) REVERT: J 175 MET cc_start: 0.7724 (mmt) cc_final: 0.7322 (mmm) REVERT: K 104 THR cc_start: 0.9039 (m) cc_final: 0.8695 (p) REVERT: M 80 MET cc_start: 0.8802 (mtp) cc_final: 0.8601 (mtp) REVERT: N 110 ASN cc_start: 0.8930 (t0) cc_final: 0.8587 (t0) REVERT: Q 79 SER cc_start: 0.7589 (t) cc_final: 0.7284 (m) REVERT: R 1 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7327 (ttm) REVERT: S 71 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7857 (mp0) REVERT: T 51 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.6999 (mtm-85) REVERT: T 89 ASP cc_start: 0.8140 (t0) cc_final: 0.7400 (t0) REVERT: V 53 GLU cc_start: 0.8491 (tt0) cc_final: 0.8281 (tm-30) REVERT: V 70 ASP cc_start: 0.8206 (t0) cc_final: 0.7951 (t70) REVERT: X 45 GLN cc_start: 0.8465 (tp40) cc_final: 0.8026 (mp10) REVERT: X 69 MET cc_start: 0.8887 (ttp) cc_final: 0.8604 (ttp) REVERT: c 57 MET cc_start: 0.8826 (mmm) cc_final: 0.8451 (mmt) REVERT: c 90 TYR cc_start: 0.8106 (m-80) cc_final: 0.7636 (m-80) REVERT: e 49 MET cc_start: 0.8610 (mmm) cc_final: 0.8342 (mmm) REVERT: e 60 MET cc_start: 0.8822 (tpp) cc_final: 0.8370 (tpp) REVERT: h 66 MET cc_start: 0.7730 (tpp) cc_final: 0.7449 (tpp) REVERT: h 70 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7935 (mtm) REVERT: h 142 HIS cc_start: 0.8612 (m-70) cc_final: 0.8083 (m90) REVERT: j 46 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8402 (tm-30) REVERT: j 110 MET cc_start: 0.8755 (mmt) cc_final: 0.8527 (mmt) REVERT: j 126 GLN cc_start: 0.7947 (tt0) cc_final: 0.7649 (tt0) REVERT: k 24 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8127 (tttm) REVERT: k 66 GLU cc_start: 0.7998 (pt0) cc_final: 0.7670 (pm20) REVERT: l 56 LYS cc_start: 0.9170 (tppt) cc_final: 0.8957 (tppp) REVERT: l 64 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8828 (tm-30) REVERT: l 68 GLU cc_start: 0.9073 (tt0) cc_final: 0.8389 (tm-30) REVERT: l 72 LYS cc_start: 0.8746 (mmpt) cc_final: 0.8444 (mmpt) REVERT: n 36 ASN cc_start: 0.9375 (m110) cc_final: 0.9039 (p0) REVERT: p 41 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8258 (mm-30) REVERT: q 58 ASP cc_start: 0.9071 (t70) cc_final: 0.8837 (t0) REVERT: q 73 ILE cc_start: 0.9150 (mp) cc_final: 0.8734 (mp) REVERT: q 77 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8156 (mp0) REVERT: r 83 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7909 (tm-30) REVERT: s 24 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.8132 (t80) REVERT: s 34 LYS cc_start: 0.8806 (mtpm) cc_final: 0.8219 (mtmt) REVERT: t 44 PHE cc_start: 0.8972 (m-10) cc_final: 0.8415 (m-80) REVERT: u 28 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.9220 (tmm) REVERT: u 51 ASN cc_start: 0.8722 (m-40) cc_final: 0.8420 (m-40) REVERT: u 66 ILE cc_start: 0.9178 (pt) cc_final: 0.8937 (pp) outliers start: 141 outliers final: 82 residues processed: 755 average time/residue: 1.9886 time to fit residues: 2213.5328 Evaluate side-chains 747 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 649 time to evaluate : 6.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 139 LEU Chi-restraints excluded: chain 0 residue 216 ASP Chi-restraints excluded: chain 0 residue 319 ILE Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 0 residue 369 LYS Chi-restraints excluded: chain 1 residue 58 ARG Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 47 GLU Chi-restraints excluded: chain 8 residue 24 MET Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 49 ASN Chi-restraints excluded: chain J residue 115 HIS Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 54 LYS Chi-restraints excluded: chain P residue 58 MET Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain T residue 115 ASP Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 79 THR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 109 ASP Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 39 ASN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain g residue 45 ASP Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 78 ASN Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 56 ASN Chi-restraints excluded: chain h residue 70 MET Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 37 GLU Chi-restraints excluded: chain j residue 58 LYS Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 24 LYS Chi-restraints excluded: chain k residue 52 ILE Chi-restraints excluded: chain k residue 55 THR Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain l residue 34 ILE