Starting phenix.real_space_refine on Wed Feb 21 13:55:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3k_13180/02_2024/7p3k_13180_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3k_13180/02_2024/7p3k_13180.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3k_13180/02_2024/7p3k_13180_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3k_13180/02_2024/7p3k_13180_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3k_13180/02_2024/7p3k_13180_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3k_13180/02_2024/7p3k_13180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3k_13180/02_2024/7p3k_13180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3k_13180/02_2024/7p3k_13180_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3k_13180/02_2024/7p3k_13180_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 sd= 0.223 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 Zn 2 6.06 5 P 4469 5.49 5 Mg 308 5.21 5 S 147 5.16 5 Cl 2 4.86 5 C 70233 2.51 5 N 26089 2.21 5 O 38804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 114": "OD1" <-> "OD2" Residue "p TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 140054 Number of models: 1 Model: "" Number of chains: 63 Chain: "A" Number of atoms: 32611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32611 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 121, 'rna2p_pyr': 81, 'rna3p': 9, 'rna3p_pur': 742, 'rna3p_pyr': 565} Link IDs: {'rna2p': 203, 'rna3p': 1315} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "a" Number of atoms: 59130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 6, 'rna2p_pur': 266, 'rna2p_pyr': 139, 'rna3p': 17, 'rna3p_pur': 1319, 'rna3p_pyr': 1006} Link IDs: {'rna2p': 410, 'rna3p': 2342} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 586 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "X" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "V" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1609 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 64} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Unusual residues: {' MG': 93} Classifications: {'undetermined': 93} Link IDs: {None: 92} Chain: "a" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 226 Unusual residues: {' MG': 206, 'CLM': 1} Classifications: {'undetermined': 207} Link IDs: {None: 206} Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0STQ SG CYS 3 11 71.021 149.627 159.786 1.00 38.77 S ATOM A0SUF SG CYS 3 14 70.898 148.945 156.085 1.00 34.24 S ATOM A0SXA SG CYS 3 27 72.515 152.076 157.371 1.00 35.79 S ATOM A0T3D SG CYS 4 16 63.345 48.643 206.941 1.00 53.49 S ATOM A0T3P SG CYS 4 18 60.362 49.108 209.354 1.00 53.38 S ATOM A0T7N SG CYS 4 37 60.424 50.617 206.019 1.00 51.87 S ATOM A0T88 SG CYS 4 40 62.746 52.049 208.698 1.00 53.39 S Time building chain proxies: 49.91, per 1000 atoms: 0.36 Number of scatterers: 140054 At special positions: 0 Unit cell: (231.504, 241.332, 286.104, 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 2 29.99 Cl 2 17.00 S 147 16.00 P 4469 15.00 Mg 308 11.99 O 38804 8.00 N 26089 7.00 C 70233 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: 56.41 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 37 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " Number of angles added : 9 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10262 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: 172 helices and 67 sheets defined 39.2% alpha, 19.8% beta 1581 base pairs and 2493 stacking pairs defined. Time for finding SS restraints: 72.69 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.632A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 6.816A pdb=" N THR B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 12 Processing helix chain 'C' and resid 28 through 48 Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 113 removed outlier: 5.116A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'D' and resid 7 through 16 Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 5.213A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 110 through 121 Processing helix chain 'D' and resid 146 through 153 removed outlier: 4.628A pdb=" N GLN D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N SER D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 166 removed outlier: 4.775A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 4.899A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 206 Processing helix chain 'E' and resid 55 through 71 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 14 through 33 removed outlier: 3.656A pdb=" N VAL F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Proline residue: F 19 - end of helix Processing helix chain 'F' and resid 67 through 82 removed outlier: 5.531A pdb=" N ASP F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 57 through 70 Processing helix chain 'G' and resid 92 through 112 removed outlier: 5.660A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 149 Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 112 through 120 Processing helix chain 'I' and resid 34 through 40 removed outlier: 4.465A pdb=" N GLY I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 33 Processing helix chain 'J' and resid 80 through 90 Processing helix chain 'K' and resid 46 through 51 Processing helix chain 'K' and resid 54 through 59 removed outlier: 4.253A pdb=" N THR K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 76 removed outlier: 4.768A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 104 Processing helix chain 'L' and resid 3 through 11 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 113 through 118 Processing helix chain 'M' and resid 14 through 22 removed outlier: 4.258A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 44 through 49 removed outlier: 5.230A pdb=" N SER M 49 " --> pdb=" O ILE M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 64 removed outlier: 4.374A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 52 Proline residue: N 52 - end of helix Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 Processing helix chain 'O' and resid 49 through 74 Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 Processing helix chain 'R' and resid 11 through 17 Processing helix chain 'R' and resid 25 through 34 removed outlier: 5.449A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 70 through 76 Proline residue: S 76 - end of helix Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 65 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 37 removed outlier: 4.992A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 4.524A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 17 removed outlier: 4.797A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL c 16 " --> pdb=" O GLY c 12 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL c 17 " --> pdb=" O ARG c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 131 through 136 Proline residue: c 136 - end of helix Processing helix chain 'c' and resid 197 through 203 removed outlier: 4.774A pdb=" N MET c 201 " --> pdb=" O ASN c 197 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU c 202 " --> pdb=" O ALA c 198 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG c 203 " --> pdb=" O GLU c 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 197 through 203' Processing helix chain 'c' and resid 207 through 215 Processing helix chain 'c' and resid 221 through 226 removed outlier: 4.997A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 260 through 268 removed outlier: 4.657A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.927A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 Processing helix chain 'd' and resid 97 through 103 removed outlier: 4.609A pdb=" N PHE d 101 " --> pdb=" O SER d 97 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'e' and resid 24 through 41 removed outlier: 5.764A pdb=" N GLN e 41 " --> pdb=" O ALA e 37 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.899A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'e' and resid 16 through 21 removed outlier: 3.863A pdb=" N ARG e 21 " --> pdb=" O GLU e 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 16 through 21' Processing helix chain 'f' and resid 2 through 21 removed outlier: 5.237A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 29 Proline residue: f 29 - end of helix Processing helix chain 'f' and resid 42 through 47 Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 93 through 111 removed outlier: 5.228A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 Processing helix chain 'f' and resid 134 through 139 Proline residue: f 139 - end of helix Processing helix chain 'g' and resid 2 through 8 Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 5.462A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 Processing helix chain 'h' and resid 22 through 29 removed outlier: 3.524A pdb=" N PHE h 29 " --> pdb=" O TYR h 25 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 38 Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 123 removed outlier: 5.489A pdb=" N LYS i 123 " --> pdb=" O PHE i 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 109 removed outlier: 4.637A pdb=" N ARG j 108 