Starting phenix.real_space_refine on Wed Apr 17 13:10:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj0_12937/04_2024/7oj0_12937_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj0_12937/04_2024/7oj0_12937.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj0_12937/04_2024/7oj0_12937_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj0_12937/04_2024/7oj0_12937_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj0_12937/04_2024/7oj0_12937_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj0_12937/04_2024/7oj0_12937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj0_12937/04_2024/7oj0_12937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj0_12937/04_2024/7oj0_12937_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj0_12937/04_2024/7oj0_12937_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.016 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 4525 5.49 5 Mg 308 5.21 5 S 169 5.16 5 C 74049 2.51 5 N 27235 2.21 5 O 40219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 236": "OE1" <-> "OE2" Residue "l PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 146507 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 32612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32612 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 122, 'rna2p_pyr': 81, 'rna3p': 10, 'rna3p_pur': 740, 'rna3p_pyr': 565} Link IDs: {'rna2p': 204, 'rna3p': 1314} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 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: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 952 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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: 60285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2807, 60285 Classifications: {'RNA': 2807} Modifications used: {'rna2p': 6, 'rna2p_pur': 273, 'rna2p_pyr': 145, 'rna3p': 17, 'rna3p_pur': 1343, 'rna3p_pyr': 1023} Link IDs: {'rna2p': 423, 'rna3p': 2383} Chain breaks: 2 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 3} 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: "6" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "8" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2800 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 345} Chain breaks: 1 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: "5" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "9" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 966 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 9, 'TRANS': 123} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Unusual residues: {' MG': 93} Classifications: {'undetermined': 93} Link IDs: {None: 92} Chain: "a" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 223 Unusual residues: {' MG': 208} Classifications: {'peptide': 1, 'undetermined': 208} Modifications used: {'COO': 1} Link IDs: {None: 208} 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: "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 A0TPR SG CYS 3 11 116.587 150.048 175.441 1.00 93.59 S ATOM A0TQG SG CYS 3 14 115.152 153.085 174.825 1.00 91.36 S ATOM A0TTB SG CYS 3 27 118.592 153.148 175.545 1.00 96.64 S ATOM A0TZE SG CYS 4 16 55.968 70.211 127.175 1.00162.54 S ATOM A0TZQ SG CYS 4 18 54.574 67.966 130.082 1.00166.03 S ATOM A0U3O SG CYS 4 37 54.663 71.645 130.333 1.00157.77 S ATOM A0U49 SG CYS 4 40 57.912 69.614 130.392 1.00160.16 S Time building chain proxies: 56.46, per 1000 atoms: 0.39 Number of scatterers: 146507 At special positions: 0 Unit cell: (265.58, 278.588, 237.396, 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 169 16.00 P 4525 15.00 Mg 308 11.99 O 40219 8.00 N 27235 7.00 C 74049 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: 55.77 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " 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=" ND1 HIS 3 33 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 37 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " Number of angles added : 9 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11526 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: 197 helices and 74 sheets defined 40.8% alpha, 19.4% beta 1620 base pairs and 2512 stacking pairs defined. Time for finding SS restraints: 76.91 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: 4.590A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 6.770A 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 150 through 155 removed outlier: 5.064A pdb=" N MET B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 150 through 155' 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 25 through 48 removed outlier: 4.502A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) 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: 5.054A 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: 5.056A 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: 3.777A pdb=" N GLN