Starting phenix.real_space_refine on Fri Apr 12 16:44:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw1_26822/04_2024/7uw1_26822_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw1_26822/04_2024/7uw1_26822.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw1_26822/04_2024/7uw1_26822_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw1_26822/04_2024/7uw1_26822_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw1_26822/04_2024/7uw1_26822_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw1_26822/04_2024/7uw1_26822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw1_26822/04_2024/7uw1_26822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw1_26822/04_2024/7uw1_26822_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw1_26822/04_2024/7uw1_26822_updated.pdb" } resolution = 2.21 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= 0.003 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 95 atoms to isotropic. 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 1 6.06 5 P 4368 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 68958 2.51 5 N 25548 2.21 5 O 38174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 31": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "H GLU 41": "OE1" <-> "OE2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "I GLU 99": "OE1" <-> "OE2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "K GLU 12": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K GLU 88": "OE1" <-> "OE2" Residue "K GLU 117": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 91": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 30": "OE1" <-> "OE2" Residue "N GLU 79": "OE1" <-> "OE2" Residue "N GLU 115": "OE1" <-> "OE2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O GLU 74": "OE1" <-> "OE2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "O TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 111": "OE1" <-> "OE2" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q GLU 18": "OE1" <-> "OE2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "S GLU 53": "OE1" <-> "OE2" Residue "T GLU 35": "OE1" <-> "OE2" Residue "U GLU 13": "OE1" <-> "OE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U GLU 40": "OE1" <-> "OE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U GLU 50": "OE1" <-> "OE2" Residue "U PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 66": "OE1" <-> "OE2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "W GLU 30": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 43": "OE1" <-> "OE2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "b GLU 138": "OE1" <-> "OE2" Residue "c GLU 31": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 90": "OE1" <-> "OE2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "c PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "d GLU 52": "OE1" <-> "OE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d GLU 204": "OE1" <-> "OE2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "e GLU 161": "OE1" <-> "OE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 93": "OE1" <-> "OE2" Residue "g GLU 11": "OE1" <-> "OE2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "h GLU 54": "OE1" <-> "OE2" Residue "h GLU 68": "OE1" <-> "OE2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 90": "OE1" <-> "OE2" Residue "i GLU 108": "OE1" <-> "OE2" Residue "j GLU 66": "OE1" <-> "OE2" Residue "k GLU 67": "OE1" <-> "OE2" Residue "m GLU 41": "OE1" <-> "OE2" Residue "m GLU 59": "OE1" <-> "OE2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "n GLU 10": "OE1" <-> "OE2" Residue "n GLU 14": "OE1" <-> "OE2" Residue "n GLU 43": "OE1" <-> "OE2" Residue "o GLU 10": "OE1" <-> "OE2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "o GLU 76": "OE1" <-> "OE2" Residue "p GLU 66": "OE1" <-> "OE2" Residue "p GLU 87": "OE1" <-> "OE2" Residue "q GLU 27": "OE1" <-> "OE2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "r GLU 35": "OE1" <-> "OE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "t GLU 49": "OE1" <-> "OE2" Residue "u ARG 21": "NH1" <-> "NH2" Residue "u GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 137191 Number of models: 1 Model: "" Number of chains: 57 Chain: "0" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 427 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 58481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2726, 58481 Classifications: {'RNA': 2726} Modifications used: {'rna2p': 3, 'rna2p_pur': 261, 'rna2p_pyr': 156, 'rna3p': 11, 'rna3p_pur': 1297, 'rna3p_pyr': 997} Link IDs: {'rna2p': 419, 'rna3p': 2306} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 15, 'rna3p': 99} Chain: "C" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2106 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 254} Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1572 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "E" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1516 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1370 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1318 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 458 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "I" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1125 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1071 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1087 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 865 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain: "O" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "P" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "S" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "T" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 766 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 577 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "W" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 640 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "X" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Y" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 455 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "Z" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "a" Number of atoms: 32782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32782 Classifications: {'RNA': 1528} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 115, 'rna2p_pyr': 91, 'rna3p': 8, 'rna3p_pur': 748, 'rna3p_pyr': 565} Link IDs: {'rna2p': 207, 'rna3p': 1320} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "d" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "e" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "f" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "g" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1073 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Chain: "h" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "k" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Chain: "m" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 705 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "r" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "s" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 515 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} 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: "A" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 288 Unusual residues: {' MG': 1, 'OIY': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'OIY:plan-4': 3, 'OIY:plan-1': 5} Unresolved non-hydrogen planarities: 36 Chain: "W" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'OIY': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 176 Unusual residues: {'OIY': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'OIY:plan-4': 2, 'OIY:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 179.964 125.363 138.999 1.00 66.66 S ATOM 1398 SG CYS 3 14 179.118 123.709 135.674 1.00 65.07 S ATOM 1503 SG CYS 3 27 180.610 121.653 138.486 1.00 65.05 S Time building chain proxies: 55.14, per 1000 atoms: 0.40 Number of scatterers: 137191 At special positions: 0 Unit cell: (227.52, 244.08, 273.6, 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 1 29.99 S 141 16.00 P 4368 15.00 Mg 1 11.99 O 38174 8.00 N 25548 7.00 C 68958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 56.56 Conformation dependent library (CDL) restraints added in 7.5 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 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " Number of angles added : 3 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10102 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: 170 helices and 66 sheets defined 39.5% alpha, 18.3% beta 1474 base pairs and 2227 stacking pairs defined. Time for finding SS restraints: 70.40 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.155A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.405A 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 31 through 36 removed outlier: 4.602A