Starting phenix.real_space_refine on Sun Apr 14 05:13:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/04_2024/7oiz_12936_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/04_2024/7oiz_12936.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/04_2024/7oiz_12936_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/7oiz_12936/04_2024/7oiz_12936_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/04_2024/7oiz_12936_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/04_2024/7oiz_12936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/04_2024/7oiz_12936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/04_2024/7oiz_12936_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/04_2024/7oiz_12936_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= 0.000 sd= 0.013 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4472 5.49 5 Mg 308 5.21 5 S 147 5.16 5 C 70374 2.51 5 N 26132 2.21 5 O 38860 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 140295 Number of models: 1 Model: "" Number of chains: 64 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': 120, 'rna2p_pyr': 81, 'rna3p': 9, 'rna3p_pur': 743, 'rna3p_pyr': 565} Link IDs: {'rna2p': 202, 'rna3p': 1316} 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: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "7" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 139 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} 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': 1, 'rna3p_pur': 34, 'rna3p_pyr': 30} Link IDs: {'rna2p': 10, 'rna3p': 64} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 135 Unusual residues: {' MG': 93, 'PAR': 1} Classifications: {'undetermined': 94} Link IDs: {None: 93} Chain: "a" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 220 Unusual residues: {' MG': 205} Classifications: {'peptide': 1, 'undetermined': 205} Modifications used: {'COO': 1} Link IDs: {None: 205} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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 11 116.278 150.187 176.481 1.00 33.43 S ATOM A0SUF SG CYS 3 14 114.940 153.389 175.021 1.00 31.78 S ATOM A0SXA SG CYS 3 27 118.403 153.276 176.458 1.00 35.86 S ATOM A0T3D SG CYS 4 16 55.976 69.887 127.108 1.00 77.37 S ATOM A0T3P SG CYS 4 18 54.583 67.935 130.139 1.00 77.82 S ATOM A0T7N SG CYS 4 37 54.880 71.584 130.141 1.00 77.11 S ATOM A0T88 SG CYS 4 40 58.083 69.506 130.342 1.00 81.07 S Time building chain proxies: 56.15, per 1000 atoms: 0.40 Number of scatterers: 140295 At special positions: 0 Unit cell: (265.58, 278.588, 225.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 147 16.00 P 4472 15.00 Mg 308 11.99 O 38860 8.00 N 26132 7.00 C 70374 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: 58.92 Conformation dependent library (CDL) restraints added in 7.6 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 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10296 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: 173 helices and 67 sheets defined 39.2% alpha, 19.8% beta 1582 base pairs and 2496 stacking pairs defined. Time for finding SS restraints: 73.47 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: 4.631A 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: 4.774A 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: 3.655A 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: 5.532A 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: 4.464A 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: 5.231A 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: 5.448A 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: 4.775A 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: 5.238A 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: 4.610A pdb=" N PHE d 101 " --> pdb=" O SER d 97 " (cutoff:3.500A) removed outlier: 4.859A 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: 5.227A 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: 5.461A 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: 4.638A pdb=" N ARG j 108 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 5.656A 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: 5.683A 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: 4.880A 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: 5.105A 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: 5.206A 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: 5.857A 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: 6.068A 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: 4.154A 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: 4.434A 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: 4.890A 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: 5.353A 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: 5.554A 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 helix chain '7' and resid 11 through 16 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: 5.834A 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: 5.985A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.323A 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: 6.496A 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: 6.828A 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: 6.990A 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: 6.579A 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: 4.106A 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: 4.433A 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: 6.915A 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: 4.732A 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: 5.839A 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: 7.205A 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: 4.732A 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: 5.758A 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: 5.876A 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: 6.407A 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: 6.521A 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: 6.265A pdb=" N ALA m 111 " --> pdb=" O LYS m 99 " (cutoff:3.500A) removed outlier: 6.586A 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: 6.891A 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: 6.849A 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: 6.621A 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: 3.929A pdb=" N HIS o 56 " --> pdb=" O ARG o 53 " (cutoff:3.500A) removed outlier: 7.739A 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: 6.006A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 5.606A 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: 6.725A 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: 6.902A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 7.028A 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: 3.593A pdb=" N ARG w 27 " --> pdb=" O GLY w 15 " (cutoff:3.500A) removed outlier: 3.812A 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: 6.734A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.445A 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: 5.294A 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 2056 hydrogen bonds defined for protein. 