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N SER j 109 " --> pdb=" O ARG j 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 104 through 109' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 5.684A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 62 Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 5.617A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 Processing helix chain 'k' and resid 91 through 99 Processing helix chain 'k' and resid 128 through 139 Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 Proline residue: l 125 - end of helix Processing helix chain 'm' and resid 13 through 32 Processing helix chain 'm' and resid 38 through 58 Proline residue: m 50 - end of helix removed outlier: 4.575A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 Processing helix chain 'm' and resid 72 through 88 removed outlier: 4.881A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix Processing helix chain 'n' and resid 2 through 22 removed outlier: 4.605A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 5.104A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 Processing helix chain 'n' and resid 101 through 114 Processing helix chain 'o' and resid 2 through 13 Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.800A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) Processing helix chain 'p' and resid 6 through 22 Processing helix chain 'p' and resid 26 through 31 Processing helix chain 'p' and resid 32 through 37 Processing helix chain 'p' and resid 39 through 73 Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 Processing helix chain 'r' and resid 13 through 25 Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 Processing helix chain 'r' and resid 65 through 70 removed outlier: 3.725A pdb=" N LEU r 69 " --> pdb=" O ASP r 65 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LYS r 70 " --> pdb=" O ILE r 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 65 through 70' Processing helix chain 's' and resid 3 through 12 removed outlier: 6.067A pdb=" N ARG s 12 " --> pdb=" O LEU s 8 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 Processing helix chain 's' and resid 39 through 50 Processing helix chain 't' and resid 66 through 71 removed outlier: 5.162A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) Processing helix chain 'u' and resid 13 through 24 Processing helix chain 'u' and resid 43 through 52 Processing helix chain 'u' and resid 53 through 59 removed outlier: 4.726A pdb=" N TYR u 57 " --> pdb=" O LYS u 53 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 9 removed outlier: 4.153A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) Processing helix chain 'x' and resid 10 through 35 Processing helix chain 'x' and resid 39 through 62 removed outlier: 4.435A pdb=" N LEU x 43 " --> pdb=" O GLN x 39 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.889A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 5.133A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 Processing helix chain '2' and resid 32 through 37 removed outlier: 5.351A pdb=" N ALA 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 38 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.786A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 65 Processing sheet with id= 1, first strand: chain 'B' and resid 15 through 18 removed outlier: 5.307A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.501A pdb=" N PHE B 90 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 53 through 59 Processing sheet with id= 4, first strand: chain 'C' and resid 164 through 169 removed outlier: 5.833A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 141 through 145 removed outlier: 6.809A pdb=" N MET D 178 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 12 through 16 removed outlier: 7.016A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 84 through 88 removed outlier: 6.290A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 33 through 40 Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 43 removed outlier: 5.986A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 44 through 47 removed outlier: 6.979A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.497A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.829A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.694A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 5 through 11 Processing sheet with id= 15, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.638A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 17, first strand: chain 'K' and resid 42 through 45 removed outlier: 3.939A pdb=" N ASN K 29 " --> pdb=" O SER K 26 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 29 through 33 removed outlier: 5.217A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 36 through 41 removed outlier: 5.138A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'P' and resid 4 through 10 removed outlier: 6.991A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Q' and resid 7 through 12 removed outlier: 4.480A pdb=" N ASP Q 57 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'S' and resid 30 through 34 Processing sheet with id= 24, first strand: chain 'c' and resid 33 through 36 No H-bonds generated for sheet with id= 24 Processing sheet with id= 25, first strand: chain 'c' and resid 80 through 83 removed outlier: 6.746A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.105A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE c 164 " --> pdb=" O SER c 139 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'c' and resid 91 through 96 removed outlier: 4.434A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'd' and resid 11 through 16 removed outlier: 6.914A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 79 through 84 removed outlier: 5.735A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 179 through 182 Processing sheet with id= 31, first strand: chain 'd' and resid 24 through 28 Processing sheet with id= 32, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.531A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'e' and resid 1 through 6 removed outlier: 4.302A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.855A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'f' and resid 65 through 69 removed outlier: 5.838A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'g' and resid 15 through 20 removed outlier: 6.369A pdb=" N GLN g 22 " --> pdb=" O LEU g 37 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY g 31 " --> pdb=" O GLY g 28 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'g' and resid 41 through 44 removed outlier: 5.224A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'g' and resid 94 through 99 removed outlier: 6.853A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'g' and resid 121 through 125 removed outlier: 6.060A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'h' and resid 16 through 20 removed outlier: 5.759A pdb=" N LYS h 35 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'i' and resid 52 through 57 removed outlier: 4.946A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.285A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'j' and resid 18 through 21 removed outlier: 5.877A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'k' and resid 120 through 123 removed outlier: 3.580A pdb=" N LYS k 141 " --> pdb=" O VAL k 120 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'l' and resid 62 through 66 removed outlier: 6.408A pdb=" N LEU l 102 " --> pdb=" O ARG l 66 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.209A pdb=" N ARG m 103 " --> pdb=" O ASN m 107 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY m 101 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA m 111 " --> pdb=" O LYS m 99 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS m 99 " --> pdb=" O ALA m 111 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE m 113 " --> pdb=" O ILE m 97 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE m 97 " --> pdb=" O ILE m 113 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU m 115 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR m 95 " --> pdb=" O LEU m 115 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'n' and resid 49 through 53 removed outlier: 6.848A pdb=" N ILE n 35 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.620A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'o' and resid 49 through 53 removed outlier: 4.647A pdb=" N ARG o 53 " --> pdb=" O HIS o 56 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N HIS o 56 " --> pdb=" O ARG o 53 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'q' and resid 11 through 15 removed outlier: 7.090A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'q' and resid 17 through 22 removed outlier: 6.589A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU q 31 " --> pdb=" O VAL q 63 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 53, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 54, first strand: chain 'q' and resid 69 through 78 removed outlier: 5.556A pdb=" N GLU q 70 " --> pdb=" O GLN q 91 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLN q 91 " --> pdb=" O GLU q 70 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 56, first strand: chain 's' and resid 28 through 34 removed outlier: 6.005A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 't' and resid 83 through 87 Processing sheet with id= 58, first strand: chain 'u' and resid 69 through 72 Processing sheet with id= 59, first strand: chain 'v' and resid 51 through 54 Processing sheet with id= 60, first strand: chain 'v' and resid 66 through 71 Processing sheet with id= 61, first strand: chain 'w' and resid 12 through 19 removed outlier: 3.592A pdb=" N ARG w 27 " --> pdb=" O GLY w 15 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER w 19 " --> pdb=" O ASN w 23 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'w' and resid 35 through 41 Processing sheet with id= 63, first strand: chain 'y' and resid 33 through 39 removed outlier: 7.574A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '0' and resid 19 through 26 removed outlier: 6.618A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '2' and resid 22 through 25 removed outlier: 5.578A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '3' and resid 1 through 5 removed outlier: 5.295A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '4' and resid 20 through 25 2054 hydrogen bonds defined for protein. 