Chi-restraints excluded: chain l residue 58 SER Chi-restraints excluded: chain l residue 64 GLN Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 75 LEU Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 41 GLU Chi-restraints excluded: chain p residue 80 GLU Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 67 THR Chi-restraints excluded: chain s residue 24 TYR Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain u residue 28 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 626 optimal weight: 9.9990 chunk 404 optimal weight: 40.0000 chunk 605 optimal weight: 5.9990 chunk 305 optimal weight: 70.0000 chunk 199 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 644 optimal weight: 8.9990 chunk 690 optimal weight: 40.0000 chunk 500 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 796 optimal weight: 40.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 431 ASN 0 534 ASN ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS d 122 GLN ** d 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 117 HIS f 135 ASN ** j 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 20 GLN ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 3 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 159815 Z= 0.331 Angle : 0.590 23.909 238703 Z= 0.308 Chirality : 0.039 1.897 30482 Planarity : 0.004 0.056 13023 Dihedral : 23.128 179.276 78643 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.70 % Allowed : 18.95 % Favored : 78.35 % 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: 1.73 (0.11), residues: 2081 sheet: 0.01 (0.15), residues: 1172 loop : -0.19 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F 108 HIS 0.009 0.001 HIS J 115 PHE 0.032 0.002 PHE h 62 TYR 0.021 0.002 TYR Z 6 ARG 0.013 0.000 ARG 5 24 *********************** 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 799 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 660 time to evaluate : 6.969 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: 0 74 MET cc_start: 0.7568 (pmm) cc_final: 0.7181 (pmm) REVERT: 0 121 TRP cc_start: 0.8708 (m100) cc_final: 0.8428 (m100) REVERT: 0 139 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7614 (mp) REVERT: 0 220 GLN cc_start: 0.8787 (mt0) cc_final: 0.8475 (mt0) REVERT: 0 369 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8502 (mttp) REVERT: 1 9 LEU cc_start: 0.9215 (mt) cc_final: 0.8996 (mp) REVERT: 1 58 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8396 (tpt-90) REVERT: 3 33 GLU cc_start: 0.8484 (pm20) cc_final: 0.8066 (pm20) REVERT: 5 1 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7858 (tpp) REVERT: 8 24 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8395 (mtt) REVERT: F 120 MET cc_start: 0.7661 (ptt) cc_final: 0.6414 (ppp) REVERT: F 129 ARG cc_start: 0.8551 (tpp80) cc_final: 0.8296 (tmm160) REVERT: F 164 ARG cc_start: 0.8585 (ttt180) cc_final: 0.8266 (mtp180) REVERT: F 189 PHE cc_start: 0.6588 (OUTLIER) cc_final: 0.5954 (t80) REVERT: F 211 ASN cc_start: 0.7965 (t0) cc_final: 0.7740 (t0) REVERT: F 218 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7840 (m-80) REVERT: I 27 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8309 (tp30) REVERT: I 149 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8584 (p0) REVERT: J 78 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.7784 (ttp80) REVERT: J 83 MET cc_start: 0.8995 (mmm) cc_final: 0.8716 (mmm) REVERT: J 175 MET cc_start: 0.7711 (mmt) cc_final: 0.7313 (mmm) REVERT: K 104 THR cc_start: 0.9048 (m) cc_final: 0.8706 (p) REVERT: M 80 MET cc_start: 0.8843 (mtp) cc_final: 0.8627 (mtp) REVERT: N 110 ASN cc_start: 0.8932 (t0) cc_final: 0.8567 (t0) REVERT: Q 79 SER cc_start: 0.7660 (t) cc_final: 0.7354 (m) REVERT: R 1 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7449 (ttm) REVERT: T 51 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.7055 (mtm-85) REVERT: T 89 ASP cc_start: 0.8180 (t0) cc_final: 0.7444 (t0) REVERT: U 37 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8394 (mt-10) REVERT: V 53 GLU cc_start: 0.8508 (tt0) cc_final: 0.8301 (tm-30) REVERT: V 70 ASP cc_start: 0.8147 (t0) cc_final: 0.7918 (t70) REVERT: X 45 GLN cc_start: 0.8466 (tp40) cc_final: 0.8037 (mp10) REVERT: c 57 MET cc_start: 0.8823 (mmm) cc_final: 0.8473 (mmt) REVERT: c 90 TYR cc_start: 0.8069 (m-80) cc_final: 0.7627 (m-10) REVERT: e 49 MET cc_start: 0.8672 (mmm) cc_final: 0.8414 (mmm) REVERT: e 60 MET cc_start: 0.8821 (tpp) cc_final: 0.8376 (tpp) REVERT: f 12 