D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SER D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 166 removed outlier: 4.365A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 4.332A 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 Proline residue: F 19 - end of helix Processing helix chain 'F' and resid 67 through 81 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: 5.600A 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 39 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 Processing helix chain 'K' and resid 60 through 76 removed outlier: 5.002A 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 23 removed outlier: 5.254A pdb=" N TYR M 23 " --> pdb=" O LEU M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 64 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: 5.252A 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 63 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: 4.764A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 3.766A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 17 removed outlier: 4.771A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL c 16 " --> pdb=" O GLY c 12 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL c 17 " --> pdb=" O ARG c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 3.954A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 30 through 35' Processing helix chain 'c' and resid 131 through 136 Proline residue: c 136 - end of helix Processing helix chain 'c' and resid 199 through 204 removed outlier: 6.270A pdb=" N VAL c 204 " --> pdb=" O HIS c 200 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 215 Processing helix chain 'c' and resid 221 through 226 removed outlier: 4.924A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 260 through 268 removed outlier: 4.500A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 72 Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.541A 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 'e' and resid 24 through 41 removed outlier: 5.705A pdb=" N GLN e 41 " --> pdb=" O ALA e 37 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.428A pdb=" N THR e 53 " --> pdb=" O ARG e 49 " (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: 4.852A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 184 removed outlier: 6.274A pdb=" N ASP e 184 " --> pdb=" O LEU e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'e' and resid 16 through 21 Processing helix chain 'f' and resid 2 through 21 removed outlier: 5.453A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 30 Proline residue: f 29 - end of helix Processing helix chain 'f' and resid 46 through 62 removed outlier: 3.992A pdb=" N LEU f 50 " --> pdb=" O ASP f 46 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 111 removed outlier: 5.528A 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 134 through 139 removed outlier: 4.697A pdb=" N PHE f 138 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Proline residue: f 139 - end of helix No H-bonds generated for 'chain 'f' and resid 134 through 139' Processing helix chain 'f' and resid 162 through 174 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: 5.327A 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 28 Processing helix chain 'h' and resid 29 through 34 removed outlier: 3.913A pdb=" N GLN h 33 " --> pdb=" O PHE h 29 " (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: 5.225A pdb=" N LYS i 123 " --> pdb=" O PHE i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 72 removed outlier: 4.190A pdb=" N LYS i 72 " --> pdb=" O ASN i 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 67 through 72' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'j' and resid 104 through 109 removed outlier: 3.873A pdb=" N LEU j 107 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SER j 109 " --> pdb=" O GLU j 106 " (cutoff:3.500A) Processing helix chain 'k' and resid 37 through 42 removed outlier: 5.643A 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: 5.640A 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: 4.619A 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: 5.253A 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: 4.577A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 62 removed outlier: 5.257A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (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: 4.951A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 4.960A 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 's' and resid 3 through 12 removed outlier: 5.591A pdb=" N ARG s 12 " --> pdb=" O LEU s 8 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 26 Processing helix chain 's' and resid 39 through 50 Processing helix chain 't' and resid 66 through 71 removed outlier: 5.018A 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: 4.925A 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 10 removed