6039 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3966 hydrogen bonds 6138 hydrogen bond angles 0 basepair planarities 1581 basepair parallelities 2493 stacking parallelities Total time for adding SS restraints: 284.51 Time building geometry restraints manager: 61.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 11349 1.29 - 1.42: 67647 1.42 - 1.55: 63648 1.55 - 1.69: 8941 1.69 - 1.82: 266 Bond restraints: 151851 Sorted by residual: bond pdb=" N9 CLM a6206 " pdb=" O9A CLM a6206 " ideal model delta sigma weight residual 1.209 1.397 -0.188 2.00e-02 2.50e+03 8.82e+01 bond pdb=" C5 U a2449 " pdb=" C6 U a2449 " ideal model delta sigma weight residual 1.337 1.486 -0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" CA VAL F 18 " pdb=" CB VAL F 18 " ideal model delta sigma weight residual 1.534 1.575 -0.041 6.80e-03 2.16e+04 3.63e+01 bond pdb=" C2 U a2449 " pdb=" N3 U a2449 " ideal model delta sigma weight residual 1.373 1.483 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C1' C X 16 " pdb=" N1 C X 16 " ideal model delta sigma weight residual 1.480 1.551 -0.071 1.50e-02 4.44e+03 2.25e+01 ... (remaining 151846 not shown) Histogram of bond angle deviations from ideal: 96.06 - 105.29: 21528 105.29 - 114.51: 102489 114.51 - 123.73: 81260 123.73 - 132.96: 21714 132.96 - 142.18: 140 Bond angle restraints: 227131 Sorted by residual: angle pdb=" C1' G7M a2069 " pdb=" N9 G7M a2069 " pdb=" C8 G7M a2069 " ideal model delta sigma weight residual 94.96 125.24 -30.28 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 126.90 -20.58 3.00e+00 1.11e-01 4.70e+01 angle pdb=" C1' G7M a2069 " pdb=" N9 G7M a2069 " pdb=" C4 G7M a2069 " ideal model delta sigma weight residual 142.80 125.38 17.42 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C3' G a2505 " pdb=" O3' G a2505 " pdb=" P U a2506 " ideal model delta sigma weight residual 120.20 128.82 -8.62 1.50e+00 4.44e-01 3.30e+01 angle pdb=" C GLU M 66 " pdb=" CA GLU M 66 " pdb=" CB GLU M 66 " ideal model delta sigma weight residual 117.23 109.50 7.73 1.36e+00 5.41e-01 3.23e+01 ... (remaining 227126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 86481 35.98 - 71.96: 9583 71.96 - 107.93: 1109 107.93 - 143.91: 10 143.91 - 179.89: 10 Dihedral angle restraints: 97193 sinusoidal: 81283 harmonic: 15910 Sorted by residual: dihedral pdb=" CA ASP g 47 " pdb=" C ASP g 47 " pdb=" N ASN g 48 " pdb=" CA ASN g 48 " ideal model delta harmonic sigma weight residual -180.00 -116.72 -63.28 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" O4' U a1779 " pdb=" C1' U a1779 " pdb=" N1 U a1779 " pdb=" C2 U a1779 " ideal model delta sinusoidal sigma weight residual 200.00 48.35 151.65 1 1.50e+01 4.44e-03 8.02e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 52.78 147.22 1 1.50e+01 4.44e-03 7.85e+01 ... (remaining 97190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 27438 0.099 - 0.198: 1402 0.198 - 0.296: 69 0.296 - 0.395: 9 0.395 - 0.494: 1 Chirality restraints: 28919 Sorted by residual: chirality pdb=" C1* PSU a2580 " pdb=" O4* PSU a2580 " pdb=" C2* PSU a2580 " pdb=" C5 PSU a2580 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" C1* PSU A 516 " pdb=" O4* PSU A 516 " pdb=" C2* PSU A 516 " pdb=" C5 PSU A 516 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C3' U a2506 " pdb=" C4' U a2506 " pdb=" O3' U a2506 " pdb=" C2' U a2506 " both_signs ideal model delta sigma weight residual False -2.48 -2.81 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 28916 not shown) Planarity restraints: 12165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.064 2.00e-02 2.50e+03 5.97e-01 8.02e+03 pdb=" C4' 5MC A1407 " -0.444 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.601 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.651 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.172 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -0.989 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.220 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.907 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.062 2.00e-02 2.50e+03 5.81e-01 7.59e+03 pdb=" C4' 2MG A1516 " -0.425 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.556 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.592 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.627 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.170 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -0.981 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.233 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.867 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG a2251 " -0.014 2.00e-02 2.50e+03 5.72e-01 7.37e+03 pdb=" C4' OMG a2251 " -0.434 2.00e-02 2.50e+03 pdb=" O4' OMG a2251 " -0.697 2.00e-02 2.50e+03 pdb=" C3' OMG a2251 " 0.597 2.00e-02 2.50e+03 pdb=" O3' OMG a2251 " 0.546 2.00e-02 2.50e+03 pdb=" C2' OMG a2251 " 0.231 2.00e-02 2.50e+03 pdb=" O2' OMG a2251 " -0.878 2.00e-02 2.50e+03 pdb=" C1' OMG a2251 " -0.217 2.00e-02 2.50e+03 pdb=" N9 OMG a2251 " 0.866 2.00e-02 2.50e+03 ... (remaining 12162 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 730 2.48 - 3.08: 84665 3.08 - 3.69: 253534 3.69 - 4.29: 394995 4.29 - 4.90: 540331 Nonbonded interactions: 1274255 Sorted by model distance: nonbonded pdb=" O2 C A 720 " pdb=" NZ LYS R 60 " model vdw 1.871 2.520 nonbonded pdb=" O2 C a 335 " pdb=" OG SER t 68 " model vdw 1.983 2.440 nonbonded pdb=" OP2 G a 370 " pdb="MG MG a6065 " model vdw 1.986 2.170 nonbonded pdb=" OP2 A a 422 " pdb="MG MG a6065 " model vdw 1.987 2.170 nonbonded pdb=" O2 C a2499 " pdb="MG MG a6059 " model vdw 1.989 2.170 ... (remaining 1274250 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: 5.450 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: 0.160 Extract box with map and model: 21.580 Check model and map are aligned: 1.350 Set scattering table: 0.880 Process input model: 581.970 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.380 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: 0.030 Load rotamer database and sin/cos tables:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 628.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.007 0.188 151851 Z= 0.436 Angle : 0.827 30.280 227131 Z= 0.424 Chirality : 0.047 0.494 28919 Planarity : 0.018 0.597 12165 Dihedral : 22.406 179.890 86931 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.46 % Favored : 96.43 % Rotamer: Outliers : 0.09 % Allowed : 0.42 % Favored : 99.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.61 (0.11), residues: 5484 helix: 0.15 (0.11), residues: 1969 sheet: -0.21 (0.15), residues: 1085 loop : -0.86 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 201 HIS 0.022 0.002 HIS l 13 PHE 0.033 0.002 PHE S 74 TYR 0.052 0.003 TYR 0 49 ARG 0.021 0.001 ARG c 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1724 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1720 time to evaluate : 5.832 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: B 72 THR cc_start: 0.7232 (m) cc_final: 0.6947 (p) REVERT: D 9 LEU cc_start: 0.5803 (mt) cc_final: 0.5540 (mp) REVERT: D 154 ARG cc_start: 0.5100 (mpt180) cc_final: 0.3740 (ttp-170) REVERT: E 112 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7803 (ttm-80) REVERT: H 2 SER cc_start: 0.8065 (p) cc_final: 0.7813 (t) REVERT: H 101 ILE cc_start: 0.8801 (pt) cc_final: 0.8428 (pt) REVERT: H 111 MET cc_start: 0.8091 (ptp) cc_final: 0.7848 (ptm) REVERT: L 111 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7110 (ttpt) REVERT: O 65 LYS cc_start: 0.8688 (mttt) cc_final: 0.8432 (mtmt) REVERT: O 84 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7569 (mtp180) REVERT: S 66 MET cc_start: 0.5947 (tmm) cc_final: 0.5150 (tmm) REVERT: d 167 ASN cc_start: 0.8404 (t0) cc_final: 0.8154 (t0) REVERT: e 115 GLN cc_start: 0.7196 (mt0) cc_final: 0.6894 (mt0) REVERT: f 52 ASN cc_start: 0.7969 (m110) cc_final: 0.7608 (m-40) REVERT: m 45 ARG cc_start: 0.7488 (mtm180) cc_final: 0.7055 (ttp80) REVERT: p 76 TYR cc_start: 0.8665 (t80) cc_final: 0.8449 (t80) REVERT: r 30 SER cc_start: 0.8427 (p) cc_final: 0.8086 (p) REVERT: r 34 ASP cc_start: 0.6576 (m-30) cc_final: 0.6308 (m-30) REVERT: x 16 THR cc_start: 0.8559 (t) cc_final: 0.8223 (p) REVERT: z 11 SER cc_start: 0.8707 (t) cc_final: 0.8453 (m) REVERT: z 15 MET cc_start: 0.8227 (mtt) cc_final: 0.7985 (mtm) outliers start: 4 outliers final: 5 residues processed: 1721 average time/residue: 2.2474 time to fit residues: 5389.8021 Evaluate side-chains 1109 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1104 time to evaluate : 5.