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: h 70 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7942 (mtm) REVERT: h 142 HIS cc_start: 0.8580 (m-70) cc_final: 0.8047 (m90) REVERT: j 6 TYR cc_start: 0.6751 (m-10) cc_final: 0.5967 (m-10) REVERT: j 46 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8421 (tm-30) REVERT: j 89 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8246 (pt0) REVERT: j 110 MET cc_start: 0.8740 (mmt) cc_final: 0.8521 (mmt) REVERT: j 126 GLN cc_start: 0.7898 (tt0) cc_final: 0.7634 (tt0) REVERT: k 24 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8118 (tttm) REVERT: k 66 GLU cc_start: 0.8025 (pt0) cc_final: 0.7646 (pm20) REVERT: l 20 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.7865 (p) REVERT: l 64 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8863 (pp30) REVERT: l 68 GLU cc_start: 0.9084 (tt0) cc_final: 0.8395 (tm-30) REVERT: l 72 LYS cc_start: 0.8740 (mmpt) cc_final: 0.8373 (mmpt) REVERT: p 34 GLU cc_start: 0.9084 (tp30) cc_final: 0.8599 (mm-30) REVERT: p 41 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: q 58 ASP cc_start: 0.9060 (t70) cc_final: 0.8824 (t0) REVERT: q 77 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8164 (mp0) REVERT: r 83 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7874 (tm-30) REVERT: s 24 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.8123 (t80) REVERT: s 34 LYS cc_start: 0.8781 (mtpm) cc_final: 0.8266 (mtmp) REVERT: t 13 ASP cc_start: 0.8952 (p0) cc_final: 0.8667 (p0) REVERT: t 44 PHE cc_start: 0.8965 (m-10) cc_final: 0.8428 (m-80) REVERT: u 28 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9163 (tmm) REVERT: u 51 ASN cc_start: 0.8725 (m-40) cc_final: 0.8433 (m-40) REVERT: u 66 ILE cc_start: 0.9194 (pt) cc_final: 0.8955 (pp) outliers start: 139 outliers final: 87 residues processed: 741 average time/residue: 2.0401 time to fit residues: 2230.7972 Evaluate side-chains 747 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 640 time to evaluate : 6.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 84 LEU Chi-restraints excluded: chain 0 residue 139 LEU Chi-restraints excluded: chain 0 residue 216 ASP Chi-restraints excluded: chain 0 residue 319 ILE Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 0 residue 369 LYS Chi-restraints excluded: chain 1 residue 58 ARG Chi-restraints excluded: chain 3 residue 45 LEU Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 47 GLU Chi-restraints excluded: chain 8 residue 24 MET Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 49 ASN Chi-restraints excluded: chain J residue 115 HIS Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 40 LYS Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 54 LYS Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain T residue 115 ASP Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 79 THR Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 39 ASN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain f residue 12 GLU Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 78 ASN Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 56 ASN Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 70 MET Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 37 GLU Chi-restraints excluded: chain j residue 58 LYS Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain j residue 76 SER Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain k residue 24 LYS Chi-restraints excluded: chain k residue 52 ILE Chi-restraints excluded: chain k residue 55 THR Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 58 SER Chi-restraints excluded: chain l residue 64 GLN Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 41 GLU Chi-restraints excluded: chain p residue 80 GLU Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 67 THR Chi-restraints excluded: chain s residue 24 TYR Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain u residue 28 MET Chi-restraints excluded: chain u residue 37 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 921 optimal weight: 20.0000 chunk 970 optimal weight: 30.0000 chunk 885 optimal weight: 40.0000 chunk 943 optimal weight: 7.9990 chunk 568 optimal weight: 8.9990 chunk 411 optimal weight: 30.0000 chunk 741 optimal weight: 40.0000 chunk 289 optimal weight: 20.0000 chunk 853 optimal weight: 20.0000 chunk 892 optimal weight: 10.0000 chunk 940 optimal weight: 20.