6045 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3968 hydrogen bonds 6138 hydrogen bond angles 0 basepair planarities 1582 basepair parallelities 2496 stacking parallelities Total time for adding SS restraints: 248.28 Time building geometry restraints manager: 64.05 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: 11372 1.29 - 1.42: 67574 1.42 - 1.55: 63945 1.55 - 1.69: 8952 1.69 - 1.82: 265 Bond restraints: 152108 Sorted by residual: bond pdb=" C13 PAR A1601 " pdb=" O43 PAR A1601 " ideal model delta sigma weight residual 1.402 1.633 -0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C13 PAR A1601 " pdb=" C23 PAR A1601 " ideal model delta sigma weight residual 1.524 1.344 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" C5 U a2449 " pdb=" C6 U a2449 " ideal model delta sigma weight residual 1.337 1.487 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" C1' G X 20 " pdb=" N9 G X 20 " ideal model delta sigma weight residual 1.475 1.380 0.095 1.50e-02 4.44e+03 3.97e+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 ... (remaining 152103 not shown) Histogram of bond angle deviations from ideal: 96.06 - 105.29: 21553 105.29 - 114.52: 102699 114.52 - 123.75: 81429 123.75 - 132.98: 21683 132.98 - 142.20: 136 Bond angle restraints: 227500 Sorted by residual: angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 126.87 -20.55 3.00e+00 1.11e-01 4.69e+01 angle pdb=" C GLU M 66 " pdb=" CA GLU M 66 " pdb=" CB GLU M 66 " ideal model delta sigma weight residual 117.23 109.51 7.72 1.36e+00 5.41e-01 3.23e+01 angle pdb=" C THR k 117 " pdb=" N THR k 118 " pdb=" CA THR k 118 " ideal model delta sigma weight residual 122.31 135.34 -13.03 2.34e+00 1.83e-01 3.10e+01 angle pdb=" C SER t 98 " pdb=" N ASN t 99 " pdb=" CA ASN t 99 " ideal model delta sigma weight residual 126.32 135.35 -9.03 1.74e+00 3.30e-01 2.69e+01 angle pdb=" C MET S 66 " pdb=" CA MET S 66 " pdb=" CB MET S 66 " ideal model delta sigma weight residual 110.35 119.32 -8.97 1.78e+00 3.16e-01 2.54e+01 ... (remaining 227495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 86677 35.98 - 71.97: 9601 71.97 - 107.95: 1107 107.95 - 143.93: 10 143.93 - 179.92: 10 Dihedral angle restraints: 97405 sinusoidal: 81446 harmonic: 15959 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 -116.69 -63.31 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 48.37 151.63 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 52.68 147.32 1 1.50e+01 4.44e-03 7.86e+01 ... (remaining 97402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 27512 0.099 - 0.198: 1377 0.198 - 0.298: 69 0.298 - 0.397: 8 0.397 - 0.496: 1 Chirality restraints: 28967 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 0.50 2.00e-01 2.50e+01 6.15e+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 2.83e+00 chirality pdb=" C3' A A1035 " pdb=" C4' A A1035 " pdb=" O3' A A1035 " pdb=" C2' A A1035 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 28964 not shown) Planarity restraints: 12192 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 8.03e+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 5.73e-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 12189 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 1231 2.57 - 3.15: 98572 3.15 - 3.73: 266796 3.73 - 4.32: 386163 4.32 - 4.90: 524545 Nonbonded interactions: 1277307 Sorted by model distance: 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 1.986 2.170 nonbonded pdb=" O2 C a2499 " pdb="MG MG a6059 " model vdw 1.989 2.170 nonbonded pdb=" O6 G a 776 " pdb="MG MG a6158 " model vdw 1.992 2.170 nonbonded pdb=" O4 U a1671 " pdb="MG MG a6090 " model vdw 1.993 2.170 ... (remaining 1277302 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 15.730 Check model and map are aligned: 1.630 Set scattering table: 1.010 Process input model: 563.220 Find NCS groups from input model: 2.830 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 599.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 0.231 152108 Z= 0.438 Angle : 0.824 20.549 227500 Z= 0.422 Chirality : 0.046 0.496 28967 Planarity : 0.019 0.597 12192 Dihedral : 22.404 179.916 87109 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.49 % Favored : 96.40 % Rotamer: Outliers : 0.07 % Allowed : 0.48 % Favored : 99.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.16 % 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: -0.63 (0.11), residues: 5498 helix: 0.13 (0.11), residues: 1975 sheet: -0.21 (0.15), residues: 1085 loop : -0.87 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP a6206 HIS 0.022 0.002 HIS l 13 PHE 0.033 0.002 PHE S 74 TYR 0.053 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) ************************************************ 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1140 time to evaluate : 6.241 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: G 118 LEU cc_start: 0.8718 (pp) cc_final: 0.8395 (pp) REVERT: N 7 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8051 (mmtt) REVERT: N 28 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8508 (mttt) REVERT: N 98 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8341 (ttmm) REVERT: T 78 ASN cc_start: 0.8797 (m-40) cc_final: 0.8448 (m110) REVERT: U 21 ARG cc_start: 0.7563 (mmm160) cc_final: 0.7334 (tpt170) REVERT: c 146 MET cc_start: 0.7039 (mmm) cc_final: 0.6759 (mmm) REVERT: d 139 SER cc_start: 0.8923 (m) cc_final: 0.8685 (m) REVERT: e 197 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7408 (tm-30) REVERT: l 127 LYS cc_start: 0.7881 (tppp) cc_final: 0.7549 (tptt) REVERT: p 101 PHE cc_start: 0.7968 (m-10) cc_final: 0.7714 (m-10) REVERT: r 92 ARG cc_start: 0.7916 (mtp-110) cc_final: 0.7564 (mtp-110) REVERT: s 37 ASP cc_start: 0.7538 (p0) cc_final: 0.7296 (p0) REVERT: u 48 MET cc_start: 0.7730 (mmm) cc_final: 0.7467 (tpt) REVERT: x 5 GLU cc_start: 0.7693 (pp20) cc_final: 0.7447 (pp20) REVERT: 1 15 SER cc_start: 0.8543 (m) cc_final: 0.8250 (m) outliers start: 3 outliers final: 0 residues processed: 1141 average time/residue: 2.1359 time to fit residues: 3470.9231 Evaluate side-chains 916 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 916 time to evaluate : 6.