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain e residue 152 GLU Chi-restraints excluded: chain l residue 65 ILE Chi-restraints excluded: chain y residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 827 optimal weight: 1.9990 chunk 742 optimal weight: 0.3980 chunk 412 optimal weight: 8.9990 chunk 253 optimal weight: 7.9990 chunk 501 optimal weight: 3.9990 chunk 396 optimal weight: 10.0000 chunk 768 optimal weight: 3.9990 chunk 297 optimal weight: 0.9980 chunk 467 optimal weight: 4.9990 chunk 571 optimal weight: 4.9990 chunk 889 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 103 ASN B 177 ASN B 203 ASN C 19 ASN D 71 GLN E 19 ASN E 89 HIS G 153 HIS I 126 GLN J 99 GLN K 29 ASN K 101 ASN N 62 ASN O 62 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN T 21 ASN T 70 ASN c 37 ASN c 53 HIS c 86 ASN c 117 GLN c 251 GLN d 173 GLN e 41 GLN e 136 GLN e 195 GLN g 30 ASN ** g 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 67 ASN j 3 GLN m 11 ASN m 13 ASN n 29 HIS n 104 GLN o 12 GLN p 37 GLN p 52 GLN p 59 GLN q 91 GLN s 15 HIS x 31 GLN x 45 GLN z 4 GLN 0 45 GLN 3 35 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 151851 Z= 0.195 Angle : 0.608 15.257 227131 Z= 0.329 Chirality : 0.034 0.403 28919 Planarity : 0.006 0.129 12165 Dihedral : 22.746 178.374 75904 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.21 % Favored : 96.75 % Rotamer: Outliers : 4.17 % Allowed : 18.40 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.11), residues: 5484 helix: 1.14 (0.12), residues: 1961 sheet: -0.13 (0.15), residues: 1072 loop : -0.63 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.010 0.001 HIS l 13 PHE 0.026 0.002 PHE S 74 TYR 0.024 0.002 TYR p 47 ARG 0.010 0.001 ARG 1 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1210 time to evaluate : 5.835 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: B 10 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7639 (mm) REVERT: C 138 VAL cc_start: 0.7438 (t) cc_final: 0.6691 (t) REVERT: C 187 SER cc_start: 0.8432 (t) cc_final: 0.7944 (t) REVERT: D 154 ARG cc_start: 0.5110 (mpt180) cc_final: 0.4060 (ptm160) REVERT: E 64 MET cc_start: 0.7540 (mmm) cc_final: 0.7295 (mmp) REVERT: E 65 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6688 (tp30) REVERT: E 69 ARG cc_start: 0.7752 (mtm110) cc_final: 0.7546 (mtp-110) REVERT: F 14 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: H 2 SER cc_start: 0.8621 (p) cc_final: 0.8316 (t) REVERT: H 50 LYS cc_start: 0.7776 (pptt) cc_final: 0.7387 (ptmm) REVERT: I 63 LEU cc_start: 0.8667 (mt) cc_final: 0.8454 (mp) REVERT: K 68 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7497 (mt-10) REVERT: L 54 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6947 (tpp-160) REVERT: M 104 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8581 (m) REVERT: O 38 HIS cc_start: 0.8080 (t70) cc_final: 0.7842 (t-90) REVERT: P 63 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.6694 (mp10) REVERT: c 188 CYS cc_start: 0.8136 (m) cc_final: 0.7778 (m) REVERT: c 255 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8103 (tttp) REVERT: f 94 GLU cc_start: 0.6436 (tm-30) cc_final: 0.6076 (tm-30) REVERT: i 31 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: l 75 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7385 (mm-30) REVERT: n 21 LEU cc_start: 0.8808 (mt) cc_final: 0.8529 (mt) REVERT: o 44 GLU cc_start: 0.6338 (tt0) cc_final: 0.6056 (tt0) REVERT: p 76 TYR cc_start: 0.8833 (t80) cc_final: 0.8586 (t80) REVERT: u 12 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: v 25 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7483 (mtp85) REVERT: y 21 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8729 (mtmt) REVERT: z 15 MET cc_start: 0.8325 (mtt) cc_final: 0.8110 (mtm) outliers start: 191 outliers final: 76 residues processed: 1292 average time/residue: 2.1367 time to fit residues: 3912.6478 Evaluate side-chains 1165 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1080 time to evaluate : 5.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 133 ARG Chi-restraints excluded: chain c residue 187 ASP Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 255 LYS Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 31 GLU Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 10 GLU Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 113 ILE Chi-restraints excluded: chain o residue 83 SER Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain s residue 21 SER Chi-restraints excluded: chain s residue 25 GLU Chi-restraints excluded: chain s residue 49 LYS Chi-restraints excluded: chain s residue 50 LEU Chi-restraints excluded: chain s residue 78 SER Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain v residue 25 ARG Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain y residue 48 ILE Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 30 VAL Chi-restraints excluded: chain 0 residue 23 THR Chi-restraints excluded: chain 3 residue 7 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 494 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 chunk 740 optimal weight: 2.9990 chunk 606 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 891 optimal weight: 10.0000 chunk 963 optimal weight: 2.9990 chunk 794 optimal weight: 0.0870 chunk 884 optimal weight: 0.9990 chunk 303 optimal weight: 10.0000 chunk 715 optimal weight: 10.0000 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN C 3 GLN D 59 GLN E 19 ASN E 78 ASN E 82 GLN G 153 HIS J 99 GLN K 101 ASN L 73 ASN N 49 GLN N 62 ASN O 62 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 HIS T 21 ASN c 117 GLN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN e 195 GLN f 52 ASN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 HIS g 116 GLN m 23 ASN m 107 ASN n 61 GLN n 104 GLN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 71 GLN q 6 GLN r 31 GLN s 28 ASN x 31 GLN 0 45 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 151851 Z= 0.265 Angle : 0.627 13.810 227131 Z= 0.337 Chirality : 0.036 0.401 28919 Planarity : 0.006 0.140 12165 Dihedral : 22.767 179.883 75894 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 5.09 % Allowed : 20.06 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.11), residues: 5484 helix: 1.49 (0.12), residues: 1949 sheet: 0.04 (0.15), residues: 1060 loop : -0.54 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 42 HIS 0.007 0.001 HIS l 13 PHE 0.025 0.002 PHE S 74 TYR 0.024 0.002 TYR p 47 ARG 0.010 0.001 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1141 time to evaluate : 5.376 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: B 10 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7959 (mm) REVERT: B 169 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6979 (mm-30) REVERT: B 175 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7946 (tt0) REVERT: C 42 TYR cc_start: 0.8174 (t80) cc_final: 0.7972 (t80) REVERT: D 128 ARG cc_start: 0.5043 (OUTLIER) cc_final: 0.4841 (ttp-170) REVERT: D 143 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8230 (t) REVERT: D 154 ARG cc_start: 0.5600 (mpt180) cc_final: 0.4592 (ptm160) REVERT: G 137 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8149 (ttmm) REVERT: L 88 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8475 (mmmm) REVERT: N 62 ASN cc_start: 0.8537 (m-40) cc_final: 0.8299 (m-40) REVERT: O 38 HIS cc_start: 0.8018 (t70) cc_final: 0.7758 (t-90) REVERT: P 63 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: R 24 LYS cc_start: 0.8360 (mppt) cc_final: 0.7918 (mttt) REVERT: S 37 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7952 (ttm170) REVERT: T 3 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7975 (p0) REVERT: c 185 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: c 188 CYS cc_start: 0.8056 (m) cc_final: 0.7815 (m) REVERT: c 255 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8175 (tttp) REVERT: c 270 ARG cc_start: 0.7730 (mmm160) cc_final: 0.7514 (tpt90) REVERT: e 136 GLN cc_start: 0.7801 (tp-100) cc_final: 0.7188 (tp-100) REVERT: e 176 ASP cc_start: 0.7705 (p0) cc_final: 0.7490 (p0) REVERT: f 98 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6750 (mt-10) REVERT: i 1 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6091 (pmt) REVERT: i 69 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7576 (ttt90) REVERT: i 71 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7772 (t0) REVERT: k 13 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7842 (mptp) REVERT: k 55 MET cc_start: 0.8479 (tpp) cc_final: 0.8255 (mmm) REVERT: o 44 GLU cc_start: 0.6683 (tt0) cc_final: 0.6465 (tt0) REVERT: x 23 ARG cc_start: 0.8241 (mpp80) cc_final: 0.7994 (mpp80) REVERT: 2 30 ARG cc_start: 0.8897 (mmt180) cc_final: 0.8645 (mmt180) outliers start: 233 outliers final: 97 residues processed: 1244 average time/residue: 2.1837 time to fit residues: 3865.8298 Evaluate side-chains 1151 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1040 time to evaluate : 5.