pdb=" N LYS 2 35 " --> pdb=" O ILE 2 31 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER 2 36 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 31 through 36' Processing helix chain '2' and resid 37 through 45 removed outlier: 3.891A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLY 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.493A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER 2 56 " --> pdb=" O SER 2 52 " (cutoff:3.500A) Proline residue: 2 62 - end of helix Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.542A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.733A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.556A 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 207 through 215 removed outlier: 3.864A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.974A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 4.959A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.436A pdb=" N ASN C 201 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.154A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.659A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.864A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 Processing helix chain 'E' and resid 153 through 162 removed outlier: 4.568A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.667A pdb=" N PHE E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 4 through 21 removed outlier: 4.522A pdb=" N TYR F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.251A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 Processing helix chain 'F' and resid 93 through 111 removed outlier: 3.626A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE 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 'G' and resid 2 through 8 Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.540A pdb=" N SER G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 4.043A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 50 removed outlier: 3.818A pdb=" N ARG H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 59 removed outlier: 5.576A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 removed outlier: 4.143A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 88 through 96 removed outlier: 3.635A pdb=" N ALA I 94 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.714A pdb=" N PHE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 122 removed outlier: 3.544A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 118 Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.863A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LYS K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.746A pdb=" N LEU K 63 " --> pdb=" O ILE K 59 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 4.058A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 85 removed outlier: 3.990A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 85' Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'L' and resid 43 through 59 Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.837A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Proline residue: L 126 - end of helix Processing helix chain 'M' and resid 13 through 32 Processing helix chain 'M' and resid 37 through 57 removed outlier: 3.837A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.513A pdb=" N ASN M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.662A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.537A 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 3 through 23 removed outlier: 4.500A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 Processing helix chain 'N' and resid 100 through 113 Processing helix chain 'O' and resid 5 through 16 removed outlier: 4.256A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.731A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N SER O 107 " --> pdb=" O LEU O 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 107' Processing helix chain 'P' and resid 6 through 22 removed outlier: 3.716A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.773A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.977A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) 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 removed outlier: 3.847A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 4.149A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 10 removed outlier: 4.577A pdb=" N LEU S 10 " --> pdb=" O ILE S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 26 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.064A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'U' and resid 12 through 17 removed outlier: 5.248A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 47 through 58 removed outlier: 3.757A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASN U 58 " --> pdb=" O ALA U 54 " (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: 3.775A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 35 Processing helix chain 'X' and resid 39 through 61 removed outlier: 4.564A pdb=" N VAL X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.655A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 4.938A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 6.707A pdb=" N LEU b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.353A pdb=" N PHE b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 removed outlier: 3.910A pdb=" N THR b 48 " --> pdb=" O ASN b 44 " (cutoff:3.500A) Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 75 through 90 removed outlier: 4.705A pdb=" N ASN b 80 " --> pdb=" O ARG b 76 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 126 removed outlier: 3.566A pdb=" N LEU b 109 " --> pdb=" O ASN b 105 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 132 removed outlier: 4.909A pdb=" N THR b 132 " --> pdb=" O PHE b 128 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 150 Processing helix chain 'b' and resid 167 through 172 Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 227 removed outlier: 4.565A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.750A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 removed outlier: 3.811A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.529A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.091A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 Processing helix chain 'c' and resid 129 through 145 Processing helix chain 'c' and resid 210 through 215 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.387A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 Processing helix chain 'd' and resid 51 through 68 removed outlier: 3.518A pdb=" N ILE d 66 " --> pdb=" O LYS d 62 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR d 67 " --> pdb=" O VAL d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.103A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.776A pdb=" N ARG d 99 " --> pdb=" O LEU d 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 108 Processing helix chain 'd' and resid 112 through 123 removed outlier: 3.695A pdb=" N ARG d 123 " --> pdb=" O LEU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 153 removed outlier: 5.270A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 168 removed outlier: 3.673A pdb=" N GLN d 166 " --> pdb=" O GLU d 162 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG d 167 " --> pdb=" O LEU d 163 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 removed outlier: 3.522A pdb=" N LEU d 193 " --> pdb=" O ASP d 189 " (cutoff:3.500A) Proline residue: d 194 - end of helix No H-bonds generated for 'chain 'd' and resid 189 through 194' Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.614A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.151A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.747A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 164 Processing helix chain 'f' and resid 14 through 33 removed outlier: 3.835A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLY f 20 " --> pdb=" O ASP f 16 " (cutoff:3.500A) 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 54 removed outlier: 3.541A pdb=" N GLN g 51 " --> pdb=" O LEU g 47 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.721A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS g 110 " --> pdb=" O ASP g 106 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 148 removed outlier: 3.591A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 113 through 121 Processing helix chain 'i' and resid 32 through 37 Processing helix chain 'i' and resid 39 through 54 removed outlier: 3.532A pdb=" N ARG i 43 " --> pdb=" O ARG i 39 " (cutoff:3.500A) Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 90 removed outlier: 3.599A pdb=" N GLU i 90 " --> pdb=" O ILE i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 100 Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.556A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.228A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.701A