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 828 optimal weight: 0.6980 chunk 743 optimal weight: 8.9990 chunk 412 optimal weight: 10.0000 chunk 253 optimal weight: 0.4980 chunk 501 optimal weight: 3.9990 chunk 397 optimal weight: 10.0000 chunk 768 optimal weight: 5.9990 chunk 297 optimal weight: 0.9980 chunk 467 optimal weight: 6.9990 chunk 572 optimal weight: 5.9990 chunk 890 optimal weight: 10.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN E 19 ASN E 43 ASN E 70 ASN E 73 ASN ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN P 26 ASN R 31 ASN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN T 70 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN g 22 GLN h 18 GLN h 28 ASN n 116 GLN o 10 GLN r 15 GLN t 40 ASN x 45 GLN 0 45 GLN 3 13 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 152108 Z= 0.208 Angle : 0.610 14.734 227500 Z= 0.332 Chirality : 0.035 0.459 28967 Planarity : 0.006 0.128 12192 Dihedral : 22.751 179.307 76032 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 2.13 % Allowed : 13.06 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.04 (0.11), residues: 5498 helix: 1.07 (0.12), residues: 1974 sheet: -0.17 (0.15), residues: 1078 loop : -0.67 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a6206 HIS 0.009 0.001 HIS l 13 PHE 0.025 0.001 PHE U 12 TYR 0.023 0.002 TYR p 47 ARG 0.009 0.000 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 981 time to evaluate : 6.156 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: E 29 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7481 (mtp85) REVERT: E 70 ASN cc_start: 0.7497 (t0) cc_final: 0.7284 (t0) REVERT: N 98 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8304 (ttmm) REVERT: O 64 ARG cc_start: 0.8063 (tpp80) cc_final: 0.7833 (tpp-160) REVERT: O 68 ASP cc_start: 0.7685 (m-30) cc_final: 0.7341 (m-30) REVERT: P 5 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7415 (ptt90) REVERT: S 37 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7647 (ptm-80) REVERT: T 74 ARG cc_start: 0.8639 (mtm-85) cc_final: 0.7846 (mtm-85) REVERT: T 78 ASN cc_start: 0.8792 (m-40) cc_final: 0.8466 (m110) REVERT: c 146 MET cc_start: 0.7117 (mmm) cc_final: 0.6778 (mmm) REVERT: f 7 TYR cc_start: 0.8699 (t80) cc_final: 0.8487 (t80) REVERT: f 98 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7511 (mt-10) REVERT: j 93 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: j 108 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7389 (mtt-85) REVERT: r 92 ARG cc_start: 0.7904 (mtp-110) cc_final: 0.7622 (mtp-110) REVERT: s 37 ASP cc_start: 0.7387 (p0) cc_final: 0.7126 (p0) REVERT: s 76 ARG cc_start: 0.7553 (tpt90) cc_final: 0.7337 (tpt-90) REVERT: s 87 LEU cc_start: 0.8049 (mt) cc_final: 0.7834 (mt) REVERT: 1 15 SER cc_start: 0.8494 (m) cc_final: 0.8225 (m) outliers start: 98 outliers final: 45 residues processed: 1012 average time/residue: 2.0860 time to fit residues: 3006.9477 Evaluate side-chains 981 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 931 time to evaluate : 6.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain c residue 38 SER Chi-restraints excluded: chain c residue 157 SER Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 30 ASN Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 93 GLN Chi-restraints excluded: chain j residue 108 ARG Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain r residue 24 ILE Chi-restraints excluded: chain r residue 81 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain x residue 14 LEU Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 32 ILE Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 4 residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 495 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 chunk 741 optimal weight: 7.9990 chunk 606 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 892 optimal weight: 6.9990 chunk 964 optimal weight: 4.9990 chunk 794 optimal weight: 0.9990 chunk 885 optimal weight: 0.6980 chunk 304 optimal weight: 8.9990 chunk 715 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN D 74 ASN F 46 GLN H 16 ASN ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN P 59 HIS R 54 GLN ** T 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN T 55 GLN T 61 GLN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN h 18 GLN n 61 GLN o 10 GLN u 49 ASN 0 45 GLN 7 22 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 152108 Z= 0.233 Angle : 0.600 13.421 227500 Z= 0.325 Chirality : 0.034 0.447 28967 Planarity : 0.006 0.134 12192 Dihedral : 22.665 179.643 76032 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 3.00 % Allowed : 15.55 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.34 (0.11), residues: 5498 helix: 1.46 (0.12), residues: 1968 sheet: -0.06 (0.15), residues: 1078 loop : -0.61 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a6206 HIS 0.009 0.001 HIS l 13 PHE 0.028 0.001 PHE G 26 TYR 0.024 0.002 TYR p 47 ARG 0.009 0.001 ARG f 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 970 time to evaluate : 6.052 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: E 29 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7652 (mtt90) REVERT: E 70 ASN cc_start: 0.7629 (t0) cc_final: 0.7389 (t0) REVERT: O 68 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7570 (m-30) REVERT: P 5 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8412 (ptt180) REVERT: T 74 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8424 (mtm110) REVERT: T 78 ASN cc_start: 0.8718 (m-40) cc_final: 0.8422 (m110) REVERT: c 146 MET cc_start: 0.7135 (mmm) cc_final: 0.6863 (mmm) REVERT: c 181 MET cc_start: 0.7062 (mmm) cc_final: 0.6747 (mtm) REVERT: j 93 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: n 81 ARG cc_start: 0.8435 (mtt180) cc_final: 0.8212 (mtt180) REVERT: s 2 ILE cc_start: 0.8779 (mp) cc_final: 0.8369 (mm) REVERT: s 26 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8338 (tmtt) REVERT: s 37 ASP cc_start: 0.7359 (p0) cc_final: 0.7114 (p0) REVERT: y 31 ARG cc_start: 0.8507 (ptp90) cc_final: 0.8149 (ptp90) outliers start: 138 outliers final: 72 residues processed: 1018 average time/residue: 2.1339 time to fit residues: 3096.1740 Evaluate side-chains 1000 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 924 time to evaluate : 6.