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 255 LYS Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 69 ARG Chi-restraints excluded: chain i residue 71 ASP Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 113 ILE Chi-restraints excluded: chain m residue 114 GLU Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 62 ILE Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain r residue 52 GLU Chi-restraints excluded: chain s residue 11 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 17 SER Chi-restraints excluded: chain s residue 21 SER Chi-restraints excluded: chain s residue 49 LYS Chi-restraints excluded: chain s residue 50 LEU Chi-restraints excluded: chain s residue 78 SER Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 48 MET Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 17 GLU Chi-restraints excluded: chain v residue 81 SER Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 23 THR Chi-restraints excluded: chain 0 residue 24 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 880 optimal weight: 4.9990 chunk 670 optimal weight: 1.9990 chunk 462 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 425 optimal weight: 10.0000 chunk 598 optimal weight: 10.0000 chunk 894 optimal weight: 3.9990 chunk 947 optimal weight: 3.9990 chunk 467 optimal weight: 6.9990 chunk 848 optimal weight: 0.8980 chunk 255 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN E 19 ASN E 78 ASN E 82 GLN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS K 29 ASN K 101 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 GLN S 57 HIS T 20 HIS c 21 ASN c 117 GLN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN e 195 GLN f 27 GLN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 54 GLN n 61 GLN n 104 GLN o 12 GLN p 71 GLN p 72 ASN q 6 GLN v 76 ASN x 31 GLN 0 45 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 151851 Z= 0.308 Angle : 0.647 13.584 227131 Z= 0.345 Chirality : 0.038 0.397 28919 Planarity : 0.007 0.136 12165 Dihedral : 22.794 179.233 75892 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 4.94 % Allowed : 22.22 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.11), residues: 5484 helix: 1.53 (0.12), residues: 1952 sheet: 0.01 (0.15), residues: 1103 loop : -0.56 (0.12), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 42 HIS 0.006 0.001 HIS c 53 PHE 0.029 0.002 PHE S 74 TYR 0.021 0.002 TYR p 47 ARG 0.019 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1326 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1100 time to evaluate : 5.837 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: B 6 MET cc_start: 0.7533 (tmm) cc_final: 0.7328 (tpt) REVERT: B 10 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7871 (mm) REVERT: D 154 ARG cc_start: 0.5693 (mpt180) cc_final: 0.4854 (ptm160) REVERT: E 13 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6635 (mt-10) REVERT: F 88 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8010 (ttt) REVERT: G 137 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8111 (ttmm) REVERT: K 68 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7448 (mt-10) REVERT: L 54 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7146 (tpp-160) REVERT: L 73 ASN cc_start: 0.8100 (p0) cc_final: 0.7863 (p0) REVERT: O 38 HIS cc_start: 0.7998 (t70) cc_final: 0.7672 (t-90) REVERT: P 31 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7706 (ttp-170) REVERT: R 24 LYS cc_start: 0.8434 (mppt) cc_final: 0.8175 (mttt) REVERT: S 37 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7356 (ttm170) REVERT: c 185 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: c 255 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8182 (tttp) REVERT: i 1 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.5971 (pmt) REVERT: i 13 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7875 (mtt90) REVERT: i 69 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7400 (ttm110) REVERT: k 55 MET cc_start: 0.8451 (tpp) cc_final: 0.8233 (mmm) REVERT: o 110 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8666 (mt) REVERT: r 95 ARG cc_start: 0.7531 (ttm110) cc_final: 0.7175 (ttm170) REVERT: t 86 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7886 (mtm180) REVERT: z 15 MET cc_start: 0.8392 (mtt) cc_final: 0.8168 (mtm) outliers start: 226 outliers final: 117 residues processed: 1205 average time/residue: 2.1154 time to fit residues: 3633.0537 Evaluate side-chains 1161 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1032 time to evaluate : 5.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 56 GLN Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 28 MET Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 187 ASP Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 255 LYS Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 69 ARG Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 97 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 63 ILE Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 113 ILE Chi-restraints excluded: chain m residue 114 GLU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 62 ILE Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 52 GLU Chi-restraints excluded: chain s residue 11 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 21 SER Chi-restraints excluded: chain s residue 49 LYS Chi-restraints excluded: chain s residue 50 LEU Chi-restraints excluded: chain s residue 78 SER Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain t residue 86 ARG Chi-restraints excluded: chain u residue 25 LYS Chi-restraints excluded: chain u residue 48 MET Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain z residue 30 VAL Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 23 THR Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 4 residue 31 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 788 optimal weight: 6.9990 chunk 537 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 705 optimal weight: 0.8980 chunk 390 optimal weight: 10.0000 chunk 808 optimal weight: 0.7980 chunk 654 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 483 optimal weight: 7.9990 chunk 850 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN D 59 GLN D 89 ASN E 78 ASN E 82 GLN G 153 HIS L 46 ASN O 62 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 69 HIS T 20 HIS c 117 GLN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN e 195 GLN f 27 GLN ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 23 ASN n 61 GLN n 104 GLN o 12 GLN p 71 GLN q 43 ASN r 15 GLN 0 45 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 151851 Z= 0.268 Angle : 0.619 13.670 227131 Z= 0.333 Chirality : 0.036 0.390 28919 Planarity : 0.006 0.134 12165 Dihedral : 22.758 178.875 75892 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 4.96 % Allowed : 23.47 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.11), residues: 5484 helix: 1.65 (0.12), residues: 1959 sheet: 0.03 (0.15), residues: 1084 loop : -0.53 (0.12), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.005 0.001 HIS c 53 PHE 0.020 0.002 PHE C 130 TYR 0.026 0.002 TYR N 20 ARG 0.013 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1299 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1072 time to evaluate : 6.135 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: B 85 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6391 (tm) REVERT: B 109 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: B 169 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6861 (mm-30) REVERT: B 175 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7977 (tt0) REVERT: C 123 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: C 185 ASN cc_start: 0.8165 (t0) cc_final: 0.7804 (m110) REVERT: D 154 ARG cc_start: 0.5698 (mpt180) cc_final: 0.5156 (ptm160) REVERT: E 82 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7902 (mp-120) REVERT: F 88 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8035 (ttt) REVERT: K 68 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7438 (mt-10) REVERT: L 54 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7171 (tpp-160) REVERT: L 73 ASN cc_start: 0.8125 (p0) cc_final: 0.7868 (p0) REVERT: N 62 ASN cc_start: 0.8499 (m-40) cc_final: 0.8256 (m-40) REVERT: O 38 HIS cc_start: 0.7985 (t70) cc_final: 0.7643 (t-90) REVERT: P 31 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7637 (ttp-170) REVERT: R 24 LYS cc_start: 0.8491 (mppt) cc_final: 0.8221 (mttt) REVERT: S 37 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7209 (ttm170) REVERT: c 255 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8185 (tttp) REVERT: f 98 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6946 (mt-10) REVERT: i 69 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7389 (ttm110) REVERT: k 13 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7813 (mptp) REVERT: k 55 MET cc_start: 0.8462 (tpp) cc_final: 0.8256 (mmm) REVERT: q 22 LEU cc_start: 0.8681 (mp) cc_final: 0.8379 (mp) REVERT: t 86 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7915 (mtm180) REVERT: u 12 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: v 70 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6982 (pt0) outliers start: 227 outliers final: 121 residues processed: 1189 average time/residue: 2.1461 time to fit residues: 3649.9666 Evaluate side-chains 1186 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1051 time to evaluate : 5.