pdb=" N GLN k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 45 through 50' Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.751A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 53 through 58' Processing helix chain 'k' and resid 59 through 77 removed outlier: 3.801A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 3.822A pdb=" N LEU k 99 " --> pdb=" O ALA k 95 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY k 100 " --> pdb=" O VAL k 96 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.578A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.203A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 49 through 64 removed outlier: 4.187A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Proline residue: m 64 - end of helix 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 33 removed outlier: 5.129A pdb=" N ALA n 22 " --> pdb=" O ALA n 18 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LYS n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 51 Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'n' and resid 52 through 57 Proline residue: n 57 - end of helix Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.313A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS o 47 " --> pdb=" O PHE o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.914A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 71 through 82 removed outlier: 3.506A pdb=" N GLN p 81 " --> pdb=" O HIS p 77 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY p 82 " --> pdb=" O TRP p 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 86 through 100 Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.892A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.647A 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 removed outlier: 4.538A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 removed outlier: 3.534A pdb=" N VAL t 28 " --> pdb=" O LEU t 24 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 65 Proline residue: t 56 - end of helix removed outlier: 3.598A pdb=" N GLY t 65 " --> pdb=" O MET t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 3.831A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 37 removed outlier: 3.684A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 Processing sheet with id= 1, first strand: chain '0' and resid 15 through 21 removed outlier: 5.925A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N MET 0 30 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 21 through 24 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain '3' and resid 1 through 5 removed outlier: 6.623A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N SER 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.838A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.042A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.229A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 13.488A pdb=" N GLY D 201 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 11.746A pdb=" N LYS D 117 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 80 through 85 removed outlier: 4.862A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 9, first strand: chain 'D' and resid 25 through 29 No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.301A pdb=" N SER E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 43 through 46 removed outlier: 6.885A pdb=" N ARG E 43 " --> pdb=" O PRO E 88 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA E 86 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 116 through 119 removed outlier: 5.941A pdb=" N ARG E 116 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.032A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 15, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 16, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.198A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 18, first strand: chain 'H' and resid 1 through 5 removed outlier: 4.757A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 52 through 57 removed outlier: 5.006A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.225A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.180A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'L' and resid 63 through 66 removed outlier: 3.618A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE L 34 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS L 101 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 74 through 77 removed outlier: 6.915A pdb=" N ILE L 74 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 31 through 37 removed outlier: 8.045A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS L 128 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 33 through 36 Processing sheet with id= 26, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.837A pdb=" N ALA N 50 " --> pdb=" O VAL N 40 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.945A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 52 through 55 removed outlier: 3.754A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Q' and resid 11 through 15 removed outlier: 3.938A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Q' and resid 18 through 23 removed outlier: 4.164A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 32, first strand: chain 'Q' and resid 65 through 69 removed outlier: 3.772A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 71 through 78 removed outlier: 4.222A pdb=" N TYR Q 83 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 35, first strand: chain 'S' and resid 28 through 32 removed outlier: 4.276A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'U' and resid 4 through 7 Processing sheet with id= 37, first strand: chain 'U' and resid 41 through 46 Processing sheet with id= 38, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.493A pdb=" N GLN U 82 " --> pdb=" O MET U 91 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR U 89 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 45 through 48 removed outlier: 6.136A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 50 through 54 removed outlier: 7.178A pdb=" N ASN V 50 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.504A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'W' and resid 34 through 40 Processing sheet with id= 43, first strand: chain 'Y' and resid 32 through 38 removed outlier: 4.254A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS Y 5 " --> pdb=" O GLU Y 57 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'b' and resid 17 through 20 removed outlier: 4.440A pdb=" N HIS b 17 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N HIS b 41 " --> pdb=" O GLY b 19 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 69 through 73 Processing sheet with id= 46, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.737A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.593A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'd' and resid 143 through 147 removed outlier: 6.867A pdb=" N LEU d 180 " --> pdb=" O VAL d 147 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 11 through 15 removed outlier: 6.764A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.783A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 32 through 39 Processing sheet with id= 52, first strand: chain 'f' and resid 38 through 42 removed outlier: 3.559A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.719A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.393A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'h' and resid 75 through 78 removed outlier: 4.691A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'i' and resid 3 through 9 removed outlier: 4.199A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 35 through 38 Processing sheet with id= 58, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.722A pdb=" N LYS j 71 " --> pdb=" O MET j 42 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 44 through 53 removed outlier: 8.512A pdb=" N ALA j 61 " --> pdb=" O THR j 53 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 28 through 35 removed outlier: 4.077A pdb=" N ASN k 28 " --> pdb=" O SER k 25 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL k 83 " --> pdb=" O ASN k 107 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.150A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 36 through 41 removed outlier: 4.981A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.670A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'q' and resid 7 through 12 removed outlier: 5.968A pdb=" N ARG q 7 " --> pdb=" O GLU q 64 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 20 through 31 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 's' and resid 47 through 52 removed outlier: 4.386A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) 1874 hydrogen bonds defined for protein. 