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain O residue 68 ASP Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain c residue 38 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 157 SER Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 19 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 93 GLN Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 135 ILE Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain p residue 98 ILE Chi-restraints excluded: chain q residue 26 ASP Chi-restraints excluded: chain r residue 24 ILE Chi-restraints excluded: chain r residue 81 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 62 GLU Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 32 ILE Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 4 residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 881 optimal weight: 0.9990 chunk 670 optimal weight: 5.9990 chunk 463 optimal weight: 6.9990 chunk 98 optimal weight: 50.0000 chunk 425 optimal weight: 10.0000 chunk 599 optimal weight: 7.9990 chunk 895 optimal weight: 0.0970 chunk 948 optimal weight: 7.9990 chunk 467 optimal weight: 8.9990 chunk 848 optimal weight: 3.9990 chunk 255 optimal weight: 9.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN D 74 ASN F 46 GLN H 16 ASN ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN R 52 GLN R 54 GLN T 55 GLN T 61 GLN T 70 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 260 ASN f 81 GLN o 10 GLN u 49 ASN ** x 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 45 GLN 3 13 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 152108 Z= 0.277 Angle : 0.618 13.886 227500 Z= 0.333 Chirality : 0.035 0.458 28967 Planarity : 0.006 0.135 12192 Dihedral : 22.626 179.549 76032 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 3.92 % Allowed : 17.11 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.41 (0.11), residues: 5498 helix: 1.52 (0.12), residues: 1988 sheet: -0.09 (0.16), residues: 1071 loop : -0.55 (0.12), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a6206 HIS 0.011 0.001 HIS P 59 PHE 0.021 0.001 PHE G 26 TYR 0.024 0.002 TYR p 47 ARG 0.010 0.001 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 955 time to evaluate : 6.275 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: E 29 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7350 (mtp85) REVERT: J 7 ARG cc_start: 0.7640 (mmt-90) cc_final: 0.7277 (mmt180) REVERT: P 5 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8491 (ptt180) REVERT: R 65 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8456 (mp) REVERT: S 66 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7532 (ppp) REVERT: T 74 ARG cc_start: 0.8728 (mtm-85) cc_final: 0.8376 (ttm110) REVERT: T 78 ASN cc_start: 0.8653 (m-40) cc_final: 0.8380 (m110) REVERT: U 21 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7411 (tpm170) REVERT: c 181 MET cc_start: 0.7110 (mmm) cc_final: 0.6832 (mtm) REVERT: h 1 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7485 (ttt) REVERT: j 93 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: m 32 GLU cc_start: 0.8154 (mp0) cc_final: 0.7893 (mp0) REVERT: s 2 ILE cc_start: 0.8804 (mp) cc_final: 0.8413 (mm) REVERT: s 26 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8362 (tmtt) REVERT: s 37 ASP cc_start: 0.7406 (p0) cc_final: 0.7168 (p0) REVERT: 4 37 CYS cc_start: 0.8098 (p) cc_final: 0.7483 (p) outliers start: 180 outliers final: 85 residues processed: 1040 average time/residue: 2.1092 time to fit residues: 3139.9423 Evaluate side-chains 1006 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 914 time to evaluate : 6.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain c residue 38 SER Chi-restraints excluded: chain c residue 53 HIS Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 157 SER Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 20 VAL 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 121 THR Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 93 GLN Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain l residue 84 LYS Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain p residue 98 ILE Chi-restraints excluded: chain q residue 22 LEU Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 26 ASP Chi-restraints excluded: chain q residue 85 LYS Chi-restraints excluded: chain r residue 24 ILE Chi-restraints excluded: chain r residue 81 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 5 ASN Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain x residue 6 LEU Chi-restraints excluded: chain y residue 32 ILE Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 62 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 789 optimal weight: 1.9990 chunk 538 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 706 optimal weight: 4.9990 chunk 391 optimal weight: 10.0000 chunk 809 optimal weight: 2.9990 chunk 655 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 484 optimal weight: 6.9990 chunk 851 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN C 123 GLN D 74 ASN E 61 GLN F 46 GLN G 153 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN P 26 ASN P 63 GLN Q 45 HIS R 31 ASN R 54 GLN T 70 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN h 28 ASN j 90 ASN o 10 GLN r 9 HIS u 49 ASN ** x 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 45 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 152108 Z= 0.396 Angle : 0.689 13.546 227500 Z= 0.365 Chirality : 0.040 0.475 28967 Planarity : 0.007 0.142 12192 Dihedral : 22.656 179.839 76032 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 4.18 % Allowed : 18.92 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.30 (0.11), residues: 5498 helix: 1.48 (0.12), residues: 1979 sheet: -0.14 (0.16), residues: 1045 loop : -0.66 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a6206 HIS 0.011 0.001 HIS P 59 PHE 0.022 0.002 PHE G 26 TYR 0.024 0.002 TYR F 59 ARG 0.010 0.001 ARG n 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 971 time to evaluate : 10.