Starting phenix.real_space_refine on Tue Mar 19 11:31:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/03_2024/7oiz_12936_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/03_2024/7oiz_12936.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/03_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_12936/03_2024/7oiz_12936_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/03_2024/7oiz_12936_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/03_2024/7oiz_12936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/03_2024/7oiz_12936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/03_2024/7oiz_12936_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiz_12936/03_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 53.16, per 1000 atoms: 0.38 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: 54.06 Conformation dependent library (CDL) restraints added in 7.1 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: 69.40 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: 251.82 Time building geometry restraints manager: 58.91 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=" C1' MA6 A1518 " pdb=" N9 MA6 A1518 " pdb=" C8 MA6 A1518 " ideal model delta sigma weight residual 126.14 141.29 -15.15 3.00e+00 1.11e-01 2.55e+01 ... (remaining 227495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 86677 35.98 - 71.97: 9603 71.97 - 107.95: 1105 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 14.970 Check model and map are aligned: 1.490 Set scattering table: 0.950 Process input model: 545.330 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 580.610 ------------------------------------------------------------------------------- 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 : 0.825 20.549 227500 Z= 0.423 Chirality : 0.046 0.496 28967 Planarity : 0.019 0.597 12192 Dihedral : 22.403 179.916 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 : 5.778 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: 2.1044 time to fit residues: 3422.1337 Evaluate side-chains 916 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 916 time to evaluate : 5.772 ------------------------------------------------------------------------------- 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** J 15 HIS ** 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 152108 Z= 0.207 Angle : 0.609 15.520 227500 Z= 0.331 Chirality : 0.035 0.459 28967 Planarity : 0.006 0.129 12192 Dihedral : 22.744 179.271 76032 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 2.22 % Allowed : 13.06 % Favored : 84.72 % 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: 0.04 (0.11), residues: 5498 helix: 1.07 (0.12), residues: 1974 sheet: -0.17 (0.15), residues: 1085 loop : -0.67 (0.12), residues: 2439 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 0.022 0.002 TYR p 47 ARG 0.007 0.000 ARG K 69 *********************** 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 1082 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 980 time to evaluate : 5.872 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: 0.7933 (OUTLIER) cc_final: 0.7403 (mtp85) REVERT: E 70 ASN cc_start: 0.7507 (t0) cc_final: 0.7305 (t0) REVERT: O 64 ARG cc_start: 0.8073 (tpp80) cc_final: 0.7858 (tpp-160) REVERT: O 68 ASP cc_start: 0.7727 (m-30) cc_final: 0.7398 (m-30) REVERT: P 5 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7897 (ptt180) REVERT: S 37 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7614 (ptm-80) REVERT: T 74 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.7846 (mtm-85) REVERT: T 78 ASN cc_start: 0.8798 (m-40) cc_final: 0.8465 (m110) REVERT: c 146 MET cc_start: 0.7113 (mmm) cc_final: 0.6883 (mmm) REVERT: f 98 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7509 (mt-10) REVERT: j 93 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7557 (mp10) REVERT: j 108 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7381 (mtt-85) REVERT: r 92 ARG cc_start: 0.7904 (mtp-110) cc_final: 0.7624 (mtp-110) REVERT: s 37 ASP cc_start: 0.7383 (p0) cc_final: 0.7125 (p0) REVERT: s 76 ARG cc_start: 0.7529 (tpt90) cc_final: 0.7310 (tpt-90) REVERT: s 87 LEU cc_start: 0.8034 (mt) cc_final: 0.7833 (mt) REVERT: 1 15 SER cc_start: 0.8491 (m) cc_final: 0.8219 (m) outliers start: 102 outliers final: 45 residues processed: 1014 average time/residue: 2.0718 time to fit residues: 3008.1658 Evaluate side-chains 979 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 929 time to evaluate : 5.