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 275 GLN ** 0 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 534 ASN 1 36 GLN ** I 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN N 4 GLN ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS d 122 GLN ** e 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 113 GLN e 117 HIS ** j 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 20 GLN ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 3 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 159815 Z= 0.425 Angle : 0.640 24.007 238703 Z= 0.333 Chirality : 0.042 1.896 30482 Planarity : 0.005 0.059 13023 Dihedral : 23.146 179.722 78643 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.82 % Allowed : 18.97 % Favored : 78.21 % 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: 0.59 (0.11), residues: 6001 helix: 1.57 (0.11), residues: 2065 sheet: -0.05 (0.15), residues: 1192 loop : -0.24 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP F 108 HIS 0.008 0.001 HIS c 15 PHE 0.034 0.002 PHE h 62 TYR 0.025 0.002 TYR Z 6 ARG 0.015 0.001 ARG 5 24 *********************** 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 800 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 655 time to evaluate : 6.945 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: 0 6 MET cc_start: 0.9007 (mtp) cc_final: 0.8646 (mpp) REVERT: 0 74 MET cc_start: 0.7638 (pmm) cc_final: 0.7223 (pmm) REVERT: 0 121 TRP cc_start: 0.8722 (m100) cc_final: 0.8445 (m100) REVERT: 0 139 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7669 (mp) REVERT: 0 220 GLN cc_start: 0.8801 (mt0) cc_final: 0.8531 (mt0) REVERT: 0 369 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8471 (mttp) REVERT: 3 33 GLU cc_start: 0.8460 (pm20) cc_final: 0.8037 (pm20) REVERT: 5 1 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7935 (tpp) REVERT: 8 24 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8418 (mtt) REVERT: F 120 MET cc_start: 0.7554 (ptt) cc_final: 0.6494 (ppp) REVERT: F 189 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.5969 (t80) REVERT: F 211 ASN cc_start: 0.7877 (t0) cc_final: 0.7627 (t0) REVERT: I 27 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: I 149 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8621 (p0) REVERT: J 78 ARG cc_start: 0.8429 (mtp-110) cc_final: 0.7833 (ttp80) REVERT: J 175 MET cc_start: 0.7701 (mmt) cc_final: 0.7282 (mmm) REVERT: K 95 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8116 (ptp90) REVERT: M 100 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8380 (ttp80) REVERT: N 110 ASN cc_start: 0.8955 (t0) cc_final: 0.8608 (t0) REVERT: Q 79 SER cc_start: 0.7713 (t) cc_final: 0.7381 (m) REVERT: R 1 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7507 (ttm) REVERT: R 109 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8192 (mm-30) REVERT: T 51 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.7045 (mtm-85) REVERT: T 89 ASP cc_start: 0.8223 (t0) cc_final: 0.7563 (t0) REVERT: U 37 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8399 (mt-10) REVERT: V 53 GLU cc_start: 0.8527 (tt0) cc_final: 0.8324 (tm-30) REVERT: V 70 ASP cc_start: 0.8189 (t0) cc_final: 0.7965 (t70) REVERT: X 45 GLN cc_start: 0.8487 (tp40) cc_final: 0.8064 (mp10) REVERT: X 69 MET cc_start: 0.8938 (ttp) cc_final: 0.8668 (ttp) REVERT: c 57 MET cc_start: 0.8817 (mmm) cc_final: 0.8461 (mmt) REVERT: c 90 TYR cc_start: 0.8126 (m-80) cc_final: 0.7730 (m-10) REVERT: e 60 MET cc_start: 0.8833 (tpp) cc_final: 0.8431 (tpp) REVERT: f 12 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7248 (pm20) REVERT: h 66 MET cc_start: 0.7775 (tpp) cc_final: 0.7395 (tpp) REVERT: h 70 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7916 (mtm) REVERT: h 142 HIS cc_start: 0.8551 (m-70) cc_final: 0.8010 (m90) REVERT: j 75 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.6717 (mm-40) REVERT: j 110 MET cc_start: 0.8706 (mmt) cc_final: 0.8411 (tpp) REVERT: j 126 GLN cc_start: 0.7965 (tt0) cc_final: 0.7698 (tt0) REVERT: k 24 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8109 (tttm) REVERT: k 66 GLU cc_start: 0.8012 (pt0) cc_final: 0.7593 (pm20) REVERT: l 34 ILE cc_start: 0.8220 (tp) cc_final: 0.7550 (pp) REVERT: l 56 LYS cc_start: 0.9147 (tppt) cc_final: 0.8842 (tppp) REVERT: l 64 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8851 (tm-30) REVERT: l 68 GLU cc_start: 0.9099 (tt0) cc_final: 0.8400 (tm-30) REVERT: l 72 LYS cc_start: 0.8728 (mmpt) cc_final: 0.8320 (mmpt) REVERT: n 36 ASN cc_start: 0.9434 (m110) cc_final: 