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 29 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7570 (mtp85) REVERT: E 50 TYR cc_start: 0.8675 (t80) cc_final: 0.8428 (t80) REVERT: N 62 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8030 (m-40) REVERT: N 70 PRO cc_start: 0.9525 (Cg_endo) cc_final: 0.9288 (Cg_exo) REVERT: P 5 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8604 (ptt180) REVERT: R 44 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8674 (mp) REVERT: T 74 ARG cc_start: 0.8786 (mtm-85) cc_final: 0.8438 (ttm110) REVERT: T 78 ASN cc_start: 0.8692 (m-40) cc_final: 0.8405 (m110) REVERT: U 21 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7430 (tpm170) REVERT: c 181 MET cc_start: 0.7181 (mmm) cc_final: 0.6852 (mtm) REVERT: d 184 ARG cc_start: 0.8235 (mtt180) cc_final: 0.7986 (mtt180) REVERT: j 91 SER cc_start: 0.8571 (t) cc_final: 0.7787 (p) REVERT: j 93 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: r 62 ASP cc_start: 0.7983 (m-30) cc_final: 0.7575 (m-30) REVERT: s 2 ILE cc_start: 0.8784 (mp) cc_final: 0.8412 (mm) REVERT: s 37 ASP cc_start: 0.7611 (p0) cc_final: 0.7359 (p0) REVERT: u 12 GLN cc_start: 0.8634 (mp10) cc_final: 0.8360 (mt0) REVERT: z 37 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8635 (mttp) REVERT: 4 37 CYS cc_start: 0.8028 (p) cc_final: 0.7350 (p) outliers start: 192 outliers final: 114 residues processed: 1063 average time/residue: 2.0818 time to fit residues: 3185.9178 Evaluate side-chains 1045 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 924 time to evaluate : 6.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain N residue 6 MET Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain c residue 38 SER Chi-restraints excluded: chain c residue 53 HIS Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 157 SER Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 35 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 98 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain d residue 165 MET Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 104 ASN Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 19 VAL Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 93 GLN Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 5 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 22 LEU Chi-restraints excluded: chain q residue 26 ASP Chi-restraints excluded: chain q residue 85 LYS Chi-restraints excluded: chain r residue 24 ILE Chi-restraints excluded: chain s residue 53 VAL Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 5 ASN Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain x residue 6 LEU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 32 ILE Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 25 VAL Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 3 residue 16 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 319 optimal weight: 20.0000 chunk 853 optimal weight: 0.7980 chunk 187 optimal weight: 20.0000 chunk 556 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 949 optimal weight: 0.2980 chunk 787 optimal weight: 1.9990 chunk 439 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 498 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN D 74 ASN E 70 ASN G 153 HIS H 16 ASN ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN R 52 GLN R 54 GLN T 61 GLN T 70 ASN T 84 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN j 90 ASN o 10 GLN q 86 GLN u 49 ASN 0 45 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 152108 Z= 0.189 Angle : 0.589 14.017 227500 Z= 0.319 Chirality : 0.033 0.453 28967 Planarity : 0.006 0.128 12192 Dihedral : 22.611 179.635 76032 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 3.29 % Allowed : 21.29 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.51 (0.11), residues: 5498 helix: 1.70 (0.12), residues: 1980 sheet: -0.10 (0.15), residues: 1083 loop : -0.54 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a6206 HIS 0.011 0.001 HIS P 59 PHE 0.027 0.001 PHE H 66 TYR 0.022 0.001 TYR p 47 ARG 0.008 0.000 ARG U 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 989 time to evaluate : 6.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 29 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7615 (mtt90) REVERT: E 132 ASN cc_start: 0.7756 (m-40) cc_final: 0.7550 (m110) REVERT: F 79 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7644 (ttm-80) REVERT: G 66 LEU cc_start: 0.8869 (tp) cc_final: 0.8577 (tt) REVERT: J 7 ARG cc_start: 0.7599 (mmt-90) cc_final: 0.7257 (mmt180) REVERT: P 5 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8485 (ptt180) REVERT: T 78 ASN cc_start: 0.8575 (m-40) cc_final: 0.8276 (m110) REVERT: U 47 ARG cc_start: 0.5820 (mpt180) cc_final: 0.5326 (mmt-90) REVERT: c 181 MET cc_start: 0.7103 (mmm) cc_final: 0.6790 (mtm) REVERT: j 93 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: l 63 ILE cc_start: 0.8632 (mt) cc_final: 0.8313 (tt) REVERT: m 32 GLU cc_start: 0.8100 (mp0) cc_final: 0.7894 (mp0) REVERT: q 1 MET cc_start: 0.7037 (ttm) cc_final: 0.6749 (mmt) REVERT: q 43 ASN cc_start: 0.8003 (t0) cc_final: 0.7770 (t0) REVERT: q 71 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.7662 (tppp) REVERT: s 2 ILE cc_start: 0.8803 (mp) cc_final: 0.8448 (mm) REVERT: s 26 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8178 (tmtt) REVERT: s 37 ASP cc_start: 0.7467 (p0) cc_final: 0.7193 (p0) REVERT: y 37 GLU cc_start: 0.7028 (tt0) cc_final: 0.6813 (tp30) REVERT: z 37 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8593 (mttp) REVERT: 1 15 SER cc_start: 0.8624 (m) cc_final: 0.8389 (m) REVERT: 4 37 CYS cc_start: 0.7921 (p) cc_final: 0.7212 (p) outliers start: 151 outliers final: 96 residues processed: 1063 average time/residue: 2.0308 time to fit residues: 3118.1416 Evaluate side-chains 1022 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 921 time to evaluate : 6.