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 153 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 44 ILE 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 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 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: 5.9990 chunk 741 optimal weight: 4.9990 chunk 606 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 892 optimal weight: 3.9990 chunk 964 optimal weight: 4.9990 chunk 794 optimal weight: 1.9990 chunk 885 optimal weight: 0.6980 chunk 304 optimal weight: 7.9990 chunk 715 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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** C 3 GLN D 74 ASN F 46 GLN H 16 ASN 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: 0.8363 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 152108 Z= 0.234 Angle : 0.600 13.398 227500 Z= 0.325 Chirality : 0.034 0.451 28967 Planarity : 0.006 0.134 12192 Dihedral : 22.663 179.564 76032 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 3.09 % Allowed : 15.61 % Favored : 81.30 % 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: 0.36 (0.11), residues: 5498 helix: 1.48 (0.12), residues: 1972 sheet: -0.03 (0.16), residues: 1070 loop : -0.60 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a6206 HIS 0.009 0.001 HIS J 15 PHE 0.027 0.001 PHE G 26 TYR 0.024 0.001 TYR p 47 ARG 0.010 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 1112 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 970 time to evaluate : 5.907 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: E 29 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7656 (mtt90) REVERT: E 70 ASN cc_start: 0.7619 (t0) cc_final: 0.7371 (t0) REVERT: K 32 VAL cc_start: 0.9219 (t) cc_final: 0.9018 (t) REVERT: O 68 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: P 5 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8419 (ptt180) REVERT: S 66 MET cc_start: 0.7927 (ppp) cc_final: 0.6851 (ppp) REVERT: T 74 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8419 (mtm110) REVERT: T 78 ASN cc_start: 0.8723 (m-40) cc_final: 0.8426 (m110) REVERT: c 146 MET cc_start: 0.7135 (mmm) cc_final: 0.6865 (mmm) REVERT: c 181 MET cc_start: 0.7062 (mmm) cc_final: 0.6754 (mtm) REVERT: f 7 TYR cc_start: 0.8736 (t80) cc_final: 0.8469 (t80) REVERT: j 93 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: s 2 ILE cc_start: 0.8780 (mp) cc_final: 0.8369 (mm) REVERT: s 26 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8335 (tmtt) REVERT: s 37 ASP cc_start: 0.7327 (p0) cc_final: 0.7079 (p0) REVERT: u 78 GLN cc_start: 0.8225 (mt0) cc_final: 0.8023 (mt0) REVERT: y 31 ARG cc_start: 0.8503 (ptp90) cc_final: 0.8140 (ptp90) REVERT: 4 1 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7800 (mmm) outliers start: 142 outliers final: 70 residues processed: 1018 average time/residue: 2.2241 time to fit residues: 3273.6847 Evaluate side-chains 999 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 924 time to evaluate : 5.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 199 VAL 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 Q residue 18 GLU 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: 0.8980 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: 0.9980 chunk 948 optimal weight: 8.9990 chunk 467 optimal weight: 8.9990 chunk 848 optimal weight: 0.9990 chunk 255 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 F 46 GLN H 16 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN R 31 ASN R 52 GLN R 54 GLN T 55 GLN T 70 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN o 10 GLN u 49 ASN 0 45 GLN 3 13 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 152108 Z= 0.247 Angle : 0.601 13.930 227500 Z= 0.325 Chirality : 0.034 0.451 28967 Planarity : 0.006 0.133 12192 Dihedral : 22.618 179.547 76032 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 3.57 % Allowed : 17.37 % Favored : 79.06 % 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: 0.45 (0.11), residues: 5498 helix: 1.56 (0.12), residues: 1984 sheet: -0.05 (0.16), residues: 1068 loop : -0.55 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a6206 HIS 0.011 0.001 HIS P 59 PHE 0.018 0.001 PHE G 26 TYR 0.023 0.002 TYR p 47 ARG 0.009 0.000 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 1138 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 974 time to evaluate : 5.856 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: 0.7877 (OUTLIER) cc_final: 0.7628 (mtt90) REVERT: G 66 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8408 (tt) REVERT: N 98 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8262 (ttmm) REVERT: O 65 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8537 (mttp) REVERT: P 5 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8448 (ptt180) REVERT: R 65 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8404 (mp) REVERT: T 74 ARG cc_start: 0.8713 (mtm-85) cc_final: 0.8354 (mtm110) REVERT: T 78 ASN cc_start: 0.8664 (m-40) cc_final: 0.8386 (m110) REVERT: c 181 MET cc_start: 0.7057 (mmm) cc_final: 0.6772 (mtm) REVERT: j 93 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: m 32 GLU cc_start: 0.8119 (mp0) cc_final: 0.7861 (mp0) REVERT: r 62 ASP cc_start: 0.7881 (m-30) cc_final: 0.7537 (m-30) REVERT: s 2 ILE cc_start: 0.8782 (mp) cc_final: 0.8389 (mm) REVERT: s 26 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8349 (tmtt) REVERT: s 37 ASP cc_start: 0.7376 (p0) cc_final: 0.7131 (p0) REVERT: u 78 GLN cc_start: 0.8207 (mt0) cc_final: 0.7932 (mt0) REVERT: 0 7 GLU cc_start: 0.7895 (pm20) cc_final: 0.7691 (pm20) outliers start: 164 outliers final: 84 residues processed: 1045 average time/residue: 2.0636 time to fit residues: 3091.7324 Evaluate side-chains 1003 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 913 time to evaluate : 5.