5538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3681 hydrogen bonds 5742 hydrogen bond angles 0 basepair planarities 1474 basepair parallelities 2227 stacking parallelities Total time for adding SS restraints: 248.22 Time building geometry restraints manager: 61.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 13026 1.31 - 1.43: 66004 1.43 - 1.56: 60981 1.56 - 1.69: 8739 1.69 - 1.81: 253 Bond restraints: 149003 Sorted by residual: bond pdb=" C03 OIY A3007 " pdb=" C04 OIY A3007 " ideal model delta sigma weight residual 2.080 1.515 0.565 2.00e-02 2.50e+03 7.98e+02 bond pdb=" C03 OIY A3006 " pdb=" C04 OIY A3006 " ideal model delta sigma weight residual 2.080 1.515 0.565 2.00e-02 2.50e+03 7.97e+02 bond pdb=" C03 OIY a1602 " pdb=" C04 OIY a1602 " ideal model delta sigma weight residual 2.080 1.518 0.562 2.00e-02 2.50e+03 7.89e+02 bond pdb=" C03 OIY A3005 " pdb=" C04 OIY A3005 " ideal model delta sigma weight residual 2.080 1.519 0.561 2.00e-02 2.50e+03 7.88e+02 bond pdb=" C03 OIY A3004 " pdb=" C04 OIY A3004 " ideal model delta sigma weight residual 2.080 1.519 0.561 2.00e-02 2.50e+03 7.86e+02 ... (remaining 148998 not shown) Histogram of bond angle deviations from ideal: 98.30 - 107.97: 37796 107.97 - 117.64: 100708 117.64 - 127.31: 74770 127.31 - 136.99: 9533 136.99 - 146.66: 4 Bond angle restraints: 222811 Sorted by residual: angle pdb=" C LYS u 20 " pdb=" N ARG u 21 " pdb=" CA ARG u 21 " ideal model delta sigma weight residual 122.54 111.22 11.32 1.65e+00 3.67e-01 4.71e+01 angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C8 6MZ A2026 " ideal model delta sigma weight residual 126.23 146.66 -20.43 3.00e+00 1.11e-01 4.64e+01 angle pdb=" CB ARG u 21 " pdb=" CG ARG u 21 " pdb=" CD ARG u 21 " ideal model delta sigma weight residual 111.30 126.54 -15.24 2.30e+00 1.89e-01 4.39e+01 angle pdb=" C1' OMG A2247 " pdb=" N9 OMG A2247 " pdb=" C4 OMG A2247 " ideal model delta sigma weight residual 108.29 126.99 -18.70 3.00e+00 1.11e-01 3.89e+01 angle pdb=" C1' 2MG a1204 " pdb=" N9 2MG a1204 " pdb=" C8 2MG a1204 " ideal model delta sigma weight residual 110.07 128.20 -18.13 3.00e+00 1.11e-01 3.65e+01 ... (remaining 222806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 84037 35.97 - 71.94: 9910 71.94 - 107.90: 1099 107.90 - 143.87: 28 143.87 - 179.84: 65 Dihedral angle restraints: 95139 sinusoidal: 79456 harmonic: 15683 Sorted by residual: dihedral pdb=" O4' C A 912 " pdb=" C1' C A 912 " pdb=" N1 C A 912 " pdb=" C2 C A 912 " ideal model delta sinusoidal sigma weight residual -160.00 17.24 -177.24 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2473 " pdb=" C1' U A2473 " pdb=" N1 U A2473 " pdb=" C2 U A2473 " ideal model delta sinusoidal sigma weight residual -160.00 9.14 -169.14 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' C B 39 " pdb=" C1' C B 39 " pdb=" N1 C B 39 " pdb=" C2 C B 39 " ideal model delta sinusoidal sigma weight residual 200.00 32.20 167.80 1 1.50e+01 4.44e-03 8.44e+01 ... (remaining 95136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.313: 28461 0.313 - 0.626: 16 0.626 - 0.939: 13 0.939 - 1.252: 0 1.252 - 1.565: 1 Chirality restraints: 28491 Sorted by residual: chirality pdb=" C04 OIY A3007 " pdb=" C03 OIY A3007 " pdb=" C05 OIY A3007 " pdb=" N08 OIY A3007 " both_signs ideal model delta sigma weight residual False -2.62 -1.06 -1.56 2.00e-01 2.50e+01 6.12e+01 chirality pdb=" C04 OIY A3006 " pdb=" C03 OIY A3006 " pdb=" C05 OIY A3006 " pdb=" N08 OIY A3006 " both_signs ideal model delta sigma weight residual False -2.62 -1.79 -0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" C02 OIY a1602 " pdb=" C01 OIY a1602 " pdb=" C03 OIY a1602 " pdb=" O53 OIY a1602 " both_signs ideal model delta sigma weight residual False 1.98 2.69 -0.72 2.00e-01 2.50e+01 1.28e+01 ... (remaining 28488 not shown) Planarity restraints: 11990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " -0.070 2.00e-02 2.50e+03 6.24e-01 8.77e+03 pdb=" C4' 7MG A2065 " -0.459 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " -0.712 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " 0.659 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " 0.183 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " -0.980 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " -0.198 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " 0.984 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1204 " -0.057 2.00e-02 2.50e+03 5.94e-01 7.93e+03 pdb=" C4' 2MG a1204 " -0.434 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " -0.638 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " 0.598 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " 0.619 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " 0.186 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " -0.959 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " -0.224 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " 0.909 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG a 524 " 0.019 2.00e-02 2.50e+03 5.76e-01 7.46e+03 pdb=" C4' 7MG a 524 " 0.445 2.00e-02 2.50e+03 pdb=" O4' 7MG a 524 " 0.690 2.00e-02 2.50e+03 pdb=" C3' 7MG a 524 " -0.583 2.00e-02 2.50e+03 pdb=" O3' 7MG a 524 " -0.555 2.00e-02 2.50e+03 pdb=" C2' 7MG a 524 " -0.228 2.00e-02 2.50e+03 pdb=" O2' 7MG a 524 " 0.882 2.00e-02 2.50e+03 pdb=" C1' 7MG a 524 " 0.215 2.00e-02 2.50e+03 pdb=" N9 7MG a 524 " -0.886 2.00e-02 2.50e+03 ... (remaining 11987 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 513 2.56 - 3.15: 97075 3.15 - 3.73: 263071 3.73 - 4.32: 380165 4.32 - 4.90: 503377 Nonbonded interactions: 1244201 Sorted by model distance: nonbonded pdb="MG MG A3008 " pdb=" O HOH A3102 " model vdw 1.976 2.170 nonbonded pdb="MG MG A3008 " pdb=" O HOH A3101 " model vdw 2.008 2.170 nonbonded pdb="MG MG A3008 " pdb=" O HOH A3104 " model vdw 2.012 2.170 nonbonded pdb="MG MG A3008 " pdb=" O HOH A3103 " model vdw 2.070 2.170 nonbonded pdb=" OP2 C a1311 " pdb=" OG SER s 4 " model vdw 2.103 2.440 ... (remaining 1244196 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: 18.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.640 Construct map_model_manager: 0.130 Extract box with map and model: 53.780 Check model and map are aligned: 1.520 Set scattering table: 0.970 Process input model: 553.790 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.320 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: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 643.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 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 : 0.011 0.565 149003 Z= 0.689 Angle : 0.644 20.429 222811 Z= 0.327 Chirality : 0.041 1.565 28491 Planarity : 0.015 0.624 11990 Dihedral : 23.223 179.838 85037 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.14 % Favored : 97.67 % Rotamer: Outliers : 1.92 % Allowed : 21.97 % Favored : 76.11 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.86 (0.11), residues: 5412 helix: 1.76 (0.12), residues: 1872 sheet: 0.41 (0.16), residues: 1027 loop : -0.21 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 201 HIS 0.005 0.001 HIS 2 30 PHE 0.020 0.001 PHE F 177 TYR 0.018 0.001 TYR P 32 ARG 0.022 0.001 ARG u 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 859 time to evaluate : 5.527 Fit side-chains revert: symmetry clash REVERT: F 38 MET cc_start: 0.7085 (mtp) cc_final: 0.6691 (mtt) REVERT: G 170 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8479 (tt) REVERT: Q 36 ASP cc_start: 0.7937 (p0) cc_final: 0.7634 (p0) REVERT: b 107 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8370 (tmmt) REVERT: k 63 GLN cc_start: 0.8793 (tt0) cc_final: 0.8425 (tt0) REVERT: k 67 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8079 (pm20) outliers start: 86 outliers final: 74 residues processed: 937 average time/residue: 2.1738 time to fit residues: 2861.8360 Evaluate side-chains 922 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 846 time to evaluate : 6.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 ILE Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 87 GLN Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain X residue 49 THR Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 39 LYS Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 66 ILE Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain f residue 16 ASP Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain h residue 57 LYS Chi-restraints excluded: chain i residue 45 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 67 GLU Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 59 SER Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain u residue 36 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 815 optimal weight: 20.0000 chunk 732 optimal weight: 10.0000 chunk 406 optimal weight: 8.9990 chunk 250 optimal weight: 8.9990 chunk 493 optimal weight: 8.9990 chunk 391 optimal weight: 9.9990 chunk 757 optimal weight: 40.0000 chunk 293 optimal weight: 10.0000 chunk 460 optimal weight: 0.8980 chunk 563 optimal weight: 0.9990 chunk 877 optimal weight: 20.