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain c residue 38 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 157 SER Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 11 MET Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 19 VAL Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 93 GLN Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain q residue 22 LEU Chi-restraints excluded: chain q residue 26 ASP Chi-restraints excluded: chain q residue 71 LYS Chi-restraints excluded: chain q residue 85 LYS Chi-restraints excluded: chain r residue 24 ILE Chi-restraints excluded: chain r residue 81 SER Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 5 ASN Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain x residue 6 LEU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 32 ILE Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 3 residue 16 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 915 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 540 optimal weight: 10.0000 chunk 693 optimal weight: 5.9990 chunk 537 optimal weight: 7.9990 chunk 798 optimal weight: 6.9990 chunk 530 optimal weight: 20.0000 chunk 945 optimal weight: 2.9990 chunk 591 optimal weight: 7.9990 chunk 576 optimal weight: 6.9990 chunk 436 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN D 74 ASN E 43 ASN E 73 ASN F 46 GLN ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN R 54 GLN T 21 ASN T 55 GLN T 70 ASN T 84 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 ASN f 81 GLN g 38 ASN h 33 GLN n 61 GLN o 10 GLN q 86 GLN u 49 ASN 0 45 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 152108 Z= 0.400 Angle : 0.692 13.705 227500 Z= 0.365 Chirality : 0.039 0.462 28967 Planarity : 0.006 0.141 12192 Dihedral : 22.631 179.457 76032 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 3.74 % Allowed : 22.06 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.33 (0.11), residues: 5498 helix: 1.56 (0.12), residues: 1990 sheet: -0.14 (0.16), residues: 1047 loop : -0.69 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a6206 HIS 0.011 0.001 HIS P 59 PHE 0.028 0.002 PHE E 48 TYR 0.026 0.002 TYR 2 64 ARG 0.012 0.001 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 954 time to evaluate : 6.389 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: E 29 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7553 (mtp85) REVERT: F 79 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7656 (ttm-80) REVERT: G 66 LEU cc_start: 0.8893 (tp) cc_final: 0.8597 (tt) REVERT: P 5 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8591 (ptt180) REVERT: R 44 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8705 (mp) REVERT: T 78 ASN cc_start: 0.8615 (m-40) cc_final: 0.8309 (m110) REVERT: U 21 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7409 (tpm170) REVERT: c 181 MET cc_start: 0.7174 (mmm) cc_final: 0.6884 (mtm) REVERT: e 1 MET cc_start: 0.5419 (mmm) cc_final: 0.5217 (mmp) REVERT: i 95 ARG cc_start: 0.6734 (ttm110) cc_final: 0.6532 (mtm-85) REVERT: j 93 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: s 2 ILE cc_start: 0.8812 (mp) cc_final: 0.8466 (mm) REVERT: s 26 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8289 (tmtt) REVERT: s 37 ASP cc_start: 0.7526 (p0) cc_final: 0.7287 (p0) REVERT: s 49 LYS cc_start: 0.8311 (tmtp) cc_final: 0.7991 (tmtt) REVERT: u 12 GLN cc_start: 0.8641 (mp10) cc_final: 0.8364 (mt0) REVERT: z 37 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8624 (mttp) REVERT: 4 37 CYS cc_start: 0.7966 (p) cc_final: 0.7278 (p) outliers start: 172 outliers final: 115 residues processed: 1047 average time/residue: 2.0746 time to fit residues: 3124.7446 Evaluate side-chains 1048 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 927 time to evaluate : 6.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain N residue 6 MET Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain c residue 38 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 111 LYS Chi-restraints excluded: chain c residue 157 SER Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain d residue 165 MET Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 19 VAL Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 93 GLN Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 5 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain q residue 22 LEU Chi-restraints excluded: chain q residue 26 ASP Chi-restraints excluded: chain q residue 85 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 24 ILE Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 5 ASN Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain x residue 6 LEU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 32 ILE Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 25 VAL Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 3 residue 16 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 584 optimal weight: 6.9990 chunk 377 optimal weight: 3.9990 chunk 564 optimal weight: 10.0000 chunk 284 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 601 optimal weight: 8.9990 chunk 644 optimal weight: 5.9990 chunk 467 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 743 optimal weight: 3.