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 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 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 103 VAL Chi-restraints excluded: chain G residue 66 LEU 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 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 65 LYS 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 26 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 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 106 SER Chi-restraints excluded: chain g residue 171 THR 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 k residue 7 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 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 Chi-restraints excluded: chain 4 residue 25 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 789 optimal weight: 5.9990 chunk 538 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 706 optimal weight: 5.9990 chunk 391 optimal weight: 10.0000 chunk 809 optimal weight: 0.4980 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: 0.0010 overall best weight: 3.8992 ------------------------------------------------------------------------------- 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 61 GLN F 46 GLN G 153 HIS ** H 16 ASN ** 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 52 GLN R 54 GLN T 70 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 260 ASN f 81 GLN j 90 ASN o 10 GLN u 49 ASN ** x 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 45 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 152108 Z= 0.295 Angle : 0.628 13.723 227500 Z= 0.337 Chirality : 0.036 0.459 28967 Planarity : 0.006 0.136 12192 Dihedral : 22.610 179.384 76032 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 3.94 % Allowed : 19.01 % Favored : 77.05 % 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: 0.46 (0.11), residues: 5498 helix: 1.62 (0.12), residues: 1986 sheet: -0.11 (0.16), residues: 1072 loop : -0.55 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a6206 HIS 0.011 0.001 HIS P 59 PHE 0.023 0.001 PHE G 62 TYR 0.024 0.002 TYR p 47 ARG 0.009 0.000 ARG f 95 *********************** 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 1124 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 943 time to evaluate : 5.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 29 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7422 (mtp85) REVERT: E 70 ASN cc_start: 0.7729 (t0) cc_final: 0.7477 (t0) REVERT: G 66 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8462 (tt) REVERT: I 130 ARG cc_start: 0.7436 (ptp-170) cc_final: 0.7124 (ptp-170) REVERT: J 7 ARG cc_start: 0.7572 (mmt-90) cc_final: 0.7109 (mmt180) REVERT: N 70 PRO cc_start: 0.9508 (Cg_endo) cc_final: 0.9291 (Cg_exo) REVERT: O 11 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8976 (mp) REVERT: O 65 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8557 (mttp) REVERT: P 5 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8494 (ptt180) REVERT: R 44 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8759 (mp) REVERT: T 74 ARG cc_start: 0.8749 (mtm-85) cc_final: 0.8373 (ttm110) REVERT: T 78 ASN cc_start: 0.8619 (m-40) cc_final: 0.8302 (m110) REVERT: U 21 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7412 (tpm170) REVERT: c 181 MET cc_start: 0.7162 (mmm) cc_final: 0.6852 (mtm) REVERT: j 93 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: m 32 GLU cc_start: 0.8076 (mp0) cc_final: 0.7712 (mp0) REVERT: q 71 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.7725 (tppp) REVERT: r 62 ASP cc_start: 0.7711 (m-30) cc_final: 0.7495 (m-30) REVERT: s 2 ILE cc_start: 0.8822 (mp) cc_final: 0.8451 (mm) REVERT: s 26 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8289 (tmtt) REVERT: s 37 ASP cc_start: 0.7435 (p0) cc_final: 0.7193 (p0) REVERT: s 49 LYS cc_start: 0.8310 (tmtp) cc_final: 0.7925 (tmtt) REVERT: 4 37 CYS cc_start: 0.8062 (p) cc_final: 0.7338 (p) outliers start: 181 outliers final: 109 residues processed: 1038 average time/residue: 2.0663 time to fit residues: 3073.2477 Evaluate side-chains 1017 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 899 time to evaluate : 5.