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN I 67 ASN K 125 GLN M 57 ASN N 30 ASN T 84 GLN W 74 GLN X 44 GLN b 13 GLN c 139 GLN e 96 GLN f 52 ASN f 63 ASN ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN k 39 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN r 31 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 149003 Z= 0.431 Angle : 0.689 14.580 222811 Z= 0.366 Chirality : 0.044 0.483 28491 Planarity : 0.006 0.141 11990 Dihedral : 23.219 179.828 74420 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.57 % Favored : 97.27 % Rotamer: Outliers : 3.81 % Allowed : 19.23 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.11), residues: 5412 helix: 1.74 (0.12), residues: 1882 sheet: 0.37 (0.16), residues: 1039 loop : -0.28 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 201 HIS 0.007 0.001 HIS C 230 PHE 0.018 0.002 PHE M 21 TYR 0.025 0.002 TYR P 32 ARG 0.010 0.001 ARG u 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 856 time to evaluate : 6.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 152 MET cc_start: 0.7342 (mpp) cc_final: 0.7091 (mpp) REVERT: G 20 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.6888 (p0) REVERT: L 10 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7506 (mtm180) REVERT: Q 36 ASP cc_start: 0.7961 (p0) cc_final: 0.7649 (p0) REVERT: b 107 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8336 (tmmt) REVERT: b 209 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7604 (mp) REVERT: e 13 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8767 (mttm) REVERT: h 41 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: k 49 GLN cc_start: 0.8676 (mm110) cc_final: 0.8384 (mm110) REVERT: k 78 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8944 (pp) REVERT: m 3 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8142 (ttt90) REVERT: n 85 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.7848 (tmt90) REVERT: o 54 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8741 (mtp180) REVERT: q 27 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7281 (mm-30) REVERT: r 25 ASP cc_start: 0.8288 (t0) cc_final: 0.8076 (t70) REVERT: u 10 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5636 (tm-30) outliers start: 171 outliers final: 94 residues processed: 960 average time/residue: 2.1593 time to fit residues: 2903.7960 Evaluate side-chains 936 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 831 time to evaluate : 5.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 33 LYS Chi-restraints excluded: chain 0 residue 50 ILE Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 87 GLN Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 19 ASP Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain b residue 209 ILE Chi-restraints excluded: chain b residue 219 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 66 ILE Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain f residue 16 ASP Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain h residue 41 GLN Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 59 SER Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 3 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 85 ARG Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 ASP Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 GLU Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 35 GLU Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 26 ASN Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 20 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 487 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 730 optimal weight: 10.0000 chunk 597 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 878 optimal weight: 10.0000 chunk 949 optimal weight: 6.9990 chunk 782 optimal weight: 7.9990 chunk 871 optimal weight: 6.9990 chunk 299 optimal weight: 7.9990 chunk 705 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN G 104 ASN I 67 ASN K 125 GLN M 57 ASN N 2 ASN Q 87 GLN W 74 GLN X 44 GLN c 25 ASN c 139 GLN d 118 GLN f 52 ASN f 63 ASN ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN k 63 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN p 62 GLN r 31 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 149003 Z= 0.530 Angle : 0.740 15.983 222811 Z= 0.390 Chirality : 0.048 0.481 28491 Planarity : 0.007 0.149 11990 Dihedral : 23.218 179.956 74369 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.66 % Favored : 97.17 % Rotamer: Outliers : 5.11 % Allowed : 18.07 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.11), residues: 5412 helix: 1.62 (0.12), residues: 1885 sheet: 0.34 (0.16), residues: 1029 loop : -0.37 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 83 HIS 0.008 0.001 HIS C 230 PHE 0.020 0.002 PHE F 177 TYR 0.026 0.002 TYR P 32 ARG 0.012 0.001 ARG F 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 838 time to evaluate : 6.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 ARG cc_start: 0.9012 (mtp85) cc_final: 0.8804 (mtp85) REVERT: E 4 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8681 (mmmm) REVERT: F 57 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7917 (mpm) REVERT: F 92 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8309 (mtt-85) REVERT: F 152 MET cc_start: 0.7462 (mpp) cc_final: 0.7235 (mpt) REVERT: G 20 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.6948 (p0) REVERT: G 170 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8576 (tt) REVERT: G 171 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8211 (mmm160) REVERT: K 41 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.9015 (mtpp) REVERT: L 10 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7593 (mtm180) REVERT: P 12 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8122 (ttm110) REVERT: P 87 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: Q 36 ASP cc_start: 0.7979 (p0) cc_final: 0.7656 (p0) REVERT: b 81 ILE cc_start: 0.6561 (OUTLIER) cc_final: 0.6142 (tt) REVERT: b 107 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8272 (ttpt) REVERT: e 13 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8772 (mttm) REVERT: f 81 ASN cc_start: 0.8850 (t0) cc_final: 0.8583 (t0) REVERT: g 131 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6526 (ptpp) REVERT: h 41 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: i 39 ARG cc_start: 0.9371 (OUTLIER) cc_final: 0.8481 (ptm160) REVERT: k 78 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8792 (pp) REVERT: m 3 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8215 (ttt90) REVERT: n 85 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8127 (tmt90) REVERT: o 54 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8798 (mtp180) REVERT: q 27 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: r 25 ASP cc_start: 0.8336 (t0) cc_final: 0.8086 (t0) REVERT: u 10 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5694 (tm-30) outliers start: 229 outliers final: 120 residues processed: 983 average time/residue: 2.2162 time to fit residues: 3045.6866 Evaluate side-chains 966 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 825 time to evaluate : 6.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 LYS Chi-restraints excluded: chain 0 residue 33 LYS Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 87 GLN Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 19 ASP Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 39 LYS Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 81 ILE Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain b residue 219 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 66 ILE Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain f residue 16 ASP Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 131 LYS Chi-restraints excluded: chain h residue 41 GLN Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 39 ARG Chi-restraints excluded: chain i residue 58 LYS Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 59 SER Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 3 ARG Chi-restraints excluded: chain m residue 8 ASN Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 85 ARG Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 ASP Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 91 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 GLU Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 35 GLU Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 26 ASN Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 20 LYS Chi-restraints excluded: chain u residue 58 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 868 optimal weight: 1.9990 chunk 660 optimal weight: 5.9990 chunk 456 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 419 optimal weight: 0.8980 chunk 590 optimal weight: 6.9990 chunk 881 optimal weight: 9.9990 chunk 933 optimal weight: 7.9990 chunk 460 optimal weight: 0.6980 chunk 835 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN K 125 GLN M 57 ASN W 74 GLN X 41 HIS X 44 GLN Z 37 HIS c 25 ASN c 139 GLN d 118 GLN f 52 ASN f 63 ASN ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN k 63 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN o 20 ASN p 62 GLN r 31 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 149003 Z= 0.133 Angle : 0.568 13.266 222811 Z= 0.310 Chirality : 0.035 0.358 28491 Planarity : 0.005 0.127 11990 Dihedral : 23.130 179.990 74362 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.24 % Favored : 97.60 % Rotamer: Outliers : 2.88 % Allowed : 20.46 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.11), residues: 5412 helix: 1.98 (0.12), residues: 1883 sheet: 0.48 (0.16), residues: 1024 loop : -0.26 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 83 HIS 0.004 0.001 HIS C 230 PHE 0.015 0.001 PHE S 69 TYR 0.013 0.001 TYR P 32 ARG 0.012 0.000 ARG g 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 847 time to evaluate : 6.