0.9060 (p0) REVERT: n 66 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8223 (mm-30) REVERT: p 34 GLU cc_start: 0.9080 (tp30) cc_final: 0.8638 (mm-30) REVERT: p 41 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8345 (mm-30) REVERT: q 19 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8822 (mmm-85) REVERT: q 58 ASP cc_start: 0.9053 (t70) cc_final: 0.8816 (t0) REVERT: q 73 ILE cc_start: 0.9165 (mp) cc_final: 0.8746 (mp) REVERT: q 77 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8148 (mp0) REVERT: r 83 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7815 (tm-30) REVERT: s 24 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.8134 (t80) REVERT: s 34 LYS cc_start: 0.8760 (mtpm) cc_final: 0.8261 (mtmp) REVERT: t 44 PHE cc_start: 0.8994 (m-10) cc_final: 0.8484 (m-80) REVERT: u 51 ASN cc_start: 0.8730 (m-40) cc_final: 0.8443 (m-40) REVERT: u 66 ILE cc_start: 0.9218 (pt) cc_final: 0.8988 (pp) outliers start: 145 outliers final: 101 residues processed: 748 average time/residue: 2.0276 time to fit residues: 2237.2027 Evaluate side-chains 758 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 637 time to evaluate : 6.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 139 LEU Chi-restraints excluded: chain 0 residue 216 ASP Chi-restraints excluded: chain 0 residue 319 ILE Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 0 residue 369 LYS Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 3 residue 45 LEU Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 47 GLU Chi-restraints excluded: chain 8 residue 24 MET Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 49 ASN Chi-restraints excluded: chain J residue 115 HIS Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 40 LYS Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 54 LYS Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain T residue 115 ASP Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 79 THR Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain c residue 15 HIS Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 194 ASP Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 39 ASN Chi-restraints excluded: chain e residue 113 GLN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain f residue 12 GLU Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 78 ASN Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 56 ASN Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 70 MET Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 37 GLU Chi-restraints excluded: chain j residue 58 LYS Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain j residue 75 GLN Chi-restraints excluded: chain j residue 76 SER Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 24 LYS Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 52 ILE Chi-restraints excluded: chain k residue 55 THR Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain l residue 58 SER Chi-restraints excluded: chain l residue 64 GLN Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 75 LEU Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 41 GLU Chi-restraints excluded: chain p residue 80 GLU Chi-restraints excluded: chain q residue 19 ARG Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 67 THR Chi-restraints excluded: chain s residue 24 TYR Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain u residue 24 GLN Chi-restraints excluded: chain u residue 37 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 619 optimal weight: 3.9990 chunk 998 optimal weight: 30.0000 chunk 609 optimal weight: 7.9990 chunk 473 optimal weight: 5.9990 chunk 693 optimal weight: 40.0000 chunk 1047 optimal weight: 0.0980 chunk 963 optimal weight: 20.0000 chunk 833 optimal weight: 40.0000 chunk 86 optimal weight: 3.9990 chunk 644 optimal weight: 7.9990 chunk 511 optimal weight: 30.