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain D residue 88 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 103 VAL Chi-restraints excluded: chain G residue 66 LEU 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 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 L residue 40 THR Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain N residue 6 MET Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 65 LYS 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 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 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 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 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 k residue 103 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 33 ILE 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 n residue 52 SER Chi-restraints excluded: chain n residue 95 SER 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 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 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 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 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 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 319 optimal weight: 9.9990 chunk 853 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 556 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 949 optimal weight: 5.9990 chunk 787 optimal weight: 3.9990 chunk 439 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 498 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 F 46 GLN G 153 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN P 63 GLN R 52 GLN R 54 GLN T 55 GLN T 61 GLN T 70 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN f 81 GLN h 28 ASN j 90 ASN o 10 GLN q 43 ASN r 9 HIS u 49 ASN x 39 GLN 0 45 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 152108 Z= 0.370 Angle : 0.674 16.280 227500 Z= 0.358 Chirality : 0.039 0.467 28967 Planarity : 0.006 0.140 12192 Dihedral : 22.632 179.695 76032 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 4.01 % Allowed : 20.01 % Favored : 75.99 % 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: 0.35 (0.11), residues: 5498 helix: 1.57 (0.12), residues: 1976 sheet: -0.19 (0.16), residues: 1052 loop : -0.64 (0.12), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a6206 HIS 0.012 0.001 HIS P 59 PHE 0.023 0.002 PHE E 48 TYR 0.029 0.002 TYR C 42 ARG 0.010 0.001 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 1151 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 967 time to evaluate : 5.965 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: 0.8051 (OUTLIER) cc_final: 0.7555 (mtp85) REVERT: E 50 TYR cc_start: 0.8648 (t80) cc_final: 0.8425 (t80) REVERT: E 54 ARG cc_start: 0.8584 (mmm160) cc_final: 0.8379 (tpp80) REVERT: G 66 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8496 (tt) REVERT: N 62 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8030 (m-40) REVERT: N 70 PRO cc_start: 0.9516 (Cg_endo) cc_final: 0.9299 (Cg_exo) REVERT: O 65 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8662 (mttp) REVERT: P 5 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8593 (ptt180) REVERT: R 44 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8716 (mp) REVERT: T 60 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.7943 (ttm-80) REVERT: T 74 ARG cc_start: 0.8759 (mtm-85) cc_final: 0.8343 (ttm110) REVERT: T 78 ASN cc_start: 0.8654 (m-40) cc_final: 0.8419 (m110) REVERT: U 21 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7420 (tpm170) REVERT: c 181 MET cc_start: 0.7170 (mmm) cc_final: 0.6826 (mtm) REVERT: c 203 ARG cc_start: 0.8199 (ptm160) cc_final: 0.7962 (ptm160) REVERT: c 214 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7991 (tpp80) REVERT: j 91 SER cc_start: 0.8576 (t) cc_final: 0.7787 (p) REVERT: j 93 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: m 32 GLU cc_start: 0.8144 (mp0) cc_final: 0.7717 (mp0) REVERT: q 43 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7443 (t0) REVERT: q 71 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.7852 (tppp) REVERT: s 2 ILE cc_start: 0.8793 (mp) cc_final: 0.8444 (mm) REVERT: s 37 ASP cc_start: 0.7625 (p0) cc_final: 0.7377 (p0) REVERT: 4 37 CYS cc_start: 0.7983 (p) cc_final: 0.7287 (p) outliers start: 184 outliers final: 110 residues processed: 1063 average time/residue: 2.0839 time to fit residues: 3178.2876 Evaluate side-chains 1045 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 924 time to evaluate : 5.