outlier: 5.043A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 Processing helix chain 'x' and resid 39 through 62 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 21 removed outlier: 4.728A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP z 20 " --> pdb=" O ARG z 16 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA z 21 " --> pdb=" O ARG z 17 " (cutoff:3.500A) Processing helix chain '0' and resid 26 through 31 Proline residue: 0 31 - end of helix Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 5.201A 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: 5.332A 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: 4.631A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.792A 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 helix chain '7' and resid 17 through 22 removed outlier: 4.041A pdb=" N HIS 7 22 " --> pdb=" O LYS 7 18 " (cutoff:3.500A) Processing helix chain '6' and resid 14 through 23 Proline residue: 6 23 - end of helix Processing helix chain '8' and resid 4 through 26 Processing helix chain '8' and resid 27 through 44 Proline residue: 8 44 - end of helix Processing helix chain '8' and resid 45 through 50 Proline residue: 8 50 - end of helix Processing helix chain '8' and resid 51 through 88 Processing helix chain '8' and resid 92 through 119 Processing helix chain '8' and resid 138 through 160 Processing helix chain '8' and resid 187 through 193 Processing helix chain '8' and resid 235 through 240 removed outlier: 4.947A pdb=" N ARG 8 240 " --> pdb=" O PRO 8 236 " (cutoff:3.500A) Processing helix chain '8' and resid 279 through 322 removed outlier: 5.550A pdb=" N TRP 8 319 " --> pdb=" O SER 8 315 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY 8 320 " --> pdb=" O ASP 8 316 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N SER 8 321 " --> pdb=" O ILE 8 317 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN 8 322 " --> pdb=" O GLY 8 318 " (cutoff:3.500A) Processing helix chain '8' and resid 344 through 351 Processing helix chain '8' and resid 353 through 364 Processing helix chain '5' and resid 3 through 21 Processing helix chain '5' and resid 33 through 48 Processing helix chain '5' and resid 62 through 68 Proline residue: 5 68 - end of helix Processing helix chain '5' and resid 73 through 79 removed outlier: 4.289A pdb=" N VAL 5 77 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) Proline residue: 5 79 - end of helix Processing helix chain '5' and resid 94 through 106 Processing helix chain '9' and resid 23 through 29 removed outlier: 4.264A pdb=" N LEU 9 27 " --> pdb=" O VAL 9 23 " (cutoff:3.500A) Processing helix chain '9' and resid 33 through 43 Processing helix chain '9' and resid 74 through 84 Processing helix chain '9' and resid 101 through 113 Processing helix chain '9' and resid 120 through 136 Processing sheet with id= 1, first strand: chain 'B' and resid 15 through 18 removed outlier: 5.395A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.194A 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: 3.802A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 54 through 59 Processing sheet with id= 4, first strand: chain 'C' and resid 164 through 169 removed outlier: 5.884A 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: 6.559A pdb=" N MET D 178 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 11 through 15 Processing sheet with id= 7, first strand: chain 'E' and resid 84 through 88 removed outlier: 6.125A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 32 through 40 Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 43 removed outlier: 6.042A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 44 through 47 removed outlier: 6.942A 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: 6.366A 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 28 removed outlier: 6.737A 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 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: 4.630A 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: 6.566A pdb=" N GLY K 19 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL K 84 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA K 21 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL K 86 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE K 23 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLY K 88 " --> pdb=" O ILE K 23 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA K 25 " --> pdb=" O GLY K 88 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 29 through 33 removed outlier: 5.381A 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: 4.975A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 4.387A 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: 3.662A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Q' and resid 7 through 11 removed outlier: 6.952A 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 80 