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 ASN cc_start: 0.7438 (OUTLIER) cc_final: 0.6795 (p0) REVERT: N 115 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7906 (mp0) REVERT: Q 36 ASP cc_start: 0.7975 (p0) cc_final: 0.7631 (p0) REVERT: e 13 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8815 (mttm) REVERT: h 41 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: k 36 ARG cc_start: 0.8307 (mmt90) cc_final: 0.8013 (mtt-85) REVERT: k 78 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8784 (pp) REVERT: u 10 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.5632 (tm-30) outliers start: 129 outliers final: 65 residues processed: 918 average time/residue: 2.2116 time to fit residues: 2842.7276 Evaluate side-chains 902 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 832 time to evaluate : 5.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 82 ILE Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 219 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain f residue 16 ASP Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain h residue 41 GLN Chi-restraints excluded: chain h residue 54 GLU Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 59 SER Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 ASP Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain r residue 45 THR Chi-restraints excluded: chain s residue 26 ASN Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 20 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 777 optimal weight: 6.9990 chunk 530 optimal weight: 0.3980 chunk 13 optimal weight: 8.9990 chunk 695 optimal weight: 10.0000 chunk 385 optimal weight: 6.9990 chunk 796 optimal weight: 20.0000 chunk 645 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 476 optimal weight: 8.9990 chunk 838 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 ASN K 125 GLN M 57 ASN W 74 GLN X 44 GLN c 25 ASN c 139 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN f 52 ASN f 63 ASN ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 48 ASN h 86 GLN k 63 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 149003 Z= 0.481 Angle : 0.706 14.486 222811 Z= 0.373 Chirality : 0.045 0.445 28491 Planarity : 0.006 0.145 11990 Dihedral : 23.126 179.729 74345 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.64 % Favored : 97.19 % Rotamer: Outliers : 3.66 % Allowed : 20.19 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.11), residues: 5412 helix: 1.80 (0.12), residues: 1884 sheet: 0.44 (0.16), residues: 1026 loop : -0.33 (0.12), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 201 HIS 0.008 0.001 HIS C 230 PHE 0.022 0.002 PHE u 37 TYR 0.027 0.002 TYR P 32 ARG 0.010 0.001 ARG g 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 822 time to evaluate : 6.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.8711 (ttt90) REVERT: G 20 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.6675 (p0) REVERT: G 170 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8566 (tt) REVERT: G 171 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8222 (mmm160) REVERT: K 41 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9020 (mtpp) REVERT: L 10 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7497 (mtm180) REVERT: N 115 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7993 (mp0) REVERT: P 12 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8095 (ttm110) REVERT: Q 36 ASP cc_start: 0.7969 (p0) cc_final: 0.7645 (p0) REVERT: b 107 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8241 (tmmt) REVERT: c 100 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8070 (mp10) REVERT: e 13 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8772 (mttm) REVERT: h 3 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8508 (ttp) REVERT: h 41 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8524 (tt0) REVERT: i 39 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.8371 (ptm160) REVERT: k 78 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8837 (pp) REVERT: m 3 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8151 (ttt90) REVERT: q 27 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: u 10 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5629 (tm-30) outliers start: 164 outliers final: 98 residues processed: 921 average time/residue: 2.1762 time to fit residues: 2814.4663 Evaluate side-chains 924 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 810 time to evaluate : 5.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain b residue 219 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 66 ILE Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain f residue 16 ASP Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 41 GLN Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 39 ARG Chi-restraints excluded: chain i residue 58 LYS Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 3 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 ASP Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 GLU Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 35 GLU Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 26 ASN Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 20 LYS Chi-restraints excluded: chain u residue 58 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 314 optimal weight: 2.9990 chunk 840 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 548 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 chunk 934 optimal weight: 6.9990 chunk 775 optimal weight: 0.8980 chunk 432 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 309 optimal weight: 2.9990 chunk 490 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN G 104 ASN I 67 ASN K 125 GLN M 57 ASN W 74 GLN X 44 GLN c 25 ASN c 139 GLN f 52 ASN f 63 ASN ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN k 63 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN o 20 ASN p 62 GLN s 14 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 149003 Z= 0.181 Angle : 0.578 13.059 222811 Z= 0.315 Chirality : 0.036 0.358 28491 Planarity : 0.005 0.131 11990 Dihedral : 23.098 179.888 74342 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.33 % Favored : 97.54 % Rotamer: Outliers : 3.19 % Allowed : 20.61 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.11), residues: 5412 helix: 2.00 (0.12), residues: 1885 sheet: 0.50 (0.16), residues: 1029 loop : -0.28 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 201 HIS 0.004 0.001 HIS C 230 PHE 0.017 0.001 PHE S 69 TYR 0.017 0.001 TYR P 32 ARG 0.011 0.000 ARG g 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 830 time to evaluate : 6.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 26 MET cc_start: 0.8270 (mmm) cc_final: 0.8056 (mmt) REVERT: G 170 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8542 (tt) REVERT: I 1 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.6114 (tmt) REVERT: L 10 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7528 (mtm180) REVERT: N 115 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7968 (mp0) REVERT: P 12 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8033 (ttm110) REVERT: Q 36 ASP cc_start: 0.7968 (p0) cc_final: 0.7620 (p0) REVERT: b 107 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8232 (tmmt) REVERT: e 13 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8809 (mttm) REVERT: h 41 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: i 39 ARG cc_start: 0.9338 (OUTLIER) cc_final: 0.8533 (ptm160) REVERT: k 36 ARG cc_start: 0.8220 (mmt90) cc_final: 0.7916 (mtt-85) REVERT: k 78 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8794 (pp) REVERT: m 3 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8061 (ttt90) REVERT: q 27 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7214 (mm-30) REVERT: u 10 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5687 (tm-30) outliers start: 143 outliers final: 81 residues processed: 910 average time/residue: 2.1746 time to fit residues: 2783.5774 Evaluate side-chains 906 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 813 time to evaluate : 6.