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU 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 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 66 LEU 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 26 SER Chi-restraints excluded: chain K residue 32 VAL 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 N residue 62 ASN Chi-restraints excluded: chain O residue 65 LYS 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 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 214 ARG 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 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 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 k residue 103 ILE 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 33 ILE 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 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 43 ASN 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 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 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 0 residue 22 THR Chi-restraints excluded: chain 0 residue 48 ILE 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 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 915 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 540 optimal weight: 8.9990 chunk 693 optimal weight: 2.9990 chunk 537 optimal weight: 7.9990 chunk 798 optimal weight: 3.9990 chunk 530 optimal weight: 10.0000 chunk 945 optimal weight: 2.9990 chunk 591 optimal weight: 5.9990 chunk 576 optimal weight: 4.9990 chunk 436 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN E 43 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 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** f 81 GLN g 38 ASN j 90 ASN o 10 GLN q 43 ASN q 86 GLN u 49 ASN 0 45 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 152108 Z= 0.252 Angle : 0.615 14.323 227500 Z= 0.332 Chirality : 0.035 0.458 28967 Planarity : 0.006 0.133 12192 Dihedral : 22.604 179.434 76032 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 3.46 % Allowed : 21.95 % Favored : 74.59 % 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: 0.42 (0.11), residues: 5498 helix: 1.65 (0.12), residues: 1982 sheet: -0.14 (0.15), residues: 1093 loop : -0.63 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a6206 HIS 0.009 0.001 HIS J 15 PHE 0.028 0.001 PHE H 66 TYR 0.028 0.002 TYR q 2 ARG 0.010 0.000 ARG J 89 *********************** 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 1107 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 948 time to evaluate : 5.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 GLU cc_start: 0.7765 (pm20) cc_final: 0.7202 (pm20) REVERT: E 29 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7399 (mtp85) REVERT: F 79 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7647 (ttm-80) REVERT: G 66 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8506 (tt) REVERT: N 62 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8011 (m-40) REVERT: N 70 PRO cc_start: 0.9498 (Cg_endo) cc_final: 0.9289 (Cg_exo) REVERT: O 65 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8558 (mttp) REVERT: P 5 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8514 (ptt180) REVERT: T 74 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8360 (ttm110) REVERT: T 78 ASN cc_start: 0.8593 (m-40) cc_final: 0.8289 (m110) REVERT: U 21 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7407 (tpm170) REVERT: c 181 MET cc_start: 0.7137 (mmm) cc_final: 0.6799 (mtm) REVERT: j 93 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7447 (mp10) REVERT: m 32 GLU cc_start: 0.8125 (mp0) cc_final: 0.7724 (mp0) REVERT: q 71 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.7701 (tppp) REVERT: s 2 ILE cc_start: 0.8823 (mp) cc_final: 0.8474 (mm) REVERT: s 26 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8236 (tmtt) REVERT: s 37 ASP cc_start: 0.7533 (p0) cc_final: 0.7267 (p0) REVERT: s 49 LYS cc_start: 0.8310 (tmtp) cc_final: 0.7932 (tmtt) REVERT: 4 37 CYS cc_start: 0.7938 (p) cc_final: 0.7233 (p) outliers start: 159 outliers final: 112 residues processed: 1033 average time/residue: 2.0578 time to fit residues: 3078.3033 Evaluate side-chains 1027 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 907 time to evaluate : 5.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU 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 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 66 LEU 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 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 35 THR Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain O residue 65 LYS 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 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 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 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 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 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 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 k residue 103 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 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 49 VAL Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 95 SER 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 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 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 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 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 