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 187 ASP Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 255 LYS Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain f residue 136 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 31 GLU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 69 ARG Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 80 ASP Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 80 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 114 GLU Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 62 ILE Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 52 GLU Chi-restraints excluded: chain s residue 11 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 17 SER Chi-restraints excluded: chain s residue 25 GLU Chi-restraints excluded: chain s residue 49 LYS Chi-restraints excluded: chain s residue 50 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 78 SER Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain t residue 86 ARG Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 48 MET Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 23 THR Chi-restraints excluded: chain 1 residue 45 SER Chi-restraints excluded: chain 4 residue 24 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 318 optimal weight: 7.9990 chunk 853 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 556 optimal weight: 5.9990 chunk 233 optimal weight: 0.7980 chunk 948 optimal weight: 7.9990 chunk 787 optimal weight: 5.9990 chunk 439 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 313 optimal weight: 6.9990 chunk 497 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN E 82 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN K 29 ASN K 101 ASN N 49 GLN O 62 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 GLN T 20 HIS c 117 GLN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN e 195 GLN f 27 GLN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN n 61 GLN n 104 GLN o 12 GLN p 71 GLN v 76 ASN 0 45 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 151851 Z= 0.424 Angle : 0.725 14.634 227131 Z= 0.380 Chirality : 0.042 0.420 28919 Planarity : 0.007 0.143 12165 Dihedral : 22.873 179.163 75892 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 5.31 % Allowed : 24.39 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.31 (0.11), residues: 5484 helix: 1.42 (0.12), residues: 1973 sheet: -0.07 (0.15), residues: 1132 loop : -0.64 (0.12), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 42 HIS 0.007 0.001 HIS c 230 PHE 0.027 0.002 PHE S 74 TYR 0.023 0.002 TYR r 38 ARG 0.014 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1076 time to evaluate : 6.119 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: B 175 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8035 (mt-10) REVERT: C 123 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: C 185 ASN cc_start: 0.8247 (t0) cc_final: 0.7891 (m110) REVERT: D 154 ARG cc_start: 0.5964 (mpt180) cc_final: 0.5588 (ptm160) REVERT: K 68 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7512 (mt-10) REVERT: L 73 ASN cc_start: 0.8202 (p0) cc_final: 0.7971 (p0) REVERT: M 87 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7516 (mtm-85) REVERT: O 38 HIS cc_start: 0.8036 (t70) cc_final: 0.7728 (t-90) REVERT: O 81 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8937 (tp) REVERT: P 31 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7778 (ttp-170) REVERT: Q 65 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8078 (ptt90) REVERT: R 24 LYS cc_start: 0.8625 (mppt) cc_final: 0.8364 (mttt) REVERT: S 37 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7183 (ttm170) REVERT: c 132 MET cc_start: 0.8209 (mtm) cc_final: 0.7991 (mtm) REVERT: c 255 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8217 (tttp) REVERT: f 98 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7085 (mt-10) REVERT: i 1 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6026 (pmt) REVERT: i 34 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7779 (ttp-170) REVERT: i 69 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7480 (ttm110) REVERT: k 13 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7891 (mptp) REVERT: m 13 ASN cc_start: 0.8584 (p0) cc_final: 0.8335 (p0) REVERT: o 9 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7862 (mt-10) REVERT: t 37 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6700 (tp30) REVERT: t 86 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7946 (mtm180) REVERT: u 12 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8178 (mt0) REVERT: v 70 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7058 (pt0) outliers start: 243 outliers final: 148 residues processed: 1198 average time/residue: 2.1808 time to fit residues: 3722.2581 Evaluate side-chains 1202 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1039 time to evaluate : 5.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 65 ARG Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 56 GLN Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 187 ASP Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 255 LYS Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 136 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 31 GLU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 34 ARG Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 69 ARG Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 80 ASP Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 80 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 3 GLN Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 65 ILE Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 113 ILE Chi-restraints excluded: chain m residue 114 GLU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 83 SER Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 62 ILE Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 52 GLU Chi-restraints excluded: chain s residue 11 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 17 SER Chi-restraints excluded: chain s residue 21 SER Chi-restraints excluded: chain s residue 49 LYS Chi-restraints excluded: chain s residue 50 LEU Chi-restraints excluded: chain s residue 78 SER Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 37 GLU Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain t residue 86 ARG Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 48 MET Chi-restraints excluded: chain u residue 50 MET Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain v residue 81 SER Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 23 THR Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 45 SER Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 4 residue 24 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 914 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 540 optimal weight: 4.9990 chunk 692 optimal weight: 2.9990 chunk 536 optimal weight: 4.9990 chunk 798 optimal weight: 3.9990 chunk 529 optimal weight: 20.0000 chunk 944 optimal weight: 0.6980 chunk 591 optimal weight: 4.9990 chunk 575 optimal weight: 3.9990 chunk 436 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN D 85 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS K 101 ASN L 46 ASN O 62 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 GLN T 20 HIS c 117 GLN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN e 195 GLN ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 127 ASN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 23 ASN n 61 GLN n 104 GLN o 12 GLN p 71 GLN q 43 ASN v 76 ASN x 31 GLN 0 45 GLN 2 31 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 151851 Z= 0.256 Angle : 0.623 13.675 227131 Z= 0.335 Chirality : 0.036 0.380 28919 Planarity : 0.006 0.133 12165 Dihedral : 22.773 178.527 75892 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 4.17 % Allowed : 26.64 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.11), residues: 5484 helix: 1.60 (0.12), residues: 1961 sheet: -0.05 (0.15), residues: 1130 loop : -0.56 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.005 0.001 HIS G 153 PHE 0.031 0.002 PHE C 130 TYR 0.022 0.002 TYR r 38 ARG 0.014 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1086 time to evaluate : 6.039 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: B 175 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7988 (mt-10) REVERT: C 123 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: C 185 ASN cc_start: 0.8175 (t0) cc_final: 0.7833 (m110) REVERT: E 78 ASN cc_start: 0.6974 (t0) cc_final: 0.6680 (t0) REVERT: K 68 