through 83 removed outlier: 6.705A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'c' and resid 162 through 165 removed outlier: 6.515A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 91 through 96 Processing sheet with id= 27, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.797A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'd' and resid 36 through 39 removed outlier: 3.672A pdb=" N GLN d 36 " --> pdb=" O GLN d 49 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA d 47 " --> pdb=" O LYS d 38 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 179 through 182 Processing sheet with id= 30, first strand: chain 'd' and resid 24 through 28 No H-bonds generated for sheet with id= 30 Processing sheet with id= 31, first strand: chain 'd' and resid 46 through 51 removed outlier: 6.147A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'e' and resid 1 through 6 Processing sheet with id= 33, first strand: chain 'e' and resid 117 through 120 Processing sheet with id= 34, first strand: chain 'f' and resid 65 through 69 removed outlier: 5.712A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'g' and resid 15 through 19 Processing sheet with id= 36, first strand: chain 'g' and resid 41 through 44 removed outlier: 5.229A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'g' and resid 94 through 98 Processing sheet with id= 38, first strand: chain 'g' and resid 121 through 126 removed outlier: 6.877A pdb=" N GLU g 130 " --> pdb=" O PRO g 126 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'h' and resid 16 through 20 removed outlier: 6.000A pdb=" N LYS h 35 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'i' and resid 52 through 57 removed outlier: 5.118A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.324A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'j' and resid 18 through 21 removed outlier: 5.843A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'l' and resid 62 through 65 removed outlier: 6.489A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.732A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.382A 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: 5.544A pdb=" N ARG m 103 " --> pdb=" O ASN m 107 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY m 101 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA m 111 " --> pdb=" O LYS m 99 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS m 99 " --> pdb=" O ALA m 111 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE m 113 " --> pdb=" O ILE m 97 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE m 97 " --> pdb=" O ILE m 113 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU m 115 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.441A 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: 6.678A pdb=" N ILE n 35 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing sheet with id= 48, 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: 6.428A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'o' and resid 57 through 64 removed outlier: 7.861A 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 Processing sheet with id= 51, first strand: chain 'q' and resid 18 through 23 removed outlier: 6.444A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 3.911A 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 77 removed outlier: 4.966A pdb=" N GLN q 91 " --> pdb=" O GLY q 69 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS q 71 " --> pdb=" O HIS q 89 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N HIS q 89 " --> pdb=" O LYS q 71 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS q 73 " --> pdb=" O GLN q 87 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN q 87 " --> pdb=" O LYS q 73 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL q 75 " --> pdb=" O LYS q 85 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS q 85 " --> pdb=" O VAL q 75 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE q 77 " --> pdb=" O TYR q 83 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR q 83 " --> pdb=" O PHE q 77 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'r' and resid 2 through 8 removed outlier: 6.862A pdb=" N VAL r 106 " --> pdb=" O THR r 72 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'r' and resid 81 through 88 removed outlier: 4.335A pdb=" N ARG r 92 " --> pdb=" O ARG r 88 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 's' and resid 28 through 34 removed outlier: 5.982A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 't' and resid 40 through 45 No H-bonds generated for sheet with id= 57 Processing sheet with id= 58, first strand: chain 't' and resid 83 through 87 Processing sheet with id= 59, first strand: chain 'u' and resid 69 through 72 Processing sheet with id= 60, first strand: chain 'v' and resid 51 through 54 Processing sheet with id= 61, first strand: chain 'v' and resid 66 through 71 Processing