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 520 ASN 0 534 ASN ** I 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN N 4 GLN ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS d 122 GLN ** e 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 113 GLN f 135 ASN j 50 GLN k 20 GLN ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN n 50 ASN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 3 ASN u 21 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 159815 Z= 0.178 Angle : 0.552 23.737 238703 Z= 0.288 Chirality : 0.035 1.910 30482 Planarity : 0.004 0.063 13023 Dihedral : 23.178 178.862 78643 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.18 % Allowed : 19.86 % Favored : 77.96 % 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: 0.78 (0.11), residues: 6001 helix: 1.76 (0.11), residues: 2071 sheet: 0.04 (0.15), residues: 1198 loop : -0.14 (0.12), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 108 HIS 0.014 0.001 HIS c 15 PHE 0.036 0.002 PHE c 16 TYR 0.022 0.001 TYR Z 6 ARG 0.015 0.000 ARG 5 24 ********************** 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 790 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 678 time to evaluate : 7.160 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 74 MET cc_start: 0.7543 (pmm) cc_final: 0.7074 (pmm) REVERT: 0 121 TRP cc_start: 0.8665 (m100) cc_final: 0.8428 (m100) REVERT: 0 139 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7663 (mp) REVERT: 0 220 GLN cc_start: 0.8779 (mt0) cc_final: 0.8463 (mt0) REVERT: 1 9 LEU cc_start: 0.9225 (mt) cc_final: 0.8933 (mp) REVERT: 3 33 GLU cc_start: 0.8528 (pm20) cc_final: 0.8137 (pm20) REVERT: 8 24 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8338 (mtt) REVERT: F 120 MET cc_start: 0.7594 (ptt) cc_final: 0.6459 (ppp) REVERT: F 137 MET cc_start: 0.8098 (mmm) cc_final: 0.7817 (mmm) REVERT: F 164 ARG cc_start: 0.8698 (ttt180) cc_final: 0.8453 (mtp180) REVERT: F 211 ASN cc_start: 0.7773 (t0) cc_final: 0.7482 (t0) REVERT: I 27 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8322 (tp30) REVERT: I 149 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8614 (p0) REVERT: J 38 MET cc_start: 0.8633 (ttm) cc_final: 0.8358 (mtp) REVERT: J 78 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.7764 (ttp80) REVERT: J 83 MET cc_start: 0.8975 (mmm) cc_final: 0.8557 (mtp) REVERT: J 175 MET cc_start: 0.7632 (mmt) cc_final: 0.7208 (mmm) REVERT: K 104 THR cc_start: 0.9005 (m) cc_final: 0.8684 (p) REVERT: M 80 MET cc_start: 0.8827 (mtp) cc_final: 0.8592 (mtp) REVERT: M 99 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8013 (ttm110) REVERT: N 110 ASN cc_start: 0.8930 (t0) cc_final: 0.8569 (t0) REVERT: Q 79 SER cc_start: 0.7651 (t) cc_final: 0.7350 (m) REVERT: R 1 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7309 (ttm) REVERT: R 109 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8054 (mm-30) REVERT: T 51 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.7005 (mtm-85) REVERT: T 89 ASP cc_start: 0.8164 (t0) cc_final: 0.7450 (t0) REVERT: V 53 GLU cc_start: 0.8484 (tt0) cc_final: 0.8284 (tm-30) REVERT: V 70 ASP cc_start: 0.8139 (t0) cc_final: 0.7911 (t70) REVERT: X 45 GLN cc_start: 0.8448 (tp40) cc_final: 0.8067 (mp10) REVERT: c 57 MET cc_start: 0.8770 (mmm) cc_final: 0.8466 (mmt) REVERT: c 90 TYR cc_start: 0.8072 (m-80) cc_final: 0.7699 (m-10) REVERT: e 60 MET cc_start: 0.8772 (tpp) cc_final: 0.8382 (tpp) REVERT: g 59 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7843 (mmm-85) REVERT: h 66 MET cc_start: 0.7689 (tpp) cc_final: 0.7275 (tpp) REVERT: h 70 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7739 (mtm) REVERT: h 142 HIS cc_start: 0.8578 (m-70) cc_final: 0.8092 (m90) REVERT: j 46 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8353 (tm-30) REVERT: j 50 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: j 110 MET cc_start: 0.8680 (mmt) cc_final: 0.8427 (tpp) REVERT: j 126 GLN cc_start: 0.7741 (tt0) cc_final: 0.7481 (tt0) REVERT: k 24 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8133 (tttm) REVERT: k 66 GLU cc_start: 0.7958 (pt0) cc_final: 0.7607 (pm20) REVERT: l 20 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.7537 (p) REVERT: l 34 ILE cc_start: 0.8157 (tp) cc_final: 0.7592 (pp) REVERT: l 56 LYS cc_start: 0.9127 (tppt) cc_final: 0.8920 (tppp) REVERT: l 64 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8926 (tm-30) REVERT: l 68 GLU cc_start: 0.9089 (tt0) cc_final: 0.8411 (tm-30) REVERT: l 72 LYS cc_start: 0.8763 (mmpt) cc_final: 0.8443 (mmpt) REVERT: m 125 GLN cc_start: 0.8796 (mt0) cc_final: 0.8509 (mt0) REVERT: n 36 ASN cc_start: 0.9447 (m110) cc_final: 0.9140 (p0) REVERT: n 66 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8407 (mm-30) REVERT: p 13 LYS cc_start: 0.9311 (mppt) cc_final: 0.9058 (mmtm) REVERT: p 34 GLU cc_start: 0.9041 (tp30) cc_final: 0.8600 (mm-30) REVERT: p 41 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8297 (mm-30) REVERT: q 19 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8813 (mmm-85) REVERT: q 58 ASP cc_start: 0.9072 (t70) cc_final: 0.8838 (t0) REVERT: q 