48 ILE 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 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 584 optimal weight: 7.9990 chunk 377 optimal weight: 0.7980 chunk 564 optimal weight: 10.0000 chunk 284 optimal weight: 30.0000 chunk 185 optimal weight: 10.0000 chunk 183 optimal weight: 0.1980 chunk 601 optimal weight: 10.0000 chunk 644 optimal weight: 6.9990 chunk 467 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 743 optimal weight: 10.0000 overall best weight: 4.9986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN R 52 GLN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 j 90 ASN o 10 GLN q 18 GLN q 43 ASN 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: 0.8425 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 152108 Z= 0.371 Angle : 0.679 17.929 227500 Z= 0.360 Chirality : 0.039 0.460 28967 Planarity : 0.006 0.140 12192 Dihedral : 22.621 179.511 76032 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 3.68 % Allowed : 22.43 % Favored : 73.90 % 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: 0.36 (0.11), residues: 5498 helix: 1.62 (0.12), residues: 1978 sheet: -0.18 (0.16), residues: 1052 loop : -0.67 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a6206 HIS 0.017 0.001 HIS P 59 PHE 0.027 0.002 PHE E 48 TYR 0.027 0.002 TYR O 69 ARG 0.012 0.001 ARG P 56 *********************** 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 1103 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 934 time to evaluate : 5.886 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: E 29 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7548 (mtp85) REVERT: F 1 MET cc_start: 0.7192 (mmm) cc_final: 0.6658 (tpt) REVERT: F 79 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7661 (ttm-80) REVERT: G 66 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8499 (tt) REVERT: H 30 SER cc_start: 0.8356 (p) cc_final: 0.7870 (t) REVERT: N 62 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8035 (m-40) REVERT: N 70 PRO cc_start: 0.9507 (Cg_endo) cc_final: 0.9280 (Cg_exo) REVERT: O 65 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8596 (mttp) REVERT: P 5 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8607 (ptt180) REVERT: T 74 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.8366 (mtm110) REVERT: T 78 ASN cc_start: 0.8499 (m-40) cc_final: 0.8278 (m110) REVERT: U 21 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7412 (tpm170) REVERT: c 181 MET cc_start: 0.7155 (mmm) cc_final: 0.6854 (mtm) REVERT: d 184 ARG cc_start: 0.8226 (mtm180) cc_final: 0.7626 (mtt180) REVERT: e 122 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7342 (mm-30) REVERT: j 91 SER cc_start: 0.8531 (t) cc_final: 0.7737 (p) REVERT: j 93 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7512 (mp10) REVERT: m 32 GLU cc_start: 0.8136 (mp0) cc_final: 0.7893 (mp0) REVERT: o 114 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7708 (mt) REVERT: q 71 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.7793 (tppp) REVERT: s 2 ILE cc_start: 0.8834 (mp) cc_final: 0.8486 (mm) REVERT: s 26 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8283 (tmtt) REVERT: s 37 ASP cc_start: 0.7556 (p0) cc_final: 0.7327 (p0) REVERT: s 49 LYS cc_start: 0.8304 (tmtp) cc_final: 0.7917 (tmtt) REVERT: u 12 GLN cc_start: 0.8640 (mp10) cc_final: 0.8360 (mt0) REVERT: 4 25 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7881 (pmm-80) REVERT: 4 37 CYS cc_start: 0.7955 (p) cc_final: 0.7266 (p) outliers start: 169 outliers final: 123 residues processed: 1026 average time/residue: 2.0627 time to fit residues: 3053.5894 Evaluate side-chains 1042 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 909 time to evaluate : 5.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU 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 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 66 LEU 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 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 35 THR Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain N residue 6 MET Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain O residue 65 LYS 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 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 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 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 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 60 ASP 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 6 SER 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 3 LYS 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 n residue 52 SER Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 95 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 25 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 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 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 