sheet with id= 62, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.616A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'w' and resid 35 through 41 Processing sheet with id= 64, first strand: chain 'y' and resid 33 through 39 removed outlier: 7.356A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.480A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '0' and resid 19 through 24 removed outlier: 6.169A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '2' and resid 22 through 25 removed outlier: 5.283A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '3' and resid 1 through 5 removed outlier: 6.415A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '4' and resid 20 through 26 Processing sheet with id= 70, first strand: chain '8' and resid 161 through 166 removed outlier: 6.631A pdb=" N THR 8 180 " --> pdb=" O ILE 8 166 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LYS 8 177 " --> pdb=" O ALA 8 134 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASP 8 127 " --> pdb=" O GLU 8 225 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE 8 217 " --> pdb=" O GLY 8 135 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ILE 8 323 " --> pdb=" O LEU 8 336 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '8' and resid 241 through 244 Processing sheet with id= 72, first strand: chain '8' and resid 167 through 170 Processing sheet with id= 73, first strand: chain '5' and resid 23 through 28 Processing sheet with id= 74, first strand: chain '9' and resid 6 through 13 2343 hydrogen bonds defined for protein. 6882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4060 hydrogen bonds 6266 hydrogen bond angles 0 basepair planarities 1620 basepair parallelities 2512 stacking parallelities Total time for adding SS restraints: 255.38 Time building geometry restraints manager: 60.75 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: 12332 1.29 - 1.42: 70153 1.42 - 1.56: 66673 1.56 - 1.69: 9061 1.69 - 1.82: 305 Bond restraints: 158524 Sorted by residual: bond pdb=" C5 U a2449 " pdb=" C6 U a2449 " ideal model delta sigma weight residual 1.337 1.492 -0.155 2.00e-02 2.50e+03 5.97e+01 bond pdb=" C2 U a2449 " pdb=" N3 U a2449 " ideal model delta sigma weight residual 1.373 1.483 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" N1 U a2449 " pdb=" C2 U a2449 " ideal model delta sigma weight residual 1.381 1.468 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" N1 U a2449 " pdb=" C6 U a2449 " ideal model delta sigma weight residual 1.375 1.450 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" N3 U a2449 " pdb=" C4 U a2449 " ideal model delta sigma weight residual 1.380 1.448 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 158519 not shown) Histogram of bond angle deviations from ideal: 93.55 - 103.67: 12429 103.67 - 113.80: 111959 113.80 - 123.93: 90438 123.93 - 134.06: 21554 134.06 - 144.18: 24 Bond angle restraints: 236404 Sorted by residual: angle pdb=" CA MET f 96 " pdb=" CB MET f 96 " pdb=" CG MET f 96 " ideal model delta sigma weight residual 114.10 130.86 -16.76 2.00e+00 2.50e-01 7.03e+01 angle pdb=" CA MET N 89 " pdb=" CB MET N 89 " pdb=" CG MET N 89 " ideal model delta sigma weight residual 114.10 128.81 -14.71 2.00e+00 2.50e-01 5.41e+01 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 128.12 -21.80 3.00e+00 1.11e-01 5.28e+01 angle pdb=" C SER t 98 " pdb=" N ASN t 99 " pdb=" CA ASN t 99 " ideal model delta sigma weight residual 126.32 138.36 -12.04 1.74e+00 3.30e-01 4.79e+01 angle pdb=" C ASN g 48 " pdb=" N THR g 49 " pdb=" CA THR g 49 " ideal model delta sigma weight residual 121.81 135.20 -13.39 2.16e+00 2.14e-01 3.84e+01 ... (remaining 236399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 89756 35.95 - 71.91: 10359 71.91 - 107.86: 1182 107.86 - 143.82: 8 143.82 - 179.77: 11 Dihedral angle restraints: 101316 sinusoidal: 83454 harmonic: 17862 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 -115.70 -64.30 0 5.00e+00 4.00e-02 1.65e+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 42.39 157.61 1 1.50e+01 4.44e-03 8.21e+01 dihedral pdb=" O4' U a 846 " pdb=" C1' U a 846 " pdb=" N1 U a 846 " pdb=" C2 U a 846 " ideal model delta sinusoidal sigma weight residual 200.00 42.42 157.58 1 1.50e+01 4.44e-03 8.21e+01 ... (remaining 101313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 28832 0.104 - 0.207: 1091 0.207 - 0.311: 63 0.311 - 0.415: 7 0.415 - 0.518: 1 Chirality restraints: 29994 Sorted by residual: chirality pdb=" CB THR H 62 " pdb=" CA THR H 62 " pdb=" OG1 THR H 62 " pdb=" CG2 THR H 62 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CB VAL y 51 " pdb=" CA VAL y 51 " pdb=" CG1 VAL y 51 " pdb=" CG2 VAL y 51 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CB VAL 5 108 " pdb=" CA VAL 5 108 " pdb=" CG1 VAL 5 108 " pdb=" CG2 VAL 5 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 29991 not shown) Planarity restraints: 