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN D 74 ASN F 46 GLN G 153 HIS H 16 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN ** P 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN R 54 GLN T 55 GLN T 61 GLN T 70 ASN T 84 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN h 33 GLN o 10 GLN q 86 GLN u 49 ASN 0 45 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 152108 Z= 0.255 Angle : 0.625 15.134 227500 Z= 0.336 Chirality : 0.035 0.455 28967 Planarity : 0.006 0.133 12192 Dihedral : 22.604 179.139 76032 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 3.29 % Allowed : 22.99 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.41 (0.11), residues: 5498 helix: 1.63 (0.12), residues: 1988 sheet: -0.14 (0.16), residues: 1056 loop : -0.62 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a6206 HIS 0.006 0.001 HIS l 13 PHE 0.029 0.001 PHE H 66 TYR 0.030 0.001 TYR C 42 ARG 0.012 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 940 time to evaluate : 5.912 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: E 29 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7410 (mtp85) REVERT: F 1 MET cc_start: 0.7105 (mmm) cc_final: 0.6578 (tpt) REVERT: F 79 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7648 (ttm-80) REVERT: G 66 LEU cc_start: 0.8868 (tp) cc_final: 0.8586 (tt) REVERT: H 30 SER cc_start: 0.8211 (p) cc_final: 0.7783 (t) REVERT: O 11 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8989 (mp) REVERT: P 5 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8523 (ptt180) REVERT: R 44 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8717 (mp) REVERT: T 78 ASN cc_start: 0.8548 (m-40) cc_final: 0.8261 (m110) REVERT: U 21 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7402 (tpm170) REVERT: c 181 MET cc_start: 0.7141 (mmm) cc_final: 0.6852 (mtm) REVERT: j 93 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: o 11 GLU cc_start: 0.7003 (pp20) cc_final: 0.6755 (pp20) REVERT: s 2 ILE cc_start: 0.8817 (mp) cc_final: 0.8479 (mm) REVERT: s 26 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8283 (tmtt) REVERT: s 37 ASP cc_start: 0.7513 (p0) cc_final: 0.7249 (p0) REVERT: z 37 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8602 (mttp) REVERT: 4 25 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7899 (pmm-80) REVERT: 4 37 CYS cc_start: 0.7942 (p) cc_final: 0.7251 (p) outliers start: 151 outliers final: 115 residues processed: 1015 average time/residue: 1.9744 time to fit residues: 2903.4615 Evaluate side-chains 1042 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 919 time to evaluate : 5.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 63 GLU Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain c residue 38 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 111 LYS Chi-restraints excluded: chain c residue 157 SER Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 19 VAL Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 93 GLN Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 34 GLU Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 26 ASP Chi-restraints excluded: chain q residue 85 LYS Chi-restraints excluded: chain r residue 24 ILE Chi-restraints excluded: chain r residue 55 ILE Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 5 ASN Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain x residue 6 LEU Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 32 ILE Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 25 VAL Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 3 residue 16 ILE Chi-restraints excluded: chain 4 residue 25 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 860 optimal weight: 0.3980 chunk 905 optimal weight: 10.0000 chunk 826 optimal weight: 5.9990 chunk 881 optimal weight: 0.9980 chunk 530 optimal weight: 20.0000 chunk 383 optimal weight: 8.9990 chunk 691 optimal weight: 0.9980 chunk 270 optimal weight: 6.9990 chunk 796 optimal weight: 8.9990 chunk 833 optimal weight: 6.9990 chunk 878 optimal weight: 7.9990 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN D 74 ASN F 46 GLN G 142 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN R 31 ASN R 52 GLN R 54 GLN T 55 GLN T 70 ASN T 84 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN h 33 GLN n 61 GLN o 10 GLN q 43 ASN q 86 GLN u 49 ASN 0 45 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 152108 Z= 0.245 Angle : 0.616 15.006 227500 Z= 0.332 Chirality : 0.035 0.451 28967 Planarity : 0.006 0.132 12192 Dihedral : 22.591 179.629 76032 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 3.16 % Allowed : 23.30 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 5498 helix: 1.62 (0.12), residues: 1981 sheet: -0.10 (0.16), residues: 1069 loop : -0.60 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a6206 HIS 0.019 0.001 HIS P 59 PHE 0.031 0.001 PHE H 66 TYR 0.034 0.002 TYR O 69 ARG 0.015 0.000 ARG P 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 936 time to evaluate : 6.303 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: B 49 MET cc_start: 0.7659 (pmm) cc_final: 0.7211 (pmm) REVERT: E 29 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7466 (mtp85) REVERT: F 14 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7916 (mp10) REVERT: F 79 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7646 (ttm-80) REVERT: G 66 LEU cc_start: 0.8948 (tp) cc_final: 0.8600 (tt) REVERT: H 30 SER cc_start: 0.8317 (p) cc_final: 0.7848 (t) REVERT: O 11 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8986 (mp) REVERT: P 5 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8517 (ptt180) REVERT: T 78 ASN cc_start: 0.8430 (m-40) cc_final: 0.8192 (m110) REVERT: U 21 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7400 (tpm170) REVERT: c 181 MET cc_start: 0.7139 (mmm) cc_final: 0.6826 (mtm) REVERT: j 93 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7462 (mp10) REVERT: l 63 ILE cc_start: 0.8636 (mt) cc_final: 0.8364 (tt) REVERT: q 71 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.7722 (tppp) REVERT: s 2 ILE cc_start: 0.8797 (mp) cc_final: 0.8450 (mm) REVERT: s 26 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8268 (tmtt) REVERT: s 37 ASP cc_start: 0.7457 (p0) cc_final: 0.7208 (p0) REVERT: z 37 LYS cc_start: 0.8819 (mtpp) cc_final: 0.8597 (mttp) REVERT: 4 1 MET cc_start: 0.7998 (ttp) cc_final: 0.7769 (tpp) REVERT: 4 37 CYS cc_start: 0.7948 (p) cc_final: 0.7268 (p) outliers start: 145 outliers final: 112 residues processed: 1008 average time/residue: 2.0589 time to fit residues: 2995.1982 Evaluate side-chains 1013 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 895 time to evaluate : 5.