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 48 ILE 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 1 MET 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: 1.9990 chunk 905 optimal weight: 5.9990 chunk 826 optimal weight: 0.7980 chunk 881 optimal weight: 0.8980 chunk 530 optimal weight: 10.0000 chunk 383 optimal weight: 7.9990 chunk 691 optimal weight: 2.9990 chunk 270 optimal weight: 7.9990 chunk 796 optimal weight: 0.1980 chunk 833 optimal weight: 0.9980 chunk 878 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN F 46 GLN G 142 HIS G 153 HIS H 16 ASN M 8 ASN 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** f 81 GLN o 10 GLN u 49 ASN ** u 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 45 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 152108 Z= 0.135 Angle : 0.582 18.349 227500 Z= 0.317 Chirality : 0.032 0.426 28967 Planarity : 0.006 0.123 12192 Dihedral : 22.602 179.425 76032 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.09 % Favored : 96.87 % Rotamer: Outliers : 2.22 % Allowed : 24.23 % 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: 0.52 (0.11), residues: 5498 helix: 1.73 (0.12), residues: 1978 sheet: -0.10 (0.15), residues: 1109 loop : -0.55 (0.13), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a6206 HIS 0.015 0.001 HIS P 59 PHE 0.026 0.001 PHE E 48 TYR 0.031 0.001 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 1059 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 957 time to evaluate : 5.924 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: 0.7801 (OUTLIER) cc_final: 0.7562 (mtt90) REVERT: F 14 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7840 (mp10) REVERT: F 79 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7614 (ttm-80) REVERT: G 66 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8500 (tt) REVERT: H 30 SER cc_start: 0.8160 (p) cc_final: 0.7742 (t) REVERT: H 88 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.7873 (tpp-160) REVERT: P 5 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8404 (ptt180) REVERT: c 181 MET cc_start: 0.7054 (mmm) cc_final: 0.6728 (mtm) REVERT: c 251 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: j 93 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7395 (mp10) REVERT: m 32 GLU cc_start: 0.8105 (mp0) cc_final: 0.7711 (mp0) REVERT: o 114 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7605 (mt) REVERT: s 2 ILE cc_start: 0.8733 (mp) cc_final: 0.8400 (mm) REVERT: s 37 ASP cc_start: 0.7393 (p0) cc_final: 0.7150 (p0) REVERT: s 49 LYS cc_start: 0.8244 (tmtp) cc_final: 0.7891 (tmtt) REVERT: 1 15 SER cc_start: 0.8589 (m) cc_final: 0.8355 (m) REVERT: 4 37 CYS cc_start: 0.7920 (p) cc_final: 0.7224 (p) outliers start: 102 outliers final: 68 residues processed: 1015 average time/residue: 2.0026 time to fit residues: 2961.7197 Evaluate side-chains 983 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 909 time to evaluate : 5.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 199 VAL 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 90 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 66 LEU 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 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 T residue 3 ASN Chi-restraints excluded: chain c residue 38 SER Chi-restraints excluded: chain c residue 111 LYS Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 251 GLN 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 e residue 3 LEU Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 64 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 104 THR Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 103 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 n residue 27 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 86 VAL Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 26 ASP Chi-restraints excluded: chain r residue 24 ILE Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 15 THR 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 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 0 residue 54 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: 4.9990 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: 0.9980 chunk 778 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 601 optimal weight: 10.0000 chunk 477 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN 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** ** 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 84 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 ASN e 163 ASN f 81 GLN h 33 GLN o 15 GLN q 43 ASN 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: 0.8424 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 152108 Z= 0.386 Angle : 0.693 17.597 227500 Z= 0.365 Chirality : 0.039 0.452 28967 Planarity : 0.007 0.140 12192 Dihedral : 22.595 179.667 76032 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 2.31 % Allowed : 24.99 % Favored : 72.70 % 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: 0.39 (0.11), residues: 5498 helix: 1.59 (0.12), residues: 1988 sheet: -0.19 (0.16), residues: 1053 loop : -0.59 (0.12), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a6206 HIS 0.017 0.001 HIS P 59 PHE 0.031 0.002 PHE E 48 TYR 0.037 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 1027 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 921 time to evaluate : 5.900 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: 0.8057 (OUTLIER) cc_final: 0.7545 (mtp85) REVERT: F 1 MET cc_start: 0.6980 (mmm) cc_final: 0.5585 (tmm) REVERT: F 79 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7657 (ttm-80) REVERT: G 66 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8493 (tt) REVERT: H 30 SER cc_start: 0.8258 (p) cc_final: 0.7738 (t) REVERT: P 5 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8560 (ptt180) REVERT: S 34 TRP cc_start: 0.8569 (m-90) cc_final: 0.8164 (m-90) REVERT: U 21 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7398 (tpm170) REVERT: c 181 MET cc_start: 0.7188 (mmm) cc_final: 0.6848 (mtm) REVERT: c 251 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: j 93 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: m 32 GLU cc_start: 0.8121 (mp0) cc_final: 0.7874 (mp0) REVERT: o 114 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7746 (mt) REVERT: q 71 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.7720 (tppp) REVERT: s 2 ILE cc_start: 0.8821 (mp) cc_final: 0.8492 (mm) REVERT: s 37 ASP cc_start: 0.7543 (p0) cc_final: 0.7296 (p0) REVERT: s 49 LYS cc_start: 0.8337 (tmtp) cc_final: 0.7952 (tmtt) REVERT: 4 37 CYS cc_start: 0.7972 (p) cc_final: 0.7287 (p) outliers start: 106 outliers final: 76 residues processed: 986 average time/residue: 2.0376 time to fit residues: 2928.9590 Evaluate side-chains 980 residues out of total 4594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 896 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU 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 134 SER Chi-restraints excluded: chain D residue 138 SER 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 66 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 L residue 16 VAL Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 45 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 T residue 3 ASN Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain c residue 38 SER Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 251 GLN 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 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 149 VAL Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 64 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 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 n residue 27 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 95 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 25 LEU Chi-restraints excluded: chain q residue 26 ASP Chi-restraints excluded: chain q residue 71 LYS Chi-restraints excluded: chain r residue 24 ILE Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 15 THR 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 19 SER 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 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 54 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 618 optimal weight: 3.9990 chunk 829 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 717 optimal weight: 0.7980 chunk 114 optimal weight: 30.0000 chunk 216 optimal weight: 10.0000 chunk 779 optimal weight: 0.0980 chunk 326 optimal weight: 5.9990 chunk 800 optimal weight: 5.9990 chunk 98 optimal weight: 50.0000 chunk 143 optimal weight: 20.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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** H 38 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN Q 47 HIS R 52 GLN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 = 0.3925 r_free = 0.3925 target = 0.142314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094916 restraints weight = 207610.278| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.20 r_work: 0.3189 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 152108 Z= 0.245 Angle : 0.632 16.977 227500 Z= 0.340 Chirality : 0.035 0.461 28967 Planarity : 0.006 0.132 12192 Dihedral : 22.611 179.197 76032 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 2.13 % Allowed : 25.41 % Favored : 72.46 % 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: 0.37 (0.11), residues: 5498 helix: 1.56 (0.12), residues: 1988 sheet: -0.21 (0.15), residues: 1078 loop : -0.58 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP S 34 HIS 0.017 0.001 HIS P 59 PHE 0.027 0.001 PHE E 48 TYR 0.037 0.002 TYR O 69 ARG 0.021 0.001 ARG J 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44562.81 seconds wall clock time: 772 minutes 55.86 seconds (46375.86 seconds total)