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 39 LYS Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 219 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 66 ILE Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain f residue 16 ASP Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain h residue 41 GLN Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 39 ARG Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 3 ARG Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 ASP Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 GLU Chi-restraints excluded: chain r residue 35 GLU Chi-restraints excluded: chain s residue 26 ASN Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 20 LYS Chi-restraints excluded: chain u residue 21 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 901 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 532 optimal weight: 8.9990 chunk 682 optimal weight: 10.0000 chunk 528 optimal weight: 9.9990 chunk 786 optimal weight: 10.0000 chunk 521 optimal weight: 0.7980 chunk 931 optimal weight: 10.0000 chunk 582 optimal weight: 9.9990 chunk 567 optimal weight: 1.9990 chunk 429 optimal weight: 9.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 ASN I 67 ASN K 125 GLN M 57 ASN T 38 ASN W 74 GLN X 44 GLN c 21 ASN c 25 ASN c 139 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN f 52 ASN f 63 ASN ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN k 63 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 149003 Z= 0.439 Angle : 0.687 14.102 222811 Z= 0.364 Chirality : 0.044 0.697 28491 Planarity : 0.006 0.143 11990 Dihedral : 23.099 179.773 74338 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.64 % Favored : 97.21 % Rotamer: Outliers : 3.39 % Allowed : 20.54 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.11), residues: 5412 helix: 1.84 (0.12), residues: 1886 sheet: 0.44 (0.16), residues: 1030 loop : -0.33 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 201 HIS 0.008 0.001 HIS C 230 PHE 0.027 0.002 PHE u 37 TYR 0.027 0.002 TYR P 32 ARG 0.013 0.001 ARG g 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 816 time to evaluate : 6.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 8 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8719 (mtpp) REVERT: G 170 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8574 (tt) REVERT: G 171 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8205 (mmm160) REVERT: L 10 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7593 (mtm180) REVERT: P 12 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8120 (ttm110) REVERT: P 100 MET cc_start: 0.9348 (ttt) cc_final: 0.9024 (ttt) REVERT: Q 36 ASP cc_start: 0.7976 (p0) cc_final: 0.7643 (p0) REVERT: b 107 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8245 (tmmt) REVERT: e 13 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8782 (mttm) REVERT: h 41 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: i 39 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.8375 (ptm160) REVERT: k 36 ARG cc_start: 0.8302 (mmt90) cc_final: 0.7995 (mtt-85) REVERT: k 78 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8824 (pp) REVERT: m 3 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8131 (ttt90) REVERT: q 27 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: u 10 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5692 (tm-30) outliers start: 152 outliers final: 103 residues processed: 906 average time/residue: 2.2050 time to fit residues: 2806.4176 Evaluate side-chains 927 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 811 time to evaluate : 6.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain b residue 219 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 66 ILE Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain f residue 16 ASP Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain h residue 41 GLN Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 39 ARG Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 3 ARG Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 ASP Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 GLU Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 35 GLU Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 20 LYS Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 58 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 576 optimal weight: 5.9990 chunk 371 optimal weight: 0.0970 chunk 556 optimal weight: 0.7980 chunk 280 optimal weight: 20.0000 chunk 182 optimal weight: 30.0000 chunk 180 optimal weight: 9.9990 chunk 591 optimal weight: 20.0000 chunk 634 optimal weight: 10.0000 chunk 460 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 731 optimal weight: 10.0000 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN F 127 ASN G 104 ASN I 67 ASN K 125 GLN M 57 ASN X 44 GLN c 21 ASN c 139 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 52 ASN f 63 ASN ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN k 63 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN o 20 ASN p 62 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 149003 Z= 0.235 Angle : 0.619 13.090 222811 Z= 0.335 Chirality : 0.038 0.608 28491 Planarity : 0.006 0.136 11990 Dihedral : 23.140 179.712 74338 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.35 % Favored : 97.51 % Rotamer: Outliers : 3.03 % Allowed : 20.92 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.11), residues: 5412 helix: 1.89 (0.12), residues: 1885 sheet: 0.45 (0.16), residues: 1028 loop : -0.31 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 83 HIS 0.006 0.001 HIS j 15 PHE 0.020 0.001 PHE S 69 TYR 0.020 0.001 TYR P 32 ARG 0.013 0.000 ARG g 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 815 time to evaluate : 6.046 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: 3 36 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8289 (ttt180) REVERT: C 182 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8941 (ttt90) REVERT: G 170 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8556 (tt) REVERT: K 41 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9001 (mtpp) REVERT: N 115 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7829 (mp0) REVERT: P 12 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8057 (ttm110) REVERT: Q 36 ASP cc_start: 0.7965 (p0) cc_final: 0.7626 (p0) REVERT: b 107 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8245 (tmmt) REVERT: e 13 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8782 (mttm) REVERT: g 143 ARG cc_start: 0.7731 (mmp-170) cc_final: 0.7483 (mmp80) REVERT: h 3 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8488 (ttp) REVERT: h 41 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: i 39 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.8368 (ptm160) REVERT: k 36 ARG cc_start: 0.8297 (mmt90) cc_final: 0.7979 (mtt-85) REVERT: k 78 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8815 (pp) REVERT: m 3 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8156 (ttt90) REVERT: q 27 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: u 10 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5744 (tm-30) outliers start: 136 outliers final: 100 residues processed: 899 average time/residue: 2.2054 time to fit residues: 2779.6325 Evaluate side-chains 924 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 810 time to evaluate : 5.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 219 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 66 ILE Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 16 ASP Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 41 GLN Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 39 ARG Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 3 ARG Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 ASP Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain r residue 35 GLU Chi-restraints excluded: chain s residue 26 ASN Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 20 LYS Chi-restraints excluded: chain u residue 21 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 846 optimal weight: 5.9990 chunk 891 optimal weight: 2.9990 chunk 813 optimal weight: 5.9990 chunk 867 optimal weight: 3.9990 chunk 522 optimal weight: 0.0170 chunk 377 optimal weight: 5.9990 chunk 681 optimal weight: 8.9990 chunk 266 optimal weight: 10.0000 chunk 784 optimal weight: 9.9990 chunk 820 optimal weight: 10.0000 chunk 864 optimal weight: 2.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 ASN I 67 ASN K 125 GLN X 44 GLN c 21 ASN c 139 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 52 ASN f 63 ASN ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN k 63 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 149003 Z= 0.249 Angle : 0.613 12.671 222811 Z= 0.331 Chirality : 0.038 0.495 28491 Planarity : 0.006 0.136 11990 Dihedral : 23.092 179.960 74338 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.59 % Favored : 97.25 % Rotamer: Outliers : 2.90 % Allowed : 21.15 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.11), residues: 5412 helix: 1.92 (0.12), residues: 1886 sheet: 0.44 (0.16), residues: 1038 loop : -0.29 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 201 HIS 0.006 0.001 HIS C 230 PHE 0.016 0.001 PHE M 21 TYR 0.021 0.001 TYR P 32 ARG 0.015 0.000 ARG g 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 815 time to evaluate : 6.162 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: C 182 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8936 (ttt90) REVERT: F 57 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7842 (mpt) REVERT: G 170 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8551 (tt) REVERT: K 41 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9006 (mtpp) REVERT: N 115 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7956 (mp0) REVERT: P 12 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8071 (ttm110) REVERT: P 100 MET cc_start: 0.9324 (ttt) cc_final: 0.8946 (ttt) REVERT: Q 36 ASP cc_start: 0.7973 (p0) cc_final: 0.7642 (p0) REVERT: b 4 TYR cc_start: 0.4839 (OUTLIER) cc_final: 0.4613 (p90) REVERT: b 107 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8239 (tmmt) REVERT: e 13 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8792 (mttm) REVERT: g 136 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8503 (mmtt) REVERT: h 41 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8496 (tt0) REVERT: i 39 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.8376 (ptm160) REVERT: k 36 ARG cc_start: 0.8270 (mmt90) cc_final: 0.7953 (mtt-85) REVERT: k 78 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8811 (pp) REVERT: m 3 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8095 (ttt90) REVERT: q 27 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7202 (mm-30) REVERT: u 10 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5752 (tm-30) outliers start: 130 outliers final: 96 residues processed: 889 average time/residue: 2.2046 time to fit residues: 2747.1438 Evaluate side-chains 920 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 810 time to evaluate : 6.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 4 TYR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 219 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 66 ILE Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 16 ASP Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain h residue 41 GLN Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 39 ARG Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 3 ARG Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 ASP Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain r residue 35 GLU Chi-restraints excluded: chain s residue 26 ASN Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 20 LYS Chi-restraints excluded: chain u residue 21 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 569 optimal weight: 10.0000 chunk 917 optimal weight: 10.0000 chunk 559 optimal weight: 6.9990 chunk 435 optimal weight: 0.9990 chunk 637 optimal weight: 10.0000 chunk 962 optimal weight: 8.9990 chunk 885 optimal weight: 0.6980 chunk 766 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 591 optimal weight: 20.0000 chunk 469 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN F 127 ASN G 104 ASN I 67 ASN K 125 GLN X 44 GLN c 21 ASN c 25 ASN c 139 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN f 52 ASN f 63 ASN ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN k 63 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 149003 Z= 0.288 Angle : 0.618 12.803 222811 Z= 0.334 Chirality : 0.039 0.454 28491 Planarity : 0.006 0.137 11990 Dihedral : 23.073 179.876 74338 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.42 % Favored : 97.41 % Rotamer: Outliers : 2.74 % Allowed : 21.37 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.11), residues: 5412 helix: 1.92 (0.12), residues: 1888 sheet: 0.47 (0.16), residues: 1027 loop : -0.30 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 172 HIS 0.006 0.001 HIS C 230 PHE 0.031 0.002 PHE u 37 TYR 0.022 0.001 TYR P 32 ARG 0.015 0.000 ARG g 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 814 time to evaluate : 6.216 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: C 182 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8938 (ttt90) REVERT: F 26 MET cc_start: 0.8259 (mmm) cc_final: 0.8023 (mmt) REVERT: F 170 MET cc_start: 0.6936 (ppp) cc_final: 0.6419 (pp-130) REVERT: G 170 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8566 (tt) REVERT: K 41 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9008 (mtpp) REVERT: N 115 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7970 (mp0) REVERT: P 12 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8080 (ttm110) REVERT: Q 36 ASP cc_start: 0.7974 (p0) cc_final: 0.7628 (p0) REVERT: b 4 TYR cc_start: 0.4844 (OUTLIER) cc_final: 0.4618 (p90) REVERT: b 107 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8283 (tmmt) REVERT: c 100 GLN cc_start: 0.8257 (mm-40) cc_final: 0.8056 (mp10) REVERT: e 13 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8784 (mttm) REVERT: g 143 ARG cc_start: 0.7797 (mmp-170) cc_final: 0.7533 (mmp80) REVERT: h 41 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: i 39 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.8381 (ptm160) REVERT: k 78 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8824 (pp) REVERT: m 3 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8095 (ttt90) REVERT: q 27 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: s 65 HIS cc_start: 0.8468 (m-70) cc_final: 0.8203 (m-70) REVERT: u 10 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5759 (tm-30) outliers start: 123 outliers final: 99 residues processed: 888 average time/residue: 2.1652 time to fit residues: 2695.1815 Evaluate side-chains 922 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 810 time to evaluate : 5.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain b residue 4 TYR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 219 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 66 ILE Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 16 ASP Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain h residue 41 GLN Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 39 ARG Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 3 ARG Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 ASP Chi-restraints excluded: chain p residue 91 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 GLU Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain r residue 35 GLU Chi-restraints excluded: chain s residue 26 ASN Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 20 LYS Chi-restraints excluded: chain u residue 21 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 608 optimal weight: 10.0000 chunk 816 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 706 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 chunk 767 optimal weight: 5.9990 chunk 321 optimal weight: 5.9990 chunk 788 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 ASN I 67 ASN K 125 GLN X 44 GLN c 21 ASN c 25 ASN c 139 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 52 ASN f 63 ASN ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN k 63 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.070054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.044048 restraints weight = 269589.016| |-----------------------------------------------------------------------------| r_work (start): 0.2584 rms_B_bonded: 0.98 r_work: 0.2474 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2390 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9277 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 149003 Z= 0.459 Angle : 0.698 14.395 222811 Z= 0.370 Chirality : 0.045 0.438 28491 Planarity : 0.006 0.144 11990 Dihedral : 23.111 179.853 74335 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.64 % Favored : 97.19 % Rotamer: Outliers : 3.08 % Allowed : 21.17 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.11), residues: 5412 helix: 1.79 (0.12), residues: 1888 sheet: 0.43 (0.16), residues: 1029 loop : -0.36 (0.12), residues: 2495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP d 172 HIS 0.008 0.001 HIS C 230 PHE 0.019 0.002 PHE D 121 TYR 0.027 0.002 TYR P 32 ARG 0.014 0.001 ARG g 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43381.39 seconds wall clock time: 750 minutes 1.53 seconds (45001.53 seconds total)