13163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a2445 " -0.040 2.00e-02 2.50e+03 5.85e-01 7.69e+03 pdb=" C4' 2MG a2445 " -0.439 2.00e-02 2.50e+03 pdb=" O4' 2MG a2445 " -0.650 2.00e-02 2.50e+03 pdb=" C3' 2MG a2445 " 0.591 2.00e-02 2.50e+03 pdb=" O3' 2MG a2445 " 0.590 2.00e-02 2.50e+03 pdb=" C2' 2MG a2445 " 0.203 2.00e-02 2.50e+03 pdb=" O2' 2MG a2445 " -0.933 2.00e-02 2.50e+03 pdb=" C1' 2MG a2445 " -0.217 2.00e-02 2.50e+03 pdb=" N9 2MG a2445 " 0.895 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.051 2.00e-02 2.50e+03 5.81e-01 7.60e+03 pdb=" C4' 5MC A1407 " -0.439 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.606 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.591 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.611 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.191 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -0.947 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.229 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.878 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.050 2.00e-02 2.50e+03 5.76e-01 7.47e+03 pdb=" C4' 2MG A1516 " -0.433 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.580 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.605 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.186 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -0.952 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 ... (remaining 13160 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 1863 2.58 - 3.16: 108201 3.16 - 3.74: 301458 3.74 - 4.32: 403188 4.32 - 4.90: 543015 Nonbonded interactions: 1357725 Sorted by model distance: nonbonded pdb=" OP1 U a 826 " pdb="MG MG a6087 " model vdw 1.995 2.170 nonbonded pdb=" OP1 A a1783 " pdb="MG MG a6086 " model vdw 2.005 2.170 nonbonded pdb=" OP1 C a2427 " pdb="MG MG a6087 " model vdw 2.006 2.170 nonbonded pdb=" OP2 A a2518 " pdb="MG MG a6061 " model vdw 2.008 2.170 nonbonded pdb=" OP2 C a2611 " pdb="MG MG a6062 " model vdw 2.010 2.170 ... (remaining 1357720 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 group one per residue 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 14.600 Check model and map are aligned: 1.460 Set scattering table: 0.930 Process input model: 567.460 Find NCS groups from input model: 2.960 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: 0.020 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 592.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 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 : 0.006 0.155 158524 Z= 0.354 Angle : 0.837 21.801 236404 Z= 0.429 Chirality : 0.044 0.518 29994 Planarity : 0.018 0.585 13163 Dihedral : 22.622 179.773 89790 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 0.16 % Allowed : 0.72 % Favored : 99.12 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.93 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.13 % 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: -1.32 (0.10), residues: 6148 helix: -0.41 (0.10), residues: 2288 sheet: -0.68 (0.14), residues: 1170 loop : -1.26 (0.11), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP S 34 HIS 0.019 0.002 HIS 3 33 PHE 0.038 0.003 PHE f 138 TYR 0.042 0.003 TYR F 25 ARG 0.032 0.001 ARG i 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2310 residues out of total 5137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2302 time to evaluate : 6.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 HIS cc_start: 0.9212 (p-80) cc_final: 0.8849 (p90) REVERT: B 90 PHE cc_start: 0.8951 (m-80) cc_final: 0.8514 (m-80) REVERT: B 133 GLU cc_start: 0.8442 (pm20) cc_final: 0.8117 (pm20) REVERT: B 197 ASP cc_start: 0.8589 (m-30) cc_final: 0.8372 (t70) REVERT: C 20 SER cc_start: 0.9088 (m) cc_final: 0.8450 (m) REVERT: C 42 TYR cc_start: 0.9009 (t80) cc_final: 0.8760 (t80) REVERT: C 67 THR cc_start: 0.9202 (p) cc_final: 0.8431 (p) REVERT: C 121 THR cc_start: 0.9384 (t) cc_final: 0.8464 (p) REVERT: C 125 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7994 (mp0) REVERT: C 139 GLN cc_start: 0.8850 (mp10) cc_final: 0.8586 (mp10) REVERT: C 169 ARG cc_start: 0.8396 (tmm160) cc_final: 0.8119 (ttp80) REVERT: C 185 ASN cc_start: 0.8540 (t0) cc_final: 0.8254 (t0) REVERT: C 187 SER cc_start: 0.9526 (t) cc_final: 0.9279 (t) REVERT: C 203 PHE cc_start: 0.9363 (t80) cc_final: 0.8754 (t80) REVERT: D 78 GLU cc_start: 0.8791 (tp30) cc_final: 0.8264 (tp30) REVERT: D 116 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8401 (tp-100) REVERT: D 131 ASN cc_start: 0.9320 (p0) cc_final: 0.8921 (p0) REVERT: D 135 TYR cc_start: 0.9462 (t80) cc_final: 0.8969 (t80) REVERT: D 145 ILE cc_start: 0.9236 (mm) cc_final: 0.8862 (mm) REVERT: D 199 LEU cc_start: 0.9277 (tp) cc_final: 0.8250 (tp) REVERT: D 202 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7836 (mt-10) REVERT: E 62 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8848 (mmmm) REVERT: F 11 