73 ILE cc_start: 0.9160 (mp) cc_final: 0.8757 (mp) REVERT: q 77 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8190 (mp0) REVERT: r 83 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7817 (tm-30) REVERT: s 34 LYS cc_start: 0.8779 (mtpm) cc_final: 0.8301 (mtmp) REVERT: t 44 PHE cc_start: 0.8960 (m-10) cc_final: 0.8413 (m-80) REVERT: t 66 MET cc_start: 0.7859 (ptp) cc_final: 0.7289 (pmm) REVERT: u 51 ASN cc_start: 0.8706 (m-40) cc_final: 0.8412 (m-40) outliers start: 112 outliers final: 79 residues processed: 746 average time/residue: 2.0536 time to fit residues: 2264.0597 Evaluate side-chains 739 residues out of total 5145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 646 time to evaluate : 6.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 139 LEU Chi-restraints excluded: chain 0 residue 216 ASP Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 346 TYR Chi-restraints excluded: chain 0 residue 534 ASN Chi-restraints excluded: chain 3 residue 45 LEU Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 5 residue 47 GLU Chi-restraints excluded: chain 8 residue 24 MET Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 49 ASN Chi-restraints excluded: chain J residue 115 HIS Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 99 ARG Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 54 LYS Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain T residue 115 ASP Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 79 THR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain c residue 154 MET Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 194 ASP Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 39 ASN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain f residue 160 SER Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 78 ASN Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 56 ASN Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 70 MET Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain j residue 37 GLU Chi-restraints excluded: chain j residue 50 GLN Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 75 GLN Chi-restraints excluded: chain j residue 76 SER Chi-restraints excluded: chain k residue 24 LYS Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 58 SER Chi-restraints excluded: chain l residue 64 GLN Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 75 LEU Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 41 GLU Chi-restraints excluded: chain p residue 80 GLU Chi-restraints excluded: chain q residue 19 ARG Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 67 THR Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain u residue 24 GLN Chi-restraints excluded: chain u residue 37 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 662 optimal weight: 20.0000 chunk 888 optimal weight: 0.8980 chunk 255 optimal weight: 30.0000 chunk 768 optimal weight: 30.0000 chunk 123 optimal weight: 40.0000 chunk 231 optimal weight: 20.0000 chunk 835 optimal weight: 20.0000 chunk 349 optimal weight: 20.0000 chunk 857 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 overall best weight: 13.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 342 HIS ** 0 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 534 ASN I 141 GLN I 145 ASN ** I 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 99 HIS ** e 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 117 HIS f 135 ASN j 50 GLN k 20 GLN ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 3 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.043991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031782 restraints weight = 842553.422| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.50 r_work: 0.2640 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 159815 Z= 0.443 Angle : 0.645 23.918 238703 Z= 0.334 Chirality : 0.042 1.893 30482 Planarity : 0.005 0.059 13023 Dihedral : 23.090 179.660 78643 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.37 % Allowed : 19.90 % Favored : 77.73 % 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: 0.59 (0.11), residues: 6001 helix: 1.55 (0.11), residues: 2072 sheet: -0.04 (0.15), residues: 1182 loop : -0.22 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP F 108 HIS 0.007 0.001 HIS c 15 PHE 0.034 0.002 PHE h 62 TYR 0.025 0.002 TYR Z 6 ARG 0.016 0.001 ARG 5 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38512.24 seconds wall clock time: 675 minutes 16.59 seconds (40516.59 seconds total)