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 63 GLU Chi-restraints excluded: chain c residue 38 SER Chi-restraints excluded: chain c residue 53 HIS Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 111 LYS Chi-restraints excluded: chain c residue 157 SER Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 19 VAL Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 93 GLN Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 5 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 34 GLU Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 26 ASP Chi-restraints excluded: chain q residue 71 LYS Chi-restraints excluded: chain q residue 85 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 24 ILE Chi-restraints excluded: chain s residue 53 VAL Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 32 ILE Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 25 VAL Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 3 residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 578 optimal weight: 6.9990 chunk 931 optimal weight: 0.9990 chunk 568 optimal weight: 10.0000 chunk 442 optimal weight: 10.0000 chunk 647 optimal weight: 10.0000 chunk 977 optimal weight: 10.0000 chunk 899 optimal weight: 0.7980 chunk 778 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 601 optimal weight: 10.0000 chunk 477 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 HIS C 123 GLN D 74 ASN F 46 GLN G 142 HIS G 153 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN T 55 GLN T 61 GLN T 70 ASN T 84 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN h 33 GLN o 10 GLN o 15 GLN q 18 GLN q 43 ASN q 86 GLN u 49 ASN x 39 GLN x 45 GLN 0 45 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 152108 Z= 0.264 Angle : 0.632 20.890 227500 Z= 0.338 Chirality : 0.035 0.454 28967 Planarity : 0.006 0.133 12192 Dihedral : 22.583 179.484 76032 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 3.14 % Allowed : 23.47 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.38 (0.11), residues: 5498 helix: 1.58 (0.12), residues: 1988 sheet: -0.13 (0.16), residues: 1079 loop : -0.64 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a6206 HIS 0.018 0.001 HIS P 59 PHE 0.031 0.001 PHE H 66 TYR 0.036 0.002 TYR O 69 ARG 0.017 0.001 ARG P 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 911 time to evaluate : 6.305 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 49 MET cc_start: 0.7554 (pmm) cc_final: 0.7229 (pmm) REVERT: E 29 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7456 (mtp85) REVERT: F 1 MET cc_start: 0.6865 (mmm) cc_final: 0.5478 (tmm) REVERT: F 79 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7675 (ttm-80) REVERT: G 66 LEU cc_start: 0.8941 (tp) cc_final: 0.8600 (tt) REVERT: H 30 SER cc_start: 0.8189 (p) cc_final: 0.7743 (t) REVERT: O 11 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8985 (mp) REVERT: P 5 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8502 (ptt180) REVERT: U 21 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7401 (tpm170) REVERT: c 181 MET cc_start: 0.7138 (mmm) cc_final: 0.6821 (mtm) REVERT: j 93 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7445 (mp10) REVERT: l 63 ILE cc_start: 0.8658 (mt) cc_final: 0.8361 (tt) REVERT: q 71 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.7724 (tppp) REVERT: s 2 ILE cc_start: 0.8795 (mp) cc_final: 0.8461 (mm) REVERT: s 26 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8272 (tmtt) REVERT: s 37 ASP cc_start: 0.7432 (p0) cc_final: 0.7193 (p0) REVERT: x 57 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8255 (mp) REVERT: z 37 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8600 (mttp) REVERT: 4 1 MET cc_start: 0.8053 (ttp) cc_final: 0.7825 (tpp) REVERT: 4 37 CYS cc_start: 0.7953 (p) cc_final: 0.7276 (p) outliers start: 144 outliers final: 117 residues processed: 987 average time/residue: 1.9990 time to fit residues: 2859.6593 Evaluate side-chains 1016 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 891 time to evaluate : 6.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 63 GLU Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain c residue 38 SER Chi-restraints excluded: chain c residue 53 HIS Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 157 SER Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 19 VAL Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 93 GLN Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 5 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 34 GLU Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 22 LEU Chi-restraints excluded: chain q residue 26 ASP Chi-restraints excluded: chain q residue 71 LYS Chi-restraints excluded: chain q residue 85 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 24 ILE Chi-restraints excluded: chain s residue 53 VAL Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 57 LEU Chi-restraints excluded: chain y residue 32 ILE Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 25 VAL Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 3 residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 618 optimal weight: 5.9990 chunk 829 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 717 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 216 optimal weight: 5.9990 chunk 779 optimal weight: 0.7980 chunk 326 optimal weight: 0.0010 chunk 800 optimal weight: 2.9990 chunk 98 optimal weight: 50.0000 chunk 143 optimal weight: 20.0000 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 HIS D 74 ASN F 46 GLN G 142 HIS G 153 HIS H 16 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN Q 47 HIS R 31 ASN R 52 GLN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 GLN T 70 ASN T 84 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 ASN f 81 GLN h 33 GLN o 10 GLN q 43 ASN q 86 GLN u 49 ASN 0 45 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.144391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.097445 restraints weight = 207852.710| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.13 r_work: 0.3228 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 152108 Z= 0.154 Angle : 0.603 19.540 227500 Z= 0.327 Chirality : 0.033 0.452 28967 Planarity : 0.006 0.126 12192 Dihedral : 22.631 179.497 76032 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 2.42 % Allowed : 24.43 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.47 (0.11), residues: 5498 helix: 1.64 (0.12), residues: 1982 sheet: -0.09 (0.15), residues: 1106 loop : -0.55 (0.13), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP S 34 HIS 0.017 0.001 HIS P 59 PHE 0.029 0.001 PHE H 66 TYR 0.038 0.001 TYR O 69 ARG 0.016 0.000 ARG P 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45080.38 seconds wall clock time: 780 minutes 40.19 seconds (46840.19 seconds total)