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7380 (mt-10) REVERT: L 73 ASN cc_start: 0.8169 (p0) cc_final: 0.7906 (p0) REVERT: O 6 GLU cc_start: 0.6520 (pm20) cc_final: 0.6224 (pm20) REVERT: O 38 HIS cc_start: 0.7971 (t70) cc_final: 0.7621 (t-90) REVERT: O 81 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8906 (tp) REVERT: P 31 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7678 (ttp-170) REVERT: Q 65 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8059 (ptt90) REVERT: Q 75 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8440 (tt) REVERT: R 24 LYS cc_start: 0.8542 (mppt) cc_final: 0.8297 (mttt) REVERT: S 37 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7263 (ttm170) REVERT: c 255 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8187 (tttp) REVERT: f 98 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7103 (mt-10) REVERT: i 69 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7423 (ttm110) REVERT: k 13 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7811 (mptp) REVERT: q 22 LEU cc_start: 0.8637 (mp) cc_final: 0.8428 (mp) REVERT: t 86 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7853 (mtm180) REVERT: v 70 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6967 (pt0) REVERT: 0 8 LYS cc_start: 0.8455 (mtmp) cc_final: 0.8239 (mtmp) REVERT: 3 18 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8380 (tttt) outliers start: 191 outliers final: 131 residues processed: 1179 average time/residue: 2.1109 time to fit residues: 3561.6269 Evaluate side-chains 1202 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1059 time to evaluate : 5.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 65 ARG Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 28 MET Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 187 ASP Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 255 LYS Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 130 MET Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 31 GLU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 69 ARG Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 80 ASP Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 80 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 113 ILE Chi-restraints excluded: chain m residue 114 GLU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 62 ILE Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 23 GLU Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 52 GLU Chi-restraints excluded: chain s residue 11 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 17 SER Chi-restraints excluded: chain s residue 21 SER Chi-restraints excluded: chain s residue 25 GLU Chi-restraints excluded: chain s residue 49 LYS Chi-restraints excluded: chain s residue 50 LEU Chi-restraints excluded: chain s residue 78 SER Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain t residue 86 ARG Chi-restraints excluded: chain u residue 48 MET Chi-restraints excluded: chain u residue 50 MET Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 23 THR Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 45 SER Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 24 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 584 optimal weight: 6.9990 chunk 377 optimal weight: 5.9990 chunk 564 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 600 optimal weight: 6.9990 chunk 643 optimal weight: 7.9990 chunk 467 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 742 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 HIS D 59 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS I 5 GLN J 99 GLN K 101 ASN L 46 ASN M 105 ASN N 49 GLN N 62 ASN O 62 GLN T 20 HIS ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN e 195 GLN f 27 GLN f 127 ASN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 61 GLN n 104 GLN o 12 GLN p 71 GLN t 45 HIS v 76 ASN x 31 GLN 0 45 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.093 151851 Z= 0.580 Angle : 0.837 18.056 227131 Z= 0.427 Chirality : 0.048 0.423 28919 Planarity : 0.008 0.149 12165 Dihedral : 22.984 179.297 75892 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 4.76 % Allowed : 26.46 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.06 (0.11), residues: 5484 helix: 1.22 (0.12), residues: 1960 sheet: -0.15 (0.15), residues: 1140 loop : -0.80 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 34 HIS 0.011 0.002 HIS 2 31 PHE 0.036 0.003 PHE S 74 TYR 0.029 0.003 TYR r 38 ARG 0.016 0.001 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1072 time to evaluate : 6.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8287 (mt-10) REVERT: C 123 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: C 185 ASN cc_start: 0.8335 (t0) cc_final: 0.8036 (m110) REVERT: D 113 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7361 (mm-30) REVERT: F 37 HIS cc_start: 0.8237 (m-70) cc_final: 0.8030 (m-70) REVERT: H 52 GLU cc_start: 0.6719 (mp0) cc_final: 0.6437 (mp0) REVERT: H 91 GLU cc_start: 0.7807 (mp0) cc_final: 0.7566 (mp0) REVERT: K 68 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7456 (mt-10) REVERT: K 98 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7684 (mtp85) REVERT: L 73 ASN cc_start: 0.8203 (p0) cc_final: 0.7930 (p0) REVERT: N 62 ASN cc_start: 0.8527 (m-40) cc_final: 0.8244 (m-40) REVERT: O 38 HIS cc_start: 0.8043 (t70) cc_final: 0.7727 (t-90) REVERT: O 81 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9001 (tp) REVERT: O 85 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8607 (mt) REVERT: P 31 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7767 (ttp-170) REVERT: Q 65 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8095 (ptt90) REVERT: R 24 LYS cc_start: 0.8692 (mppt) cc_final: 0.8456 (mttt) REVERT: S 37 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7118 (ttm170) REVERT: c 185 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: c 255 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8250 (tttp) REVERT: f 94 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6977 (tm-30) REVERT: f 98 GLU cc_start: 0.7619 (mt-10) cc_final: 0.6872 (mt-10) REVERT: i 1 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6062 (pmt) REVERT: i 34 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7813 (ttp-170) REVERT: i 69 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7573 (ttm110) REVERT: k 13 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7910 (mptp) REVERT: o 9 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7827 (mt-10) REVERT: o 111 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8269 (mtmm) REVERT: t 7 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.7131 (ttp80) REVERT: t 86 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8019 (mtm180) REVERT: u 12 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: v 70 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7094 (pt0) REVERT: 3 36 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8030 (ttt-90) outliers start: 218 outliers final: 151 residues processed: 1184 average time/residue: 2.1516 time to fit residues: 3637.2643 Evaluate side-chains 1210 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1040 time to evaluate : 5.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 65 ARG Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 187 ASP Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 255 LYS Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 173 PHE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 31 GLU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 34 ARG Chi-restraints excluded: chain i residue 69 ARG Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 80 ASP Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 80 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 3 GLN Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 65 ILE Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 113 ILE Chi-restraints excluded: chain m residue 114 GLU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 62 ILE Chi-restraints excluded: chain q residue 23 GLU Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 52 GLU Chi-restraints excluded: chain s residue 11 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 17 SER Chi-restraints excluded: chain s residue 21 SER Chi-restraints excluded: chain s residue 49 LYS Chi-restraints excluded: chain s residue 50 LEU Chi-restraints excluded: chain s residue 78 SER Chi-restraints excluded: chain t residue 7 ARG Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain t residue 86 ARG Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 48 MET Chi-restraints excluded: chain u residue 50 MET Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 23 THR Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 45 SER Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 24 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 859 optimal weight: 3.9990 chunk 904 optimal weight: 8.9990 chunk 825 optimal weight: 0.3980 chunk 880 optimal weight: 2.9990 chunk 529 optimal weight: 20.0000 chunk 383 optimal weight: 3.9990 chunk 691 optimal weight: 0.1980 chunk 270 optimal weight: 4.9990 chunk 795 optimal weight: 0.8980 chunk 832 optimal weight: 0.9990 chunk 877 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN E 82 GLN K 101 ASN O 62 GLN P 26 ASN ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 HIS c 117 GLN d 32 ASN d 130 GLN e 115 GLN e 195 GLN f 127 ASN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN n 104 GLN ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 12 GLN p 71 GLN q 43 ASN v 76 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 151851 Z= 0.143 Angle : 0.595 15.317 227131 Z= 0.323 Chirality : 0.033 0.370 28919 Planarity : 0.006 0.124 12165 Dihedral : 22.793 177.969 75892 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 2.58 % Allowed : 29.17 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.11), residues: 5484 helix: 1.64 (0.12), residues: 1965 sheet: -0.02 (0.15), residues: 1107 loop : -0.54 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP l 64 HIS 0.007 0.001 HIS B 18 PHE 0.038 0.001 PHE C 130 TYR 0.021 0.001 TYR r 38 ARG 0.014 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1102 time to evaluate : 5.957 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: C 12 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8343 (mm) REVERT: C 123 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: C 185 ASN cc_start: 0.8150 (t0) cc_final: 0.7843 (m110) REVERT: D 148 LYS cc_start: 0.2111 (OUTLIER) cc_final: 0.1729 (tmtt) REVERT: E 13 GLU cc_start: 0.6685 (mm-30) cc_final: 0.6419 (mm-30) REVERT: E 78 ASN cc_start: 0.6927 (t0) cc_final: 0.6643 (t0) REVERT: E 82 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7896 (mp-120) REVERT: K 68 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7321 (mt-10) REVERT: L 73 ASN cc_start: 0.8137 (p0) cc_final: 0.7897 (p0) REVERT: N 62 ASN cc_start: 0.8448 (m-40) cc_final: 0.8228 (m-40) REVERT: O 38 HIS cc_start: 0.7912 (t70) cc_final: 0.7555 (t-90) REVERT: O 81 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8861 (tp) REVERT: P 63 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.6819 (mp10) REVERT: R 24 LYS cc_start: 0.8514 (mppt) cc_final: 0.8273 (mttt) REVERT: S 37 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7347 (ttm170) REVERT: f 98 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6840 (mt-10) REVERT: i 69 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7428 (ttm110) REVERT: k 13 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7775 (mptp) REVERT: o 9 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7862 (mt-10) REVERT: o 111 LYS cc_start: 0.8472 (mtpp) cc_final: 0.8244 (mtmm) REVERT: s 50 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8339 (tp) REVERT: t 86 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7791 (mtm180) REVERT: u 12 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8178 (mt0) REVERT: w 56 MET cc_start: 0.8101 (ttm) cc_final: 0.7838 (mtt) outliers start: 118 outliers final: 69 residues processed: 1167 average time/residue: 2.1063 time to fit residues: 3528.1937 Evaluate side-chains 1148 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1067 time to evaluate : 5.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 31 GLU Chi-restraints excluded: chain i residue 69 ARG Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 80 ASP Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain q residue 23 GLU Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 49 LYS Chi-restraints excluded: chain s residue 50 LEU Chi-restraints excluded: chain s residue 78 SER Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 86 ARG Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 50 MET Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 45 SER Chi-restraints excluded: chain 4 residue 24 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 578 optimal weight: 5.9990 chunk 930 optimal weight: 3.9990 chunk 568 optimal weight: 10.0000 chunk 441 optimal weight: 6.9990 chunk 647 optimal weight: 10.0000 chunk 976 optimal weight: 10.0000 chunk 898 optimal weight: 0.9980 chunk 777 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 600 optimal weight: 7.9990 chunk 476 optimal weight: 6.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN D 59 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 82 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS G 153 HIS J 15 HIS K 101 ASN L 46 ASN N 49 GLN O 62 GLN P 26 ASN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 HIS ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN e 195 GLN f 27 GLN ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN n 104 GLN p 71 GLN q 12 HIS v 76 ASN x 31 GLN 0 45 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 151851 Z= 0.355 Angle : 0.691 15.926 227131 Z= 0.364 Chirality : 0.039 0.411 28919 Planarity : 0.007 0.141 12165 Dihedral : 22.793 179.115 75892 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.13 % Rotamer: Outliers : 2.34 % Allowed : 29.85 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.38 (0.11), residues: 5484 helix: 1.52 (0.12), residues: 1965 sheet: -0.06 (0.15), residues: 1127 loop : -0.61 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 201 HIS 0.008 0.001 HIS F 37 PHE 0.040 0.002 PHE C 130 TYR 0.025 0.002 TYR r 38 ARG 0.015 0.001 ARG D 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1053 time to evaluate : 5.979 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: C 123 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: C 185 ASN cc_start: 0.8219 (t0) cc_final: 0.7904 (m110) REVERT: D 148 LYS cc_start: 0.2444 (OUTLIER) cc_final: 0.2059 (tmtt) REVERT: G 15 ASP cc_start: 0.8269 (p0) cc_final: 0.8019 (p0) REVERT: K 68 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7425 (mt-10) REVERT: L 73 ASN cc_start: 0.8262 (p0) cc_final: 0.7978 (p0) REVERT: O 6 GLU cc_start: 0.6433 (pm20) cc_final: 0.6085 (pm20) REVERT: O 38 HIS cc_start: 0.7976 (t70) cc_final: 0.7617 (t-90) REVERT: O 81 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8916 (tp) REVERT: R 24 LYS cc_start: 0.8586 (mppt) cc_final: 0.8347 (mttt) REVERT: S 37 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7460 (ttm170) REVERT: c 255 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8180 (tttp) REVERT: f 94 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6559 (tm-30) REVERT: i 69 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7482 (ttm110) REVERT: k 13 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7894 (mptp) REVERT: o 9 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7760 (mt-10) REVERT: t 86 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7888 (mtm180) REVERT: u 12 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: 3 18 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8409 (tttt) REVERT: 3 36 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8018 (ttt-90) outliers start: 107 outliers final: 81 residues processed: 1111 average time/residue: 2.1120 time to fit residues: 3354.8766 Evaluate side-chains 1135 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1043 time to evaluate : 5.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 255 LYS Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 31 GLU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 69 ARG Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 80 ASP Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain q residue 23 GLU Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 49 LYS Chi-restraints excluded: chain s residue 50 LEU Chi-restraints excluded: chain s residue 78 SER Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 86 ARG Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 50 MET Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 45 SER Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 24 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 617 optimal weight: 4.9990 chunk 828 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 716 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 778 optimal weight: 7.9990 chunk 325 optimal weight: 0.7980 chunk 799 optimal weight: 0.9980 chunk 98 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN D 59 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS O 62 GLN P 26 ASN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 HIS d 32 ASN e 115 GLN e 195 GLN f 127 ASN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 23 ASN n 104 GLN p 71 GLN q 43 ASN v 76 ASN x 31 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.093871 restraints weight = 208226.236| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 0.42 r_work: 0.2891 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 151851 Z= 0.205 Angle : 0.634 17.276 227131 Z= 0.343 Chirality : 0.035 0.395 28919 Planarity : 0.006 0.133 12165 Dihedral : 22.820 179.505 75892 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 2.27 % Allowed : 30.31 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.40 (0.11), residues: 5484 helix: 1.54 (0.12), residues: 1967 sheet: -0.09 (0.15), residues: 1124 loop : -0.57 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.007 0.001 HIS B 18 PHE 0.042 0.002 PHE C 130 TYR 0.024 0.002 TYR r 38 ARG 0.016 0.001 ARG J 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49151.15 seconds wall clock time: 852 minutes 56.25 seconds (51176.25 seconds total)