HIS cc_start: 0.9090 (t-90) cc_final: 0.8676 (t-90) REVERT: F 14 GLN cc_start: 0.9110 (mp10) cc_final: 0.8720 (mp10) REVERT: F 56 LYS cc_start: 0.9242 (mtpp) cc_final: 0.8983 (mtpp) REVERT: G 37 SER cc_start: 0.9065 (p) cc_final: 0.8313 (p) REVERT: G 59 LEU cc_start: 0.8854 (mt) cc_final: 0.8653 (pp) REVERT: G 97 ASN cc_start: 0.9023 (m-40) cc_final: 0.8792 (m110) REVERT: G 136 LYS cc_start: 0.9142 (ptpp) cc_final: 0.8666 (pttp) REVERT: G 137 LYS cc_start: 0.9415 (tptp) cc_final: 0.9166 (tptt) REVERT: H 111 MET cc_start: 0.8754 (ptp) cc_final: 0.8507 (ptp) REVERT: I 88 MET cc_start: 0.8974 (mmt) cc_final: 0.8672 (mmp) REVERT: I 107 ASP cc_start: 0.8375 (t0) cc_final: 0.8018 (t0) REVERT: J 15 HIS cc_start: 0.7821 (p-80) cc_final: 0.7449 (p-80) REVERT: J 64 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7508 (mm-40) REVERT: J 88 MET cc_start: 0.8485 (ptp) cc_final: 0.7300 (ptp) REVERT: K 28 ASN cc_start: 0.9126 (m-40) cc_final: 0.8856 (m-40) REVERT: K 40 ASN cc_start: 0.8799 (m-40) cc_final: 0.8451 (m-40) REVERT: K 57 LYS cc_start: 0.9289 (ttpt) cc_final: 0.9061 (tttt) REVERT: K 59 THR cc_start: 0.8944 (m) cc_final: 0.8703 (m) REVERT: K 64 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8314 (tm-30) REVERT: K 68 GLU cc_start: 0.8775 (mt-10) cc_final: 0.7984 (mt-10) REVERT: K 101 ASN cc_start: 0.8767 (m-40) cc_final: 0.8469 (m-40) REVERT: L 51 LYS cc_start: 0.8787 (mppt) cc_final: 0.8458 (mmtm) REVERT: L 103 ASP cc_start: 0.8732 (m-30) cc_final: 0.8474 (m-30) REVERT: L 111 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8467 (mtmm) REVERT: L 116 LYS cc_start: 0.9515 (mttp) cc_final: 0.9246 (mttp) REVERT: M 13 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8558 (tttt) REVERT: M 81 MET cc_start: 0.9023 (mtp) cc_final: 0.8784 (mtp) REVERT: M 85 CYS cc_start: 0.9333 (p) cc_final: 0.9055 (p) REVERT: M 91 HIS cc_start: 0.8785 (m-70) cc_final: 0.8560 (m-70) REVERT: N 16 LEU cc_start: 0.9490 (mt) cc_final: 0.9251 (mt) REVERT: N 19 LYS cc_start: 0.8709 (pptt) cc_final: 0.8427 (pptt) REVERT: O 24 SER cc_start: 0.9014 (t) cc_final: 0.8749 (t) REVERT: O 45 GLU cc_start: 0.8333 (pp20) cc_final: 0.8071 (pp20) REVERT: P 12 LYS cc_start: 0.9108 (ttpp) cc_final: 0.8308 (ttpp) REVERT: P 51 ARG cc_start: 0.8651 (mtm110) cc_final: 0.8281 (mtm110) REVERT: P 79 ASN cc_start: 0.9092 (m110) cc_final: 0.8787 (m110) REVERT: Q 48 ASP cc_start: 0.7369 (t0) cc_final: 0.6664 (t70) REVERT: Q 71 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7794 (mtmt) REVERT: R 14 THR cc_start: 0.9308 (p) cc_final: 0.9001 (p) REVERT: R 28 THR cc_start: 0.9240 (p) cc_final: 0.9005 (p) REVERT: R 38 LYS cc_start: 0.9167 (mmmm) cc_final: 0.8299 (mmmm) REVERT: R 43 ARG cc_start: 0.9293 (ptm-80) cc_final: 0.8898 (tmm-80) REVERT: R 57 ARG cc_start: 0.8976 (ttm-80) cc_final: 0.8584 (ttm-80) REVERT: R 61 ARG cc_start: 0.9268 (mtt90) cc_final: 0.8592 (mtt90) REVERT: S 20 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8601 (pt0) REVERT: T 10 ARG cc_start: 0.9319 (mmt180) cc_final: 0.9048 (tpp-160) REVERT: T 31 PHE cc_start: 0.9159 (m-80) cc_final: 0.8735 (m-80) REVERT: T 68 HIS cc_start: 0.8353 (t-90) cc_final: 0.8150 (t70) REVERT: T 78 ASN cc_start: 0.9245 (t0) cc_final: 0.8859 (t0) REVERT: c 25 HIS cc_start: 0.8784 (t-90) cc_final: 0.8575 (t70) REVERT: c 114 ASP cc_start: 0.7297 (m-30) cc_final: 0.7006 (m-30) REVERT: c 267 ILE cc_start: 0.9029 (mm) cc_final: 0.8813 (mt) REVERT: d 97 SER cc_start: 0.8739 (p) cc_final: 0.7038 (p) REVERT: d 179 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8298 (ttm170) REVERT: d 185 ASN cc_start: 0.8652 (t0) cc_final: 0.8407 (t0) REVERT: e 24 ASN cc_start: 0.9133 (t0) cc_final: 0.8859 (t0) REVERT: e 35 TYR cc_start: 0.9214 (t80) cc_final: 0.8983 (t80) REVERT: e 119 ILE cc_start: 0.9424 (mm) cc_final: 0.9216 (mm) REVERT: e 124 PHE cc_start: 0.9062 (t80) cc_final: 0.8833 (t80) REVERT: e 136 GLN cc_start: 0.9443 (tp-100) cc_final: 0.8985 (tp-100) REVERT: e 145 ASP cc_start: 0.7862 (t70) cc_final: 0.7304 (t70) REVERT: e 168 ASP cc_start: 0.8229 (t70) cc_final: 0.7878 (t70) REVERT: e 188 MET cc_start: 0.8115 (mmp) cc_final: 0.7659 (mmp) REVERT: f 5 HIS cc_start: 0.9286 (t70) cc_final: 0.8974 (t70) REVERT: f 6 ASP cc_start: 0.9137 (m-30) cc_final: 0.8890 (m-30) REVERT: f 7 TYR cc_start: 0.8938 (t80) cc_final: 0.8317 (t80) REVERT: f 11 GLU cc_start: 0.8844 (mp0) cc_final: 0.8628 (mp0) REVERT: f 17 MET cc_start: 0.8620 (mmm) cc_final: 0.8086 (mmm) REVERT: f 46 ASP cc_start: 0.8466 (t70) cc_final: 0.8141 (t70) REVERT: f 96 MET cc_start: 0.8547 (mmt) cc_final: 0.8184 (mmt) REVERT: f 114 PHE cc_start: 0.7475 (t80) cc_final: 0.7114 (t80) REVERT: f 157 THR cc_start: 0.8912 (m) cc_final: 0.8651 (m) REVERT: f 165 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8179 (mm-30) REVERT: g 25 THR cc_start: 0.8850 (t) cc_final: 0.8581 (m) REVERT: g 117 LEU cc_start: 0.7842 (mm) cc_final: 0.7484 (mt) REVERT: g 143 GLN cc_start: 0.8984 (tp40) cc_final: 0.8778 (tp40) REVERT: i 53 TYR cc_start: 0.9221 (m-80) cc_final: 0.8983 (m-80) REVERT: i 118 MET cc_start: 0.8347 (mtt) cc_final: 0.7957 (mtt) REVERT: j 18 ARG cc_start: 0.8358 (mtp85) cc_final: 0.8016 (mmm-85) REVERT: j 53 LYS cc_start: 0.8968 (pttp) cc_final: 0.8748 (pttp) REVERT: j 88 ASN cc_start: 0.8534 (t0) cc_final: 0.8124 (t0) REVERT: j 108 ARG cc_start: 0.8745 (ttt180) cc_final: 0.8499 (ttm110) REVERT: k 5 THR cc_start: 0.8948 (p) cc_final: 0.8608 (t) REVERT: k 128 THR cc_start: 0.9291 (p) cc_final: 0.8911 (t) REVERT: l 46 ILE cc_start: 0.9538 (mm) cc_final: 0.9275 (mm) REVERT: n 17 LYS cc_start: 0.9830 (tptt) cc_final: 0.9568 (tptt) REVERT: n 52 SER cc_start: 0.9526 (p) cc_final: 0.8469 (p) REVERT: n 98 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8775 (mm-40) REVERT: o 8 LEU cc_start: 0.9121 (mp) cc_final: 0.8885 (mp) REVERT: o 63 LYS cc_start: 0.8552 (pttt) cc_final: 0.8191 (pttm) REVERT: q 43 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.7941 (p0) REVERT: r 77 ASP cc_start: 0.7812 (m-30) cc_final: 0.7526 (m-30) REVERT: r 108 SER cc_start: 0.9009 (p) cc_final: 0.8758 (p) REVERT: s 29 THR cc_start: 0.9512 (p) cc_final: 0.9300 (p) REVERT: s 87 LEU cc_start: 0.8998 (mt) cc_final: 0.8601 (mt) REVERT: t 6 ARG cc_start: 0.8767 (mtt-85) cc_final: 0.8442 (mpp80) REVERT: t 9 ASP cc_start: 0.8345 (m-30) cc_final: 0.8123 (m-30) REVERT: t 10 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7945 (tm-30) REVERT: t 40 ASN cc_start: 0.8750 (t0) cc_final: 0.8361 (t0) REVERT: u 45 ASP cc_start: 0.8140 (t70) cc_final: 0.7797 (t0) REVERT: u 71 LYS cc_start: 0.9097 (mmmm) cc_final: 0.8801 (mmmt) REVERT: x 15 ASN cc_start: 0.9527 (m110) cc_final: 0.9293 (m110) REVERT: x 16 THR cc_start: 0.9591 (p) cc_final: 0.9386 (p) REVERT: x 17 GLU cc_start: 0.9040 (tp30) cc_final: 0.8603 (mm-30) REVERT: x 19 LEU cc_start: 0.9752 (mt) cc_final: 0.9314 (mt) REVERT: x 39 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8049 (mm-40) REVERT: x 42 LEU cc_start: 0.8749 (mt) cc_final: 0.8193 (mt) REVERT: x 52 ARG cc_start: 0.9381 (ttm-80) cc_final: 0.9148 (ttm-80) REVERT: x 54 LYS cc_start: 0.9531 (ttpt) cc_final: 0.9327 (ttpt) REVERT: y 37 GLU cc_start: 0.7555 (tp30) cc_final: 0.7348 (tp30) REVERT: y 45 ARG cc_start: 0.8874 (tpp-160) cc_final: 0.8567 (tpp-160) REVERT: 0 26 ASN cc_start: 0.9026 (t0) cc_final: 0.8671 (t0) REVERT: 2 62 LEU cc_start: 0.9051 (mm) cc_final: 0.8824 (mm) REVERT: 4 20 ASN cc_start: 0.8843 (t0) cc_final: 0.8098 (t0) REVERT: 4 31 ASP cc_start: 0.9008 (m-30) cc_final: 0.8773 (m-30) REVERT: 4 61 ASN cc_start: 0.9248 (m110) cc_final: 0.8947 (m110) REVERT: 4 63 ARG cc_start: 0.8836 (ttm-80) cc_final: 0.8529 (ttm-80) REVERT: 6 1 MET cc_start: 0.7017 (mpp) cc_final: 0.6755 (mpp) REVERT: 8 148 LEU cc_start: 0.7032 (mt) cc_final: 0.6736 (tp) REVERT: 8 278 ARG cc_start: 0.4285 (ttm110) cc_final: 0.3260 (mmm160) REVERT: 8 300 MET cc_start: 0.7858 (mmp) cc_final: 0.7482 (ptm) REVERT: 9 57 VAL cc_start: 0.9697 (t) cc_final: 0.9492 (p) REVERT: 9 69 VAL cc_start: 0.9429 (t) cc_final: 0.9136 (p) outliers start: 8 outliers final: 2 residues processed: 2307 average time/residue: 1.2995 time to fit residues: 5141.8726 Evaluate side-chains 2024 residues out of total 5137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2021 time to evaluate : 6.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain q residue 43 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 887 optimal weight: 0.8980 chunk 796 optimal weight: 0.9980 chunk 442 optimal weight: 10.0000 chunk 272 optimal weight: 1.9990 chunk 537 optimal weight: 10.0000 chunk 425 optimal weight: 10.0000 chunk 823 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 500 optimal weight: 8.9990 chunk 613 optimal weight: 10.0000 chunk 954 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 69 HIS ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN D 59 GLN E 70 ASN E 78 ASN E 132 ASN E 135 ASN H 16 ASN H 18 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS L 5 ASN ** L 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 ASN N 35 ASN ** O 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN T 20 HIS c 115 GLN c 134 ASN ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 GLN ** f 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 58 ASN j 82 ASN m 107 ASN n 38 GLN ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 87 GLN t 69 ASN u 12 GLN u 49 ASN w 23 ASN ** x 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 25 GLN ** x 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 5 GLN z 6 ASN 1 29 GLN 3 35 GLN ** 7 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 22 HIS ** 6 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 8 ASN 8 280 GLN ** 5 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1018 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: