Starting phenix.real_space_refine on Sun Mar 17 22:02:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxg_11520/03_2024/6zxg_11520_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxg_11520/03_2024/6zxg_11520.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxg_11520/03_2024/6zxg_11520_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxg_11520/03_2024/6zxg_11520_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxg_11520/03_2024/6zxg_11520_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxg_11520/03_2024/6zxg_11520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxg_11520/03_2024/6zxg_11520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxg_11520/03_2024/6zxg_11520_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxg_11520/03_2024/6zxg_11520_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 1642 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 3 6.06 5 P 1654 5.49 5 Mg 131 5.21 5 S 203 5.16 5 C 43844 2.51 5 N 14681 2.21 5 O 19349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 251": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "G GLU 219": "OE1" <-> "OE2" Residue "H GLU 171": "OE1" <-> "OE2" Residue "I TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 34": "OE1" <-> "OE2" Residue "J ARG 70": "NH1" <-> "NH2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "J ARG 127": "NH1" <-> "NH2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 160": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "K GLU 13": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "O GLU 51": "OE1" <-> "OE2" Residue "O GLU 87": "OE1" <-> "OE2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ARG 121": "NH1" <-> "NH2" Residue "O ARG 146": "NH1" <-> "NH2" Residue "O ARG 150": "NH1" <-> "NH2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "P GLU 106": "OE1" <-> "OE2" Residue "P GLU 118": "OE1" <-> "OE2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "Q GLU 128": "OE1" <-> "OE2" Residue "S GLU 7": "OE1" <-> "OE2" Residue "T GLU 44": "OE1" <-> "OE2" Residue "T GLU 50": "OE1" <-> "OE2" Residue "W GLU 49": "OE1" <-> "OE2" Residue "W PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 42": "OE1" <-> "OE2" Residue "U GLU 113": "OE1" <-> "OE2" Residue "c GLU 52": "OE1" <-> "OE2" Residue "c GLU 62": "OE1" <-> "OE2" Residue "d ARG 12": "NH1" <-> "NH2" Residue "d PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 49": "OE1" <-> "OE2" Residue "g GLU 145": "OE1" <-> "OE2" Residue "g GLU 149": "OE1" <-> "OE2" Residue "j GLU 42": "OE1" <-> "OE2" Residue "k ARG 20": "NH1" <-> "NH2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k GLU 112": "OE1" <-> "OE2" Residue "k ARG 174": "NH1" <-> "NH2" Residue "k GLU 216": "OE1" <-> "OE2" Residue "k ARG 424": "NH1" <-> "NH2" Residue "z GLU 137": "OE1" <-> "OE2" Residue "z GLU 143": "OE1" <-> "OE2" Residue "z GLU 191": "OE1" <-> "OE2" Residue "z GLU 227": "OE1" <-> "OE2" Residue "z ARG 231": "NH1" <-> "NH2" Residue "z ARG 240": "NH1" <-> "NH2" Residue "z GLU 248": "OE1" <-> "OE2" Residue "z GLU 327": "OE1" <-> "OE2" Residue "z GLU 355": "OE1" <-> "OE2" Residue "z ARG 358": "NH1" <-> "NH2" Residue "z GLU 413": "OE1" <-> "OE2" Residue "z GLU 533": "OE1" <-> "OE2" Residue "z ARG 546": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 79865 Number of models: 1 Model: "" Number of chains: 47 Chain: "2" Number of atoms: 35310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1651, 35310 Classifications: {'RNA': 1651} Modifications used: {'rna2p': 4, 'rna2p_pur': 139, 'rna2p_pyr': 110, 'rna3p': 58, 'rna3p_pur': 716, 'rna3p_pyr': 612} Link IDs: {'rna2p': 252, 'rna3p': 1398} Chain breaks: 13 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 16 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "B" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1715 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "C" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1674 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "h" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 792 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "E" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2031 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 14, 'TRANS': 240} Chain: "D" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1745 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "G" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1802 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 10, 'TRANS': 212} Chain: "H" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1446 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 3 Chain: "I" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 1 Chain: "J" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1465 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "F" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1461 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Chain: "L" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1127 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Chain: "K" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 799 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 947 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 2 Chain: "P" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1077 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1116 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "S" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1162 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 137} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1094 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "V" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "Y" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 987 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "U" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 638 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 79} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "b" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 611 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Chain: "c" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "d" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 450 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "e" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 398 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 1 Chain: "f" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 465 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain breaks: 1 Chain: "g" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2306 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 10, 'TRANS': 284} Chain breaks: 3 Chain: "j" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 934 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "k" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 2886 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PTRANS': 36, 'TRANS': 393} Chain breaks: 5 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 545 Unresolved non-hydrogen dihedrals: 348 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 187 Chain: "z" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2803 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 11, 'TRANS': 337} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "2" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Unusual residues: {' MG': 123} Classifications: {'undetermined': 123} Link IDs: {None: 122} Chain: "h" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 40582 SG CYS h 23 88.818 171.309 101.590 1.00 6.86 S ATOM 40603 SG CYS h 26 88.611 169.988 97.651 1.00 7.43 S ATOM 40986 SG CYS h 74 90.875 168.134 100.178 1.00 8.52 S ATOM 41005 SG CYS h 77 92.137 171.444 98.795 1.00 8.67 S ATOM 69616 SG CYS d 21 160.038 157.791 70.369 1.00 6.66 S ATOM 69640 SG CYS d 24 157.416 155.309 69.413 1.00 7.59 S ATOM 69761 SG CYS d 39 156.560 158.528 71.249 1.00 8.83 S ATOM 69787 SG CYS d 42 157.789 155.581 73.214 1.00 9.31 S ATOM 70551 SG CYS f 121 186.452 146.595 29.086 1.00 26.15 S ATOM 70587 SG CYS f 126 185.169 144.795 33.134 1.00 27.55 S ATOM 70705 SG CYS f 141 183.284 145.029 29.872 1.00 25.13 S ATOM 70724 SG CYS f 144 183.659 148.198 31.681 1.00 23.70 S Time building chain proxies: 30.94, per 1000 atoms: 0.39 Number of scatterers: 79865 At special positions: 0 Unit cell: (218.154, 249.924, 196.974, 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 3 29.99 S 203 16.00 P 1654 15.00 Mg 131 11.99 O 19349 8.00 N 14681 7.00 C 43844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 249 " distance=2.04 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: 29.95 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d 101 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 21 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 42 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 39 " pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 141 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 144 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 126 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 121 " pdb=" ZN h 201 " pdb="ZN ZN h 201 " - pdb=" SG CYS h 26 " pdb="ZN ZN h 201 " - pdb=" SG CYS h 74 " pdb="ZN ZN h 201 " - pdb=" SG CYS h 77 " pdb="ZN ZN h 201 " - pdb=" SG CYS h 23 " Number of angles added : 18 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10468 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 191 helices and 61 sheets defined 31.3% alpha, 16.2% beta 454 base pairs and 873 stacking pairs defined. Time for finding SS restraints: 29.52 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 51 through 66 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 81 through 94 removed outlier: 5.577A pdb=" N ARG A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 86 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 87 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 168 through 186 Processing helix chain 'A' and resid 199 through 202 Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.786A pdb=" N GLU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 27 removed outlier: 3.758A pdb=" N LYS B 27 " --> pdb=" O PRO B 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 27' Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 158 through 177 Processing helix chain 'B' and resid 181 through 189 removed outlier: 3.638A pdb=" N ASN B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 147 through 160 Processing helix chain 'C' and resid 208 through 216 Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.906A pdb=" N THR C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TYR C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 265 through 268 No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'h' and resid 50 through 54 Processing helix chain 'h' and resid 75 through 80 Processing helix chain 'h' and resid 91 through 93 No H-bonds generated for 'chain 'h' and resid 91 through 93' Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 58 through 67 removed outlier: 3.754A pdb=" N GLN E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 248 through 255 Processing helix chain 'D' and resid 7 through 28 removed outlier: 3.658A pdb=" N VAL D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.532A pdb=" N LEU D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 55 through 59' Processing helix chain 'D' and resid 61 through 76 removed outlier: 6.520A pdb=" N ARG D 65 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE D 66 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG D 76 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 115 through 129 Processing helix chain 'D' and resid 163 through 167 removed outlier: 4.095A pdb=" N TYR D 167 " --> pdb=" O VAL D 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 25 No H-bonds generated for 'chain 'G' and resid 22 through 25' Processing helix chain 'G' and resid 138 through 144 Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 182 through 222 Processing helix chain 'H' and resid 18 through 30 removed outlier: 3.644A pdb=" N LEU H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 72 removed outlier: 5.503A pdb=" N LYS H 70 " --> pdb=" O PRO H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 118 through 120 No H-bonds generated for 'chain 'H' and resid 118 through 120' Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 160 through 181 removed outlier: 5.730A pdb=" N ASN H 164 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 166 " --> pdb=" O GLN H 163 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU H 167 " --> pdb=" O ASN H 164 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N HIS H 168 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL H 170 " --> pdb=" O GLU H 167 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU H 171 " --> pdb=" O HIS H 168 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 180 " --> pdb=" O TYR H 177 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR H 181 " --> pdb=" O LYS H 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 89 through 92 No H-bonds generated for 'chain 'I' and resid 89 through 92' Processing helix chain 'I' and resid 107 through 116 Processing helix chain 'I' and resid 131 through 137 Processing helix chain 'I' and resid 143 through 155 removed outlier: 4.961A pdb=" N ASN I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 168 removed outlier: 3.890A pdb=" N GLN I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 182 No H-bonds generated for 'chain 'I' and resid 179 through 182' Processing helix chain 'I' and resid 192 through 205 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 40 through 61 Processing helix chain 'J' and resid 68 through 84 Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 94 through 99 removed outlier: 3.639A pdb=" N GLY J 99 " --> pdb=" O TYR J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 108 removed outlier: 3.856A pdb=" N ARG J 108 " --> pdb=" O ASP J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 116 Processing helix chain 'J' and resid 123 through 130 Processing helix chain 'J' and resid 151 through 156 removed outlier: 4.380A pdb=" N LYS J 155 " --> pdb=" O LEU J 151 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N HIS J 156 " --> pdb=" O ASP J 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 151 through 156' Processing helix chain 'J' and resid 172 through 179 removed outlier: 4.360A pdb=" N LYS J 179 " --> pdb=" O ARG J 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 34 through 38 removed outlier: 4.239A pdb=" N ASP F 37 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 68 through 76 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.554A pdb=" N ARG F 91 " --> pdb=" O LEU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 143 through 161 removed outlier: 4.727A pdb=" N GLY F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 181 Processing helix chain 'F' and resid 188 through 203 removed outlier: 4.207A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 51 No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'K' and resid 5 through 16 Processing helix chain 'K' and resid 42 through 54 Processing helix chain 'K' and resid 73 through 83 removed outlier: 3.609A pdb=" N GLN K 77 " --> pdb=" O ASN K 73 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 47 through 58 removed outlier: 3.553A pdb=" N HIS N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 78 Processing helix chain 'N' and resid 86 through 104 Processing helix chain 'N' and resid 109 through 131 Processing helix chain 'N' and resid 145 through 149 Processing helix chain 'O' and resid 58 through 60 No H-bonds generated for 'chain 'O' and resid 58 through 60' Processing helix chain 'O' and resid 65 through 67 No H-bonds generated for 'chain 'O' and resid 65 through 67' Processing helix chain 'O' and resid 71 through 87 Processing helix chain 'O' and resid 112 through 121 Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 19 through 28 removed outlier: 3.682A pdb=" N HIS M 28 " --> pdb=" O THR M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 43 Processing helix chain 'M' and resid 61 through 71 removed outlier: 3.546A pdb=" N VAL M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU M 66 " --> pdb=" O VAL M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 89 Processing helix chain 'M' and resid 120 through 128 removed outlier: 3.530A pdb=" N TYR M 127 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE M 128 " --> pdb=" O ILE M 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 26 Processing helix chain 'P' and resid 30 through 34 Processing helix chain 'P' and resid 39 through 47 Processing helix chain 'P' and resid 51 through 65 Processing helix chain 'P' and resid 87 through 89 No H-bonds generated for 'chain 'P' and resid 87 through 89' Processing helix chain 'P' and resid 109 through 111 No H-bonds generated for 'chain 'P' and resid 109 through 111' Processing helix chain 'P' and resid 116 through 119 Processing helix chain 'P' and resid 139 through 141 No H-bonds generated for 'chain 'P' and resid 139 through 141' Processing helix chain 'R' and resid 7 through 19 removed outlier: 3.754A pdb=" N LYS R 19 " --> pdb=" O VAL R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 38 removed outlier: 3.655A pdb=" N ARG R 33 " --> pdb=" O HIS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 61 removed outlier: 3.684A pdb=" N LYS R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 82 removed outlier: 3.893A pdb=" N GLU R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 108 Processing helix chain 'Q' and resid 45 through 58 removed outlier: 4.809A pdb=" N TYR Q 49 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU Q 53 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Proline residue: Q 54 - end of helix Processing helix chain 'Q' and resid 60 through 63 No H-bonds generated for 'chain 'Q' and resid 60 through 63' Processing helix chain 'Q' and resid 77 through 98 Processing helix chain 'Q' and resid 104 through 115 Processing helix chain 'Q' and resid 117 through 119 No H-bonds generated for 'chain 'Q' and resid 117 through 119' Processing helix chain 'S' and resid 26 through 32 removed outlier: 4.178A pdb=" N THR S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA S 32 " --> pdb=" O PHE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 47 removed outlier: 3.503A pdb=" N HIS S 42 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL S 43 " --> pdb=" O ARG S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 72 removed outlier: 3.541A pdb=" N GLU S 65 " --> pdb=" O GLU S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 77 Processing helix chain 'S' and resid 81 through 83 No H-bonds generated for 'chain 'S' and resid 81 through 83' Processing helix chain 'S' and resid 102 through 116 Processing helix chain 'S' and resid 120 through 126 Processing helix chain 'T' and resid 6 through 8 No H-bonds generated for 'chain 'T' and resid 6 through 8' Processing helix chain 'T' and resid 11 through 25 Processing helix chain 'T' and resid 52 through 66 Processing helix chain 'T' and resid 72 through 78 removed outlier: 3.594A pdb=" N LYS T 77 " --> pdb=" O GLY T 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 109 Processing helix chain 'T' and resid 125 through 141 removed outlier: 3.542A pdb=" N ILE T 134 " --> pdb=" O ASP T 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 61 Processing helix chain 'V' and resid 65 through 75 Processing helix chain 'W' and resid 6 through 19 Processing helix chain 'W' and resid 32 through 43 Processing helix chain 'W' and resid 83 through 93 removed outlier: 3.571A pdb=" N LEU W 86 " --> pdb=" O LEU W 83 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU W 87 " --> pdb=" O LYS W 84 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS W 88 " --> pdb=" O ASP W 85 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN W 90 " --> pdb=" O GLU W 87 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN W 91 " --> pdb=" O LYS W 88 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU W 93 " --> pdb=" O GLN W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 118 Processing helix chain 'X' and resid 10 through 20 Processing helix chain 'X' and resid 25 through 31 Processing helix chain 'X' and resid 34 through 38 Processing helix chain 'X' and resid 90 through 93 Processing helix chain 'X' and resid 130 through 134 Processing helix chain 'Y' and resid 37 through 48 Processing helix chain 'Y' and resid 79 through 85 Processing helix chain 'Y' and resid 88 through 93 Processing helix chain 'Y' and resid 104 through 116 removed outlier: 4.013A pdb=" N LYS Y 116 " --> pdb=" O ASN Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 124 removed outlier: 3.529A pdb=" N ALA Y 123 " --> pdb=" O THR Y 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 46 removed outlier: 3.890A pdb=" N LYS U 46 " --> pdb=" O GLY U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 104 removed outlier: 3.520A pdb=" N SER U 103 " --> pdb=" O LYS U 99 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE U 104 " --> pdb=" O GLN U 100 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 60 removed outlier: 3.957A pdb=" N ASP Z 56 " --> pdb=" O LYS Z 52 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 64 No H-bonds generated for 'chain 'Z' and resid 62 through 64' Processing helix chain 'Z' and resid 70 through 76 Processing helix chain 'Z' and resid 81 through 93 removed outlier: 3.671A pdb=" N SER Z 93 " --> pdb=" O GLN Z 89 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 17 Processing helix chain 'd' and resid 16 through 18 No H-bonds generated for 'chain 'd' and resid 16 through 18' Processing helix chain 'd' and resid 33 through 35 No H-bonds generated for 'chain 'd' and resid 33 through 35' Processing helix chain 'd' and resid 40 through 50 removed outlier: 5.448A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 15 Processing helix chain 'e' and resid 31 through 42 Processing helix chain 'j' and resid 3 through 14 removed outlier: 3.685A pdb=" N ARG j 7 " --> pdb=" O GLN j 3 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS j 8 " --> pdb=" O ALA j 4 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) Processing helix chain 'j' and resid 92 through 99 removed outlier: 3.787A pdb=" N GLU j 99 " --> pdb=" O SER j 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 106 No H-bonds generated for 'chain 'j' and resid 104 through 106' Processing helix chain 'k' and resid 13 through 18 Processing helix chain 'k' and resid 29 through 37 Processing helix chain 'k' and resid 44 through 48 Processing helix chain 'k' and resid 70 through 73 No H-bonds generated for 'chain 'k' and resid 70 through 73' Processing helix chain 'k' and resid 146 through 151 removed outlier: 4.349A pdb=" N ALA k 149 " --> pdb=" O ALA k 146 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N CYS k 151 " --> pdb=" O LEU k 148 " (cutoff:3.500A) Processing helix chain 'k' and resid 196 through 200 removed outlier: 3.823A pdb=" N ALA k 199 " --> pdb=" O PRO k 196 " (cutoff:3.500A) Processing helix chain 'k' and resid 220 through 223 Processing helix chain 'k' and resid 242 through 248 removed outlier: 3.621A pdb=" N SER k 247 " --> pdb=" O GLU k 243 " (cutoff:3.500A) Processing helix chain 'k' and resid 251 through 259 Processing helix chain 'k' and resid 348 through 366 removed outlier: 6.016A pdb=" N LYS k 353 " --> pdb=" O GLY k 349 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG k 354 " --> pdb=" O ASN k 350 " (cutoff:3.500A) Processing helix chain 'k' and resid 411 through 420 Processing helix chain 'k' and resid 437 through 439 No H-bonds generated for 'chain 'k' and resid 437 through 439' Processing helix chain 'k' and resid 491 through 503 Processing helix chain 'z' and resid 131 through 146 removed outlier: 3.906A pdb=" N MET z 146 " --> pdb=" O LYS z 142 " (cutoff:3.500A) Processing helix chain 'z' and resid 152 through 155 Processing helix chain 'z' and resid 164 through 175 Processing helix chain 'z' and resid 239 through 259 Processing helix chain 'z' and resid 290 through 292 No H-bonds generated for 'chain 'z' and resid 290 through 292' Processing helix chain 'z' and resid 297 through 316 Processing helix chain 'z' and resid 327 through 329 No H-bonds generated for 'chain 'z' and resid 327 through 329' Processing helix chain 'z' and resid 353 through 370 removed outlier: 3.589A pdb=" N LEU z 357 " --> pdb=" O ALA z 353 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE z 367 " --> pdb=" O ASN z 363 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE z 368 " --> pdb=" O VAL z 364 " (cutoff:3.500A) Processing helix chain 'z' and resid 378 through 386 Processing helix chain 'z' and resid 395 through 407 removed outlier: 3.571A pdb=" N LYS z 401 " --> pdb=" O ALA z 397 " (cutoff:3.500A) Processing helix chain 'z' and resid 413 through 426 removed outlier: 4.320A pdb=" N GLU z 423 " --> pdb=" O HIS z 419 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL z 424 " --> pdb=" O VAL z 420 " (cutoff:3.500A) Processing helix chain 'z' and resid 439 through 451 Processing helix chain 'z' and resid 532 through 547 Processing helix chain 'z' and resid 552 through 558 Processing sheet with id= A, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.316A pdb=" N LEU A 121 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE A 77 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A 123 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL A 124 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 145 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 159 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N CYS A 148 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE A 161 " --> pdb=" O CYS A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.780A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.598A pdb=" N ASP B 90 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 66 through 70 removed outlier: 5.330A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 13.265A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 12.754A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 137 through 144 removed outlier: 3.643A pdb=" N LYS C 108 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 184 through 188 Processing sheet with id= G, first strand: chain 'h' and resid 20 through 22 Processing sheet with id= H, first strand: chain 'h' and resid 36 through 43 Processing sheet with id= I, first strand: chain 'E' and resid 70 through 72 removed outlier: 3.986A pdb=" N ASP E 88 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 121 through 125 removed outlier: 6.305A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 Processing sheet with id= L, first strand: chain 'E' and resid 225 through 229 removed outlier: 6.404A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 84 through 90 removed outlier: 6.756A pdb=" N THR D 46 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR D 87 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE D 48 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLU D 89 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE D 50 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 148 through 155 removed outlier: 3.644A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.597A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 72 through 77 Processing sheet with id= Q, first strand: chain 'G' and resid 160 through 162 removed outlier: 3.983A pdb=" N ARG G 170 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 54 through 57 removed outlier: 3.748A pdb=" N GLY G 54 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL G 108 " --> pdb=" O ASN G 56 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 91 through 96 removed outlier: 3.721A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 185 through 188 removed outlier: 8.462A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 62 through 67 Processing sheet with id= V, first strand: chain 'I' and resid 187 through 189 removed outlier: 3.700A pdb=" N ASP I 80 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 42 through 48 removed outlier: 6.657A pdb=" N HIS I 44 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA I 57 " --> pdb=" O HIS I 44 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL I 46 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR I 55 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL I 48 " --> pdb=" O LYS I 53 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS I 53 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 135 through 137 Processing sheet with id= Y, first strand: chain 'F' and resid 123 through 127 Processing sheet with id= Z, first strand: chain 'L' and resid 101 through 112 removed outlier: 6.209A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 15.621A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 16.656A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 20 through 23 removed outlier: 3.504A pdb=" N ALA K 23 " --> pdb=" O PHE K 67 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.855A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA O 92 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N CYS O 31 " --> pdb=" O ALA O 92 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N HIS O 94 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE O 33 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS O 96 " --> pdb=" O ILE O 33 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA O 35 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG O 98 " --> pdb=" O ALA O 35 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 108 through 111 removed outlier: 3.604A pdb=" N ILE M 77 " --> pdb=" O CYS M 50 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'P' and resid 75 through 78 removed outlier: 6.765A pdb=" N MET P 93 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR P 78 " --> pdb=" O MET P 93 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY P 95 " --> pdb=" O THR P 78 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'R' and resid 96 through 98 Processing sheet with id= AF, first strand: chain 'Q' and resid 9 through 15 Processing sheet with id= AG, first strand: chain 'S' and resid 12 through 14 Processing sheet with id= AH, first strand: chain 'T' and resid 81 through 83 Processing sheet with id= AI, first strand: chain 'T' and resid 113 through 115 Processing sheet with id= AJ, first strand: chain 'V' and resid 32 through 37 Processing sheet with id= AK, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= AL, first strand: chain 'W' and resid 72 through 74 removed outlier: 6.824A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 80 through 84 removed outlier: 3.522A pdb=" N GLU X 53 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA X 103 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL X 122 " --> pdb=" O ALA X 103 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Y' and resid 6 through 10 removed outlier: 3.544A pdb=" N THR Y 6 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id= AP, first strand: chain 'U' and resid 111 through 115 removed outlier: 4.556A pdb=" N LYS U 49 " --> pdb=" O HIS U 92 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'U' and resid 59 through 66 Processing sheet with id= AR, first strand: chain 'Z' and resid 97 through 101 removed outlier: 6.819A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'b' and resid 32 through 36 Processing sheet with id= AT, first strand: chain 'c' and resid 55 through 58 removed outlier: 6.661A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'c' and resid 19 through 21 Processing sheet with id= AV, first strand: chain 'f' and resid 132 through 135 Processing sheet with id= AW, first strand: chain 'g' and resid 20 through 22 removed outlier: 4.180A pdb=" N GLN g 20 " --> pdb=" O ALA g 34 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG g 57 " --> pdb=" O MET g 42 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'g' and resid 66 through 71 removed outlier: 6.696A pdb=" N GLY g 81 " --> pdb=" O SER g 67 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL g 69 " --> pdb=" O LEU g 79 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU g 79 " --> pdb=" O VAL g 69 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE g 71 " --> pdb=" O PHE g 77 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N PHE g 77 " --> pdb=" O ILE g 71 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER g 82 " --> pdb=" O THR g 86 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR g 86 " --> pdb=" O SER g 82 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP g 91 " --> pdb=" O THR g 97 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N THR g 97 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 108 through 113 removed outlier: 6.980A pdb=" N GLY g 123 " --> pdb=" O LEU g 109 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL g 111 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL g 121 " --> pdb=" O VAL g 111 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'g' and resid 151 through 156 removed outlier: 6.485A pdb=" N CYS g 168 " --> pdb=" O SER g 152 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL g 154 " --> pdb=" O VAL g 166 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL g 166 " --> pdb=" O VAL g 154 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE g 156 " --> pdb=" O ILE g 164 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE g 164 " --> pdb=" O PHE g 156 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'g' and resid 195 through 200 removed outlier: 7.125A pdb=" N GLY g 210 " --> pdb=" O ASN g 196 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL g 198 " --> pdb=" O ALA g 208 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA g 208 " --> pdb=" O VAL g 198 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL g 200 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU g 206 " --> pdb=" O VAL g 200 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASP g 220 " --> pdb=" O HIS g 226 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N HIS g 226 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'g' and resid 238 through 241 removed outlier: 3.828A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP g 260 " --> pdb=" O ILE g 266 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE g 266 " --> pdb=" O ASP g 260 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'g' and resid 6 through 11 removed outlier: 6.928A pdb=" N VAL g 309 " --> pdb=" O ARG g 8 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR g 10 " --> pdb=" O VAL g 307 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL g 307 " --> pdb=" O THR g 10 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'j' and resid 68 through 71 removed outlier: 6.751A pdb=" N GLU j 40 " --> pdb=" O LEU j 31 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N THR j 33 " --> pdb=" O LEU j 38 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU j 38 " --> pdb=" O THR j 33 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N SER j 52 " --> pdb=" O LYS j 81 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU j 83 " --> pdb=" O SER j 52 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE j 70 " --> pdb=" O SER j 85 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL j 87 " --> pdb=" O PHE j 68 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE j 68 " --> pdb=" O VAL j 87 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'k' and resid 23 through 26 removed outlier: 6.333A pdb=" N TYR k 54 " --> pdb=" O LEU k 24 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU k 26 " --> pdb=" O TYR k 54 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU k 56 " --> pdb=" O LEU k 26 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER k 79 " --> pdb=" O LEU k 55 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL k 57 " --> pdb=" O SER k 79 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL k 81 " --> pdb=" O VAL k 57 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL k 103 " --> pdb=" O LEU k 80 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU k 82 " --> pdb=" O VAL k 103 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP k 105 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER k 133 " --> pdb=" O LEU k 104 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER k 157 " --> pdb=" O LEU k 134 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU k 183 " --> pdb=" O LEU k 158 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR k 206 " --> pdb=" O LEU k 184 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'k' and resid 336 through 339 Processing sheet with id= BG, first strand: chain 'k' and resid 388 through 392 Processing sheet with id= BH, first strand: chain 'z' and resid 267 through 271 removed outlier: 6.792A pdb=" N VAL z 276 " --> pdb=" O ILE z 268 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU z 270 " --> pdb=" O VAL z 274 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL z 274 " --> pdb=" O LEU z 270 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER z 187 " --> pdb=" O VAL z 194 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N HIS z 196 " --> pdb=" O CYS z 185 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS z 185 " --> pdb=" O HIS z 196 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'z' and resid 330 through 333 1457 hydrogen bonds defined for protein. 4059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1145 hydrogen bonds 1816 hydrogen bond angles 0 basepair planarities 454 basepair parallelities 873 stacking parallelities Total time for adding SS restraints: 64.97 Time building geometry restraints manager: 32.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 9064 1.30 - 1.43: 31700 1.43 - 1.56: 40251 1.56 - 1.69: 3311 1.69 - 1.82: 312 Bond restraints: 84638 Sorted by residual: bond pdb=" C3' ATP z 602 " pdb=" C4' ATP z 602 " ideal model delta sigma weight residual 1.305 1.515 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C4' ATP z 602 " pdb=" O4' ATP z 602 " ideal model delta sigma weight residual 1.608 1.422 0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" C6 ATP z 602 " pdb=" N6 ATP z 602 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C1' ATP z 602 " pdb=" O4' ATP z 602 " ideal model delta sigma weight residual 1.307 1.428 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C4 ATP z 602 " pdb=" C5 ATP z 602 " ideal model delta sigma weight residual 1.343 1.463 -0.120 2.00e-02 2.50e+03 3.60e+01 ... (remaining 84633 not shown) Histogram of bond angle deviations from ideal: 84.06 - 102.05: 1824 102.05 - 120.03: 86021 120.03 - 138.02: 34266 138.02 - 156.00: 1 156.00 - 173.99: 1 Bond angle restraints: 122113 Sorted by residual: angle pdb=" O3' U 21677 " pdb=" P A2M 21678 " pdb=" OP1 A2M 21678 " ideal model delta sigma weight residual 108.00 173.99 -65.99 3.00e+00 1.11e-01 4.84e+02 angle pdb=" C1' A2M 2 27 " pdb=" N9 A2M 2 27 " pdb=" C8 A2M 2 27 " ideal model delta sigma weight residual 88.50 127.40 -38.90 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C1' A2M 2 668 " pdb=" N9 A2M 2 668 " pdb=" C8 A2M 2 668 " ideal model delta sigma weight residual 88.50 127.04 -38.54 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C1' A2M 2 484 " pdb=" N9 A2M 2 484 " pdb=" C8 A2M 2 484 " ideal model delta sigma weight residual 88.50 127.03 -38.53 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C1' A2M 21678 " pdb=" N9 A2M 21678 " pdb=" C8 A2M 21678 " ideal model delta sigma weight residual 88.50 126.27 -37.77 3.00e+00 1.11e-01 1.59e+02 ... (remaining 122108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 48934 35.95 - 71.89: 4051 71.89 - 107.84: 566 107.84 - 143.78: 19 143.78 - 179.73: 39 Dihedral angle restraints: 53609 sinusoidal: 37427 harmonic: 16182 Sorted by residual: dihedral pdb=" CA SER O 137 " pdb=" C SER O 137 " pdb=" N ASP O 138 " pdb=" CA ASP O 138 " ideal model delta harmonic sigma weight residual 180.00 131.75 48.25 0 5.00e+00 4.00e-02 9.31e+01 dihedral pdb=" O4' U 2 427 " pdb=" C1' U 2 427 " pdb=" N1 U 2 427 " pdb=" C2 U 2 427 " ideal model delta sinusoidal sigma weight residual -160.00 17.40 -177.40 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 21485 " pdb=" C1' U 21485 " pdb=" N1 U 21485 " pdb=" C2 U 21485 " ideal model delta sinusoidal sigma weight residual -160.00 16.76 -176.76 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 53606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 13726 0.093 - 0.186: 1078 0.186 - 0.279: 56 0.279 - 0.372: 9 0.372 - 0.465: 9 Chirality restraints: 14878 Sorted by residual: chirality pdb=" CB VAL h 84 " pdb=" CA VAL h 84 " pdb=" CG1 VAL h 84 " pdb=" CG2 VAL h 84 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C3' C 2 381 " pdb=" C4' C 2 381 " pdb=" O3' C 2 381 " pdb=" C2' C 2 381 " both_signs ideal model delta sigma weight residual False -2.48 -2.05 -0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CG LEU Y 18 " pdb=" CB LEU Y 18 " pdb=" CD1 LEU Y 18 " pdb=" CD2 LEU Y 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.37e+00 ... (remaining 14875 not shown) Planarity restraints: 9400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 683 " 0.162 2.00e-02 2.50e+03 7.26e-01 1.19e+04 pdb=" C4' OMG 2 683 " 0.528 2.00e-02 2.50e+03 pdb=" O4' OMG 2 683 " 0.700 2.00e-02 2.50e+03 pdb=" C3' OMG 2 683 " -0.516 2.00e-02 2.50e+03 pdb=" O3' OMG 2 683 " -0.861 2.00e-02 2.50e+03 pdb=" C2' OMG 2 683 " -0.078 2.00e-02 2.50e+03 pdb=" O2' OMG 2 683 " 1.191 2.00e-02 2.50e+03 pdb=" C1' OMG 2 683 " 0.101 2.00e-02 2.50e+03 pdb=" N9 OMG 2 683 " -1.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 509 " 0.049 2.00e-02 2.50e+03 5.97e-01 8.01e+03 pdb=" C4' OMG 2 509 " 0.451 2.00e-02 2.50e+03 pdb=" O4' OMG 2 509 " 0.668 2.00e-02 2.50e+03 pdb=" C3' OMG 2 509 " -0.590 2.00e-02 2.50e+03 pdb=" O3' OMG 2 509 " -0.617 2.00e-02 2.50e+03 pdb=" C2' OMG 2 509 " -0.195 2.00e-02 2.50e+03 pdb=" O2' OMG 2 509 " 0.940 2.00e-02 2.50e+03 pdb=" C1' OMG 2 509 " 0.217 2.00e-02 2.50e+03 pdb=" N9 OMG 2 509 " -0.925 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 436 " 0.082 2.00e-02 2.50e+03 5.88e-01 7.77e+03 pdb=" C4' OMG 2 436 " 0.409 2.00e-02 2.50e+03 pdb=" O4' OMG 2 436 " 0.549 2.00e-02 2.50e+03 pdb=" C3' OMG 2 436 " -0.608 2.00e-02 2.50e+03 pdb=" O3' OMG 2 436 " -0.641 2.00e-02 2.50e+03 pdb=" C2' OMG 2 436 " -0.155 2.00e-02 2.50e+03 pdb=" O2' OMG 2 436 " 1.002 2.00e-02 2.50e+03 pdb=" C1' OMG 2 436 " 0.238 2.00e-02 2.50e+03 pdb=" N9 OMG 2 436 " -0.875 2.00e-02 2.50e+03 ... (remaining 9397 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 581 2.57 - 3.15: 56440 3.15 - 3.74: 143209 3.74 - 4.32: 211215 4.32 - 4.90: 294009 Nonbonded interactions: 705454 Sorted by model distance: nonbonded pdb=" OP1 U 21694 " pdb="MG MG 21917 " model vdw 1.992 2.170 nonbonded pdb=" O2A ATP z 602 " pdb="MG MG z 603 " model vdw 2.001 2.170 nonbonded pdb=" OE2 GLU z 191 " pdb="MG MG z 601 " model vdw 2.023 2.170 nonbonded pdb=" OP2 C 21219 " pdb="MG MG 21941 " model vdw 2.033 2.170 nonbonded pdb=" O2G ATP z 602 " pdb="MG MG z 603 " model vdw 2.037 2.170 ... (remaining 705449 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.380 Construct map_model_manager: 0.110 Extract box with map and model: 12.030 Check model and map are aligned: 0.850 Set scattering table: 0.550 Process input model: 227.740 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 261.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.210 84638 Z= 0.445 Angle : 1.042 65.985 122113 Z= 0.495 Chirality : 0.052 0.465 14878 Planarity : 0.024 0.726 9400 Dihedral : 22.075 179.730 43138 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 0.23 % Allowed : 3.95 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.50 (0.10), residues: 5506 helix: -1.93 (0.10), residues: 1783 sheet: -0.86 (0.15), residues: 978 loop : -1.70 (0.10), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP g 291 HIS 0.029 0.002 HIS S 135 PHE 0.070 0.003 PHE C 236 TYR 0.028 0.003 TYR g 246 ARG 0.018 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1022 time to evaluate : 4.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7941 (mt-10) REVERT: C 146 GLU cc_start: 0.7744 (mp0) cc_final: 0.7537 (mp0) REVERT: D 124 ARG cc_start: 0.7493 (mtm-85) cc_final: 0.7226 (ttp-110) REVERT: D 156 LEU cc_start: 0.8134 (mt) cc_final: 0.7758 (tp) REVERT: I 55 TYR cc_start: 0.8741 (m-80) cc_final: 0.8539 (m-80) REVERT: L 37 TYR cc_start: 0.8670 (p90) cc_final: 0.8450 (p90) REVERT: N 143 SER cc_start: 0.7415 (m) cc_final: 0.7010 (m) REVERT: O 90 ILE cc_start: 0.8557 (mm) cc_final: 0.8208 (mm) REVERT: P 93 MET cc_start: 0.8241 (mmm) cc_final: 0.7975 (mmm) REVERT: Q 128 GLU cc_start: 0.8381 (tt0) cc_final: 0.7998 (tt0) REVERT: S 105 ASN cc_start: 0.8422 (m-40) cc_final: 0.8213 (m-40) REVERT: X 60 LYS cc_start: 0.7740 (mttp) cc_final: 0.7451 (mttt) REVERT: Y 48 TYR cc_start: 0.8356 (m-80) cc_final: 0.7996 (m-80) REVERT: U 21 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7818 (ttp-170) REVERT: j 3 GLN cc_start: 0.7128 (tt0) cc_final: 0.6900 (pt0) REVERT: j 61 ILE cc_start: 0.9098 (mt) cc_final: 0.8788 (mm) REVERT: k 205 LYS cc_start: 0.8310 (mtpp) cc_final: 0.8041 (mtpt) REVERT: z 173 MET cc_start: 0.7909 (mtt) cc_final: 0.7408 (mtt) REVERT: z 236 LYS cc_start: 0.7266 (ptmt) cc_final: 0.6980 (pttp) REVERT: z 246 TRP cc_start: 0.8417 (m100) cc_final: 0.8084 (m100) REVERT: z 306 GLN cc_start: 0.8421 (tt0) cc_final: 0.8201 (tt0) outliers start: 11 outliers final: 10 residues processed: 1032 average time/residue: 1.9458 time to fit residues: 2553.1222 Evaluate side-chains 782 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 772 time to evaluate : 4.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain k residue 165 LEU Chi-restraints excluded: chain k residue 242 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 599 optimal weight: 7.9990 chunk 538 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 363 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 chunk 556 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 338 optimal weight: 7.9990 chunk 414 optimal weight: 1.9990 chunk 644 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 84 GLN B 76 ASN B 177 GLN B 186 ASN B 208 HIS C 113 GLN C 136 HIS h 43 ASN h 80 HIS E 8 HIS E 50 ASN E 157 ASN E 161 GLN D 57 ASN D 74 GLN D 101 GLN G 56 ASN H 73 GLN H 91 HIS H 114 GLN H 163 GLN I 84 ASN I 116 HIS I 167 GLN J 125 HIS J 132 GLN F 31 ASN F 79 HIS F 95 HIS F 186 ASN L 108 ASN L 112 HIS L 121 GLN K 32 HIS K 39 ASN K 50 GLN N 36 GLN O 38 ASN M 28 HIS M 48 HIS P 53 GLN P 79 HIS P 137 HIS R 31 ASN R 116 ASN R 127 ASN Q 11 GLN Q 80 GLN S 19 ASN S 42 HIS S 72 GLN S 120 HIS T 91 HIS T 137 GLN V 2 GLN V 29 HIS W 16 ASN W 98 GLN X 39 ASN X 73 GLN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 124 ASN U 81 GLN Z 103 HIS d 26 ASN d 45 GLN e 15 GLN e 22 GLN f 135 HIS f 139 HIS g 64 HIS g 104 HIS ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 GLN g 143 GLN g 191 HIS g 215 GLN g 237 ASN j 18 HIS j 36 ASN j 47 GLN k 53 HIS k 109 ASN k 189 ASN k 200 HIS k 235 ASN k 250 GLN z 258 ASN z 309 GLN z 322 HIS z 363 ASN z 365 ASN z 392 HIS z 417 GLN Total number of N/Q/H flips: 93 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 84638 Z= 0.432 Angle : 0.922 20.098 122113 Z= 0.465 Chirality : 0.048 0.446 14878 Planarity : 0.008 0.152 9400 Dihedral : 23.467 179.862 31896 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.06 % Allowed : 12.07 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.10), residues: 5506 helix: -0.66 (0.11), residues: 1798 sheet: -0.45 (0.16), residues: 978 loop : -1.22 (0.11), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP g 291 HIS 0.020 0.002 HIS S 135 PHE 0.045 0.003 PHE d 14 TYR 0.020 0.002 TYR f 105 ARG 0.008 0.001 ARG X 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 784 time to evaluate : 4.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 217 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8226 (tpp) REVERT: C 73 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6593 (mtt) REVERT: C 105 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7320 (tp30) REVERT: E 242 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8144 (mptt) REVERT: D 117 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6938 (ttm-80) REVERT: D 156 LEU cc_start: 0.8206 (mt) cc_final: 0.7866 (tp) REVERT: H 91 HIS cc_start: 0.8525 (m90) cc_final: 0.8174 (m-70) REVERT: I 55 TYR cc_start: 0.8732 (m-80) cc_final: 0.8519 (m-80) REVERT: J 18 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7400 (mtp85) REVERT: F 62 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7423 (mtt180) REVERT: N 143 SER cc_start: 0.7626 (m) cc_final: 0.7232 (m) REVERT: P 93 MET cc_start: 0.8170 (mmm) cc_final: 0.7927 (mmm) REVERT: Q 32 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8566 (mm) REVERT: Q 45 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.6714 (mtp180) REVERT: Q 128 GLU cc_start: 0.8369 (tt0) cc_final: 0.7988 (tt0) REVERT: W 55 ASP cc_start: 0.8060 (p0) cc_final: 0.7807 (p0) REVERT: X 60 LYS cc_start: 0.7856 (mttp) cc_final: 0.7620 (mttt) REVERT: Y 48 TYR cc_start: 0.8396 (m-80) cc_final: 0.8000 (m-80) REVERT: Y 74 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7635 (mmt) REVERT: U 21 ARG cc_start: 0.8169 (ttm170) cc_final: 0.7927 (ttp-170) REVERT: j 7 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7691 (ptp90) REVERT: j 25 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8400 (mt0) REVERT: j 36 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8109 (t0) REVERT: j 61 ILE cc_start: 0.9049 (mt) cc_final: 0.8806 (mm) REVERT: k 205 LYS cc_start: 0.8378 (mtpp) cc_final: 0.8112 (mtpt) REVERT: z 231 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6215 (tpt170) REVERT: z 246 TRP cc_start: 0.8431 (m100) cc_final: 0.8102 (m100) REVERT: z 306 GLN cc_start: 0.8472 (tt0) cc_final: 0.8254 (tt0) outliers start: 144 outliers final: 66 residues processed: 857 average time/residue: 1.8616 time to fit residues: 2057.4433 Evaluate side-chains 828 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 748 time to evaluate : 4.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain c residue 44 ARG Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain g residue 288 SER Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 14 VAL Chi-restraints excluded: chain j residue 25 GLN Chi-restraints excluded: chain j residue 36 ASN Chi-restraints excluded: chain k residue 49 LEU Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain k residue 147 ASP Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain k residue 242 LEU Chi-restraints excluded: chain z residue 158 VAL Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain z residue 366 ASP Chi-restraints excluded: chain z residue 545 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 358 optimal weight: 20.0000 chunk 200 optimal weight: 0.9980 chunk 536 optimal weight: 7.9990 chunk 439 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 645 optimal weight: 9.9990 chunk 697 optimal weight: 4.9990 chunk 575 optimal weight: 7.9990 chunk 640 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 518 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN B 186 ASN C 267 GLN D 74 GLN F 107 ASN L 121 GLN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN Q 86 GLN Q 97 GLN S 105 ASN T 137 GLN V 2 GLN V 35 ASN X 39 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN g 117 ASN k 415 GLN z 258 ASN z 309 GLN z 392 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 84638 Z= 0.206 Angle : 0.763 19.196 122113 Z= 0.397 Chirality : 0.040 0.372 14878 Planarity : 0.007 0.137 9400 Dihedral : 23.294 179.378 31893 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.68 % Allowed : 14.37 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.11), residues: 5506 helix: 0.03 (0.12), residues: 1801 sheet: -0.28 (0.16), residues: 982 loop : -0.90 (0.11), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP g 291 HIS 0.009 0.001 HIS S 135 PHE 0.022 0.002 PHE d 14 TYR 0.014 0.001 TYR L 99 ARG 0.013 0.000 ARG k 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 783 time to evaluate : 4.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 217 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8253 (tpp) REVERT: C 105 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7306 (tp30) REVERT: C 146 GLU cc_start: 0.7730 (mp0) cc_final: 0.7524 (mp0) REVERT: C 167 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8644 (mtp180) REVERT: D 117 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7011 (ttm-80) REVERT: D 156 LEU cc_start: 0.8176 (mt) cc_final: 0.7976 (tp) REVERT: H 91 HIS cc_start: 0.8542 (m90) cc_final: 0.8199 (m-70) REVERT: J 18 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7449 (mtp85) REVERT: J 101 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7439 (ptpp) REVERT: F 62 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7521 (mtt180) REVERT: M 52 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6728 (tt) REVERT: P 93 MET cc_start: 0.8133 (mmm) cc_final: 0.7864 (mmm) REVERT: P 141 PHE cc_start: 0.7983 (m-80) cc_final: 0.7641 (m-80) REVERT: R 80 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6606 (tmm-80) REVERT: Q 32 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8525 (mm) REVERT: Q 128 GLU cc_start: 0.8307 (tt0) cc_final: 0.7918 (tt0) REVERT: W 55 ASP cc_start: 0.8067 (p0) cc_final: 0.7811 (p0) REVERT: X 60 LYS cc_start: 0.7689 (mttp) cc_final: 0.7439 (mttt) REVERT: Y 48 TYR cc_start: 0.8358 (m-80) cc_final: 0.7911 (m-80) REVERT: j 61 ILE cc_start: 0.9047 (mt) cc_final: 0.8826 (mm) REVERT: k 205 LYS cc_start: 0.8307 (mtpp) cc_final: 0.8075 (mtpt) REVERT: z 231 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6157 (tpt170) REVERT: z 246 TRP cc_start: 0.8387 (m100) cc_final: 0.8058 (m100) REVERT: z 306 GLN cc_start: 0.8359 (tt0) cc_final: 0.8106 (tt0) REVERT: z 545 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7816 (pptt) outliers start: 126 outliers final: 54 residues processed: 851 average time/residue: 1.8695 time to fit residues: 2051.6404 Evaluate side-chains 802 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 736 time to evaluate : 4.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 101 LYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain R residue 80 ARG Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 57 LYS Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain g residue 107 ASP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 288 SER Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain k residue 49 LEU Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain z residue 158 VAL Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 321 VAL Chi-restraints excluded: chain z residue 366 ASP Chi-restraints excluded: chain z residue 424 VAL Chi-restraints excluded: chain z residue 545 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 638 optimal weight: 0.9990 chunk 485 optimal weight: 8.9990 chunk 335 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 308 optimal weight: 20.0000 chunk 433 optimal weight: 30.0000 chunk 648 optimal weight: 7.9990 chunk 686 optimal weight: 0.4980 chunk 338 optimal weight: 0.9980 chunk 614 optimal weight: 6.9990 chunk 184 optimal weight: 0.0670 overall best weight: 1.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN B 186 ASN D 74 GLN J 113 GLN L 121 GLN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN Q 97 GLN T 137 GLN W 44 HIS X 39 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 415 GLN ** z 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 309 GLN z 348 HIS z 392 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 84638 Z= 0.203 Angle : 0.748 19.055 122113 Z= 0.389 Chirality : 0.040 0.349 14878 Planarity : 0.007 0.137 9400 Dihedral : 23.190 179.637 31891 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.91 % Allowed : 15.47 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 5506 helix: 0.45 (0.12), residues: 1806 sheet: -0.08 (0.16), residues: 984 loop : -0.69 (0.11), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP g 291 HIS 0.008 0.001 HIS z 273 PHE 0.021 0.002 PHE d 14 TYR 0.013 0.001 TYR B 133 ARG 0.014 0.000 ARG k 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 774 time to evaluate : 4.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7911 (mt-10) REVERT: B 217 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8231 (tpp) REVERT: C 105 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7307 (tp30) REVERT: C 167 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8652 (mtp180) REVERT: C 248 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: E 242 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8230 (mptt) REVERT: D 117 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6994 (ttm-80) REVERT: H 91 HIS cc_start: 0.8564 (m90) cc_final: 0.8234 (m-70) REVERT: H 145 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7324 (ttm-80) REVERT: I 7 ASN cc_start: 0.7526 (p0) cc_final: 0.7312 (p0) REVERT: J 18 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7425 (mtp85) REVERT: J 101 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7395 (ptpp) REVERT: F 62 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7529 (mtt180) REVERT: F 88 MET cc_start: 0.8702 (ttp) cc_final: 0.7938 (ttp) REVERT: K 53 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8568 (tmmt) REVERT: O 67 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7789 (p0) REVERT: O 124 MET cc_start: 0.8213 (mmt) cc_final: 0.7629 (mmt) REVERT: O 151 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6741 (pt) REVERT: M 52 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6705 (tt) REVERT: P 141 PHE cc_start: 0.7959 (m-80) cc_final: 0.7683 (m-80) REVERT: Q 45 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6473 (mtp180) REVERT: Q 128 GLU cc_start: 0.8311 (tt0) cc_final: 0.7938 (tt0) REVERT: W 51 GLU cc_start: 0.8003 (tt0) cc_final: 0.7558 (tt0) REVERT: W 55 ASP cc_start: 0.8108 (p0) cc_final: 0.7825 (p0) REVERT: Y 48 TYR cc_start: 0.8385 (m-80) cc_final: 0.8030 (m-80) REVERT: g 142 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7537 (p) REVERT: j 36 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7804 (t0) REVERT: j 61 ILE cc_start: 0.9043 (mt) cc_final: 0.8825 (mm) REVERT: k 205 LYS cc_start: 0.8277 (mtpp) cc_final: 0.7946 (mtpt) REVERT: z 231 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.5991 (tpt170) REVERT: z 383 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7090 (mp0) outliers start: 137 outliers final: 74 residues processed: 855 average time/residue: 1.9135 time to fit residues: 2107.8418 Evaluate side-chains 838 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 745 time to evaluate : 4.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 101 LYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 107 LYS Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 57 LYS Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain g residue 107 ASP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 288 SER Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 14 VAL Chi-restraints excluded: chain j residue 36 ASN Chi-restraints excluded: chain k residue 49 LEU Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain k residue 147 ASP Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain z residue 158 VAL Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 251 MET Chi-restraints excluded: chain z residue 259 THR Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 366 ASP Chi-restraints excluded: chain z residue 383 GLU Chi-restraints excluded: chain z residue 391 THR Chi-restraints excluded: chain z residue 424 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 571 optimal weight: 6.9990 chunk 389 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 510 optimal weight: 2.9990 chunk 283 optimal weight: 0.9980 chunk 585 optimal weight: 3.9990 chunk 474 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 350 optimal weight: 9.9990 chunk 615 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN D 74 GLN F 186 ASN L 121 GLN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN Q 48 GLN Q 97 GLN T 137 GLN X 39 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 GLN ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN e 15 GLN g 104 HIS ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 415 GLN z 309 GLN z 348 HIS z 392 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 84638 Z= 0.201 Angle : 0.743 19.062 122113 Z= 0.387 Chirality : 0.039 0.349 14878 Planarity : 0.007 0.136 9400 Dihedral : 23.153 179.373 31891 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.06 % Allowed : 16.51 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.11), residues: 5506 helix: 0.68 (0.12), residues: 1797 sheet: -0.05 (0.16), residues: 995 loop : -0.56 (0.12), residues: 2714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP g 291 HIS 0.008 0.001 HIS z 273 PHE 0.020 0.001 PHE d 14 TYR 0.014 0.001 TYR I 113 ARG 0.016 0.000 ARG k 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 766 time to evaluate : 4.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 217 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8240 (tpp) REVERT: C 105 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7304 (tp30) REVERT: C 167 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8653 (mtp180) REVERT: C 248 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: h 85 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7118 (ptp90) REVERT: E 242 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8223 (mptt) REVERT: D 117 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7041 (ttm-80) REVERT: H 91 HIS cc_start: 0.8560 (m90) cc_final: 0.8244 (m-70) REVERT: H 145 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7310 (ttm-80) REVERT: I 7 ASN cc_start: 0.7510 (p0) cc_final: 0.7286 (p0) REVERT: J 18 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7423 (mtp85) REVERT: J 101 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7429 (ptpp) REVERT: F 62 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7606 (mtt180) REVERT: F 88 MET cc_start: 0.8727 (ttp) cc_final: 0.7976 (ttp) REVERT: O 67 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7813 (p0) REVERT: O 151 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6753 (pt) REVERT: M 52 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6764 (mt) REVERT: P 141 PHE cc_start: 0.7978 (m-80) cc_final: 0.7694 (m-80) REVERT: R 81 ARG cc_start: 0.6440 (tpp-160) cc_final: 0.6159 (tpp-160) REVERT: Q 45 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6433 (mtp180) REVERT: Q 128 GLU cc_start: 0.8309 (tt0) cc_final: 0.7939 (tt0) REVERT: W 55 ASP cc_start: 0.8117 (p0) cc_final: 0.7858 (p0) REVERT: Y 48 TYR cc_start: 0.8430 (m-80) cc_final: 0.8043 (m-80) REVERT: g 142 VAL cc_start: 0.7758 (OUTLIER) cc_final: 0.7554 (p) REVERT: j 36 ASN cc_start: 0.8143 (m110) cc_final: 0.7837 (t0) REVERT: j 61 ILE cc_start: 0.9060 (mt) cc_final: 0.8846 (mm) REVERT: k 140 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6348 (mtp85) REVERT: k 205 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7988 (mtpt) REVERT: z 231 ARG cc_start: 0.6635 (OUTLIER) cc_final: 0.6004 (tpt170) outliers start: 144 outliers final: 84 residues processed: 854 average time/residue: 1.8474 time to fit residues: 2038.1643 Evaluate side-chains 847 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 745 time to evaluate : 4.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 85 ARG Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 101 LYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain g residue 107 ASP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 288 SER Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 14 VAL Chi-restraints excluded: chain k residue 49 LEU Chi-restraints excluded: chain k residue 140 ARG Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain k residue 147 ASP Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain z residue 146 MET Chi-restraints excluded: chain z residue 158 VAL Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 251 MET Chi-restraints excluded: chain z residue 259 THR Chi-restraints excluded: chain z residue 321 VAL Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 347 GLU Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain z residue 366 ASP Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain z residue 424 VAL Chi-restraints excluded: chain z residue 540 GLU Chi-restraints excluded: chain z residue 545 LYS Chi-restraints excluded: chain z residue 550 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 230 optimal weight: 0.9980 chunk 618 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 402 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 686 optimal weight: 9.9990 chunk 570 optimal weight: 7.9990 chunk 318 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 227 optimal weight: 0.6980 chunk 360 optimal weight: 0.0170 overall best weight: 2.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 120 GLN F 186 ASN L 121 GLN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN Q 97 GLN T 137 GLN X 39 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 GLN ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN g 64 HIS g 104 HIS ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 415 GLN z 309 GLN z 348 HIS z 392 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 84638 Z= 0.249 Angle : 0.772 19.339 122113 Z= 0.399 Chirality : 0.041 0.343 14878 Planarity : 0.007 0.140 9400 Dihedral : 23.159 179.835 31891 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.44 % Allowed : 16.66 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 5506 helix: 0.71 (0.12), residues: 1799 sheet: -0.01 (0.16), residues: 982 loop : -0.53 (0.12), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP g 291 HIS 0.010 0.001 HIS z 273 PHE 0.026 0.002 PHE d 14 TYR 0.016 0.001 TYR K 57 ARG 0.017 0.000 ARG k 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 760 time to evaluate : 4.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7911 (mt-10) REVERT: B 217 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8231 (tpp) REVERT: C 105 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7311 (tp30) REVERT: C 167 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8671 (mtp180) REVERT: C 248 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: h 85 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7686 (ptp-170) REVERT: E 242 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8209 (mptt) REVERT: D 117 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7050 (ttm-80) REVERT: G 186 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: H 91 HIS cc_start: 0.8570 (m90) cc_final: 0.8263 (m-70) REVERT: H 145 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7345 (ttm-80) REVERT: J 18 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7432 (mtp85) REVERT: J 101 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7441 (ptpp) REVERT: F 62 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7584 (mtt180) REVERT: F 88 MET cc_start: 0.8774 (ttp) cc_final: 0.8055 (ttp) REVERT: K 53 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8569 (tmmt) REVERT: O 67 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7820 (p0) REVERT: O 104 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7365 (mtm180) REVERT: O 124 MET cc_start: 0.8291 (mmt) cc_final: 0.7639 (mmt) REVERT: O 151 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6733 (pt) REVERT: M 52 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6801 (mt) REVERT: P 141 PHE cc_start: 0.8017 (m-80) cc_final: 0.7790 (m-80) REVERT: Q 45 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6401 (mtp180) REVERT: Q 128 GLU cc_start: 0.8311 (tt0) cc_final: 0.7933 (tt0) REVERT: W 55 ASP cc_start: 0.8095 (p0) cc_final: 0.7843 (p0) REVERT: Y 48 TYR cc_start: 0.8462 (m-80) cc_final: 0.8093 (m-80) REVERT: j 36 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7914 (t0) REVERT: k 140 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6436 (mtp85) REVERT: k 205 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7973 (mtpt) REVERT: z 231 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6079 (tpt170) REVERT: z 269 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7326 (tmm) REVERT: z 306 GLN cc_start: 0.8349 (tt0) cc_final: 0.8130 (tt0) REVERT: z 383 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7111 (mp0) outliers start: 162 outliers final: 99 residues processed: 860 average time/residue: 1.8575 time to fit residues: 2063.6786 Evaluate side-chains 859 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 737 time to evaluate : 4.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 85 ARG Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 101 LYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 104 ARG Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain g residue 107 ASP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 288 SER Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain g residue 306 LEU Chi-restraints excluded: chain j residue 14 VAL Chi-restraints excluded: chain j residue 36 ASN Chi-restraints excluded: chain k residue 49 LEU Chi-restraints excluded: chain k residue 140 ARG Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain k residue 147 ASP Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain z residue 158 VAL Chi-restraints excluded: chain z residue 172 LYS Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 251 MET Chi-restraints excluded: chain z residue 259 THR Chi-restraints excluded: chain z residue 269 MET Chi-restraints excluded: chain z residue 321 VAL Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 347 GLU Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain z residue 366 ASP Chi-restraints excluded: chain z residue 383 GLU Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain z residue 424 VAL Chi-restraints excluded: chain z residue 540 GLU Chi-restraints excluded: chain z residue 545 LYS Chi-restraints excluded: chain z residue 550 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 662 optimal weight: 40.0000 chunk 77 optimal weight: 10.0000 chunk 391 optimal weight: 7.9990 chunk 501 optimal weight: 2.9990 chunk 388 optimal weight: 9.9990 chunk 578 optimal weight: 0.0070 chunk 383 optimal weight: 2.9990 chunk 684 optimal weight: 7.9990 chunk 428 optimal weight: 20.0000 chunk 417 optimal weight: 6.9990 chunk 315 optimal weight: 0.7980 overall best weight: 2.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 120 GLN D 74 GLN G 197 GLN F 186 ASN L 121 GLN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN Q 97 GLN T 137 GLN X 39 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 GLN ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 HIS ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 415 GLN z 348 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 84638 Z= 0.265 Angle : 0.780 19.373 122113 Z= 0.403 Chirality : 0.041 0.352 14878 Planarity : 0.007 0.141 9400 Dihedral : 23.152 179.912 31891 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.36 % Allowed : 17.26 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.11), residues: 5506 helix: 0.74 (0.12), residues: 1795 sheet: 0.00 (0.16), residues: 982 loop : -0.50 (0.12), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP g 291 HIS 0.010 0.001 HIS z 273 PHE 0.026 0.002 PHE d 14 TYR 0.023 0.001 TYR T 65 ARG 0.018 0.000 ARG k 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 750 time to evaluate : 4.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7921 (mt-10) REVERT: B 217 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8211 (tpp) REVERT: C 105 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: C 167 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8677 (mtp180) REVERT: C 248 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: h 85 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7674 (ptp-170) REVERT: E 242 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8221 (mptt) REVERT: D 117 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7044 (ttm-80) REVERT: G 186 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: H 91 HIS cc_start: 0.8563 (m90) cc_final: 0.8262 (m-70) REVERT: H 145 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7390 (ttm-80) REVERT: J 18 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7437 (mtp85) REVERT: J 101 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7435 (ptpp) REVERT: F 62 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7568 (mtt180) REVERT: F 88 MET cc_start: 0.8757 (ttp) cc_final: 0.8043 (ttp) REVERT: K 53 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8575 (tmmt) REVERT: O 67 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7816 (p0) REVERT: O 104 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7362 (mtm180) REVERT: O 124 MET cc_start: 0.8252 (mmt) cc_final: 0.7617 (mmt) REVERT: O 151 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6736 (pt) REVERT: M 52 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6713 (mt) REVERT: P 141 PHE cc_start: 0.8054 (m-80) cc_final: 0.7810 (m-80) REVERT: R 73 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5939 (tm) REVERT: R 80 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6630 (tmm-80) REVERT: Q 45 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.6543 (mtp180) REVERT: Q 128 GLU cc_start: 0.8308 (tt0) cc_final: 0.7951 (tt0) REVERT: W 55 ASP cc_start: 0.8085 (p0) cc_final: 0.7821 (p0) REVERT: Y 48 TYR cc_start: 0.8458 (m-80) cc_final: 0.8127 (m-80) REVERT: j 36 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7917 (t0) REVERT: k 140 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6437 (mtp85) REVERT: k 205 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7971 (mtpt) REVERT: k 236 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7142 (mtmp) REVERT: k 419 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5633 (tm-30) REVERT: z 231 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6039 (tpt170) REVERT: z 269 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7184 (tmm) outliers start: 158 outliers final: 103 residues processed: 843 average time/residue: 1.8763 time to fit residues: 2046.3840 Evaluate side-chains 862 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 733 time to evaluate : 4.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 85 ARG Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 101 LYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 104 ARG Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 80 ARG Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 288 SER Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain g residue 306 LEU Chi-restraints excluded: chain j residue 14 VAL Chi-restraints excluded: chain j residue 36 ASN Chi-restraints excluded: chain k residue 49 LEU Chi-restraints excluded: chain k residue 140 ARG Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain k residue 147 ASP Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain k residue 236 LYS Chi-restraints excluded: chain k residue 419 GLU Chi-restraints excluded: chain z residue 158 VAL Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 251 MET Chi-restraints excluded: chain z residue 259 THR Chi-restraints excluded: chain z residue 269 MET Chi-restraints excluded: chain z residue 321 VAL Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 347 GLU Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain z residue 366 ASP Chi-restraints excluded: chain z residue 391 THR Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain z residue 424 VAL Chi-restraints excluded: chain z residue 430 ILE Chi-restraints excluded: chain z residue 540 GLU Chi-restraints excluded: chain z residue 545 LYS Chi-restraints excluded: chain z residue 550 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 423 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 408 optimal weight: 0.9980 chunk 206 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 435 optimal weight: 4.9990 chunk 466 optimal weight: 3.9990 chunk 338 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 537 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 272 HIS D 74 GLN H 114 GLN H 126 HIS I 88 ASN F 83 ASN F 186 ASN L 121 GLN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN Q 48 GLN Q 97 GLN S 76 GLN T 137 GLN X 39 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 HIS ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 415 GLN z 348 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 84638 Z= 0.413 Angle : 0.883 20.240 122113 Z= 0.447 Chirality : 0.047 0.438 14878 Planarity : 0.008 0.149 9400 Dihedral : 23.271 179.834 31891 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.74 % Favored : 96.24 % Rotamer: Outliers : 3.44 % Allowed : 17.77 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.11), residues: 5506 helix: 0.55 (0.12), residues: 1800 sheet: -0.05 (0.16), residues: 970 loop : -0.57 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP g 291 HIS 0.011 0.002 HIS z 273 PHE 0.039 0.002 PHE d 14 TYR 0.022 0.002 TYR K 57 ARG 0.019 0.001 ARG k 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 739 time to evaluate : 4.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 GLU cc_start: 0.8219 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 217 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8189 (tpp) REVERT: C 105 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7299 (tp30) REVERT: C 167 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8650 (mtp180) REVERT: h 85 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7776 (ptp-170) REVERT: E 242 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8201 (mptt) REVERT: D 117 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6970 (ttm-80) REVERT: G 186 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: H 91 HIS cc_start: 0.8571 (m90) cc_final: 0.8264 (m-70) REVERT: J 18 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7409 (mtp85) REVERT: J 101 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7481 (ptpp) REVERT: F 62 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7588 (mtt180) REVERT: F 88 MET cc_start: 0.8762 (ttp) cc_final: 0.8042 (ttp) REVERT: K 46 MET cc_start: 0.8731 (mtp) cc_final: 0.8428 (mtp) REVERT: K 60 GLU cc_start: 0.7858 (tt0) cc_final: 0.7512 (tt0) REVERT: O 67 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7890 (p0) REVERT: O 98 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.7901 (tmt-80) REVERT: O 104 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7408 (mtm180) REVERT: O 124 MET cc_start: 0.8259 (mmt) cc_final: 0.7665 (mmt) REVERT: O 151 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6719 (pt) REVERT: M 52 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6695 (tt) REVERT: P 141 PHE cc_start: 0.8024 (m-80) cc_final: 0.7750 (m-80) REVERT: R 73 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.6000 (tm) REVERT: R 80 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6664 (tmm-80) REVERT: Q 45 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6581 (mtp180) REVERT: Q 128 GLU cc_start: 0.8338 (tt0) cc_final: 0.7972 (tt0) REVERT: W 55 ASP cc_start: 0.8173 (p0) cc_final: 0.7909 (p0) REVERT: Y 48 TYR cc_start: 0.8516 (m-80) cc_final: 0.8206 (m-80) REVERT: Y 74 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7128 (mmm) REVERT: j 36 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8034 (t0) REVERT: k 205 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8056 (mtpt) REVERT: k 236 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7126 (mttp) REVERT: z 138 LYS cc_start: 0.7534 (mmtt) cc_final: 0.7324 (mmtt) REVERT: z 231 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.6139 (tpt170) REVERT: z 269 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7297 (tmm) REVERT: z 383 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7108 (mp0) outliers start: 162 outliers final: 100 residues processed: 837 average time/residue: 1.8525 time to fit residues: 2003.8784 Evaluate side-chains 845 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 721 time to evaluate : 4.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 85 ARG Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 101 LYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 104 ARG Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 80 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 288 SER Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain g residue 306 LEU Chi-restraints excluded: chain j residue 14 VAL Chi-restraints excluded: chain j residue 36 ASN Chi-restraints excluded: chain k residue 49 LEU Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain k residue 147 ASP Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain k residue 236 LYS Chi-restraints excluded: chain z residue 158 VAL Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 251 MET Chi-restraints excluded: chain z residue 259 THR Chi-restraints excluded: chain z residue 269 MET Chi-restraints excluded: chain z residue 321 VAL Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 347 GLU Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain z residue 366 ASP Chi-restraints excluded: chain z residue 383 GLU Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain z residue 424 VAL Chi-restraints excluded: chain z residue 430 ILE Chi-restraints excluded: chain z residue 540 GLU Chi-restraints excluded: chain z residue 545 LYS Chi-restraints excluded: chain z residue 550 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 622 optimal weight: 4.9990 chunk 655 optimal weight: 10.0000 chunk 598 optimal weight: 7.9990 chunk 637 optimal weight: 5.9990 chunk 383 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 chunk 500 optimal weight: 10.0000 chunk 195 optimal weight: 0.5980 chunk 576 optimal weight: 4.9990 chunk 603 optimal weight: 9.9990 chunk 635 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 114 GLN F 83 ASN F 186 ASN L 121 GLN Q 48 GLN Q 97 GLN S 76 GLN T 137 GLN X 39 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 HIS ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 415 GLN z 348 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 84638 Z= 0.265 Angle : 0.790 19.365 122113 Z= 0.408 Chirality : 0.042 0.360 14878 Planarity : 0.007 0.141 9400 Dihedral : 23.187 179.835 31891 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.17 % Allowed : 18.32 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.11), residues: 5506 helix: 0.73 (0.12), residues: 1791 sheet: -0.04 (0.16), residues: 982 loop : -0.50 (0.12), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP g 291 HIS 0.009 0.001 HIS z 273 PHE 0.025 0.002 PHE d 14 TYR 0.021 0.001 TYR T 65 ARG 0.020 0.000 ARG k 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 729 time to evaluate : 4.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6762 (tt0) REVERT: B 122 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7910 (mt-10) REVERT: B 217 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8148 (tpp) REVERT: C 105 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7308 (tp30) REVERT: C 167 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8670 (mtp180) REVERT: C 248 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: h 85 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7681 (ptp-170) REVERT: E 242 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8231 (mptt) REVERT: D 117 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6983 (ttm-80) REVERT: G 186 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: H 91 HIS cc_start: 0.8559 (m90) cc_final: 0.8257 (m-70) REVERT: J 18 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7419 (mtp85) REVERT: J 101 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7449 (ptpp) REVERT: F 62 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7546 (mtt180) REVERT: F 88 MET cc_start: 0.8730 (ttp) cc_final: 0.7995 (ttp) REVERT: O 67 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7834 (p0) REVERT: O 104 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7355 (mtm180) REVERT: O 124 MET cc_start: 0.8198 (mmt) cc_final: 0.7594 (mmt) REVERT: O 151 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6726 (pt) REVERT: M 52 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6731 (mt) REVERT: P 141 PHE cc_start: 0.8071 (m-80) cc_final: 0.7790 (m-80) REVERT: R 73 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5843 (tm) REVERT: Q 32 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8382 (mm) REVERT: Q 45 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6572 (mtp180) REVERT: Q 128 GLU cc_start: 0.8301 (tt0) cc_final: 0.7933 (tt0) REVERT: W 55 ASP cc_start: 0.8075 (p0) cc_final: 0.7802 (p0) REVERT: Y 48 TYR cc_start: 0.8485 (m-80) cc_final: 0.8179 (m-80) REVERT: Y 74 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7170 (mmm) REVERT: j 36 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7956 (t0) REVERT: k 205 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7970 (mtpt) REVERT: k 236 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7101 (mttp) REVERT: k 419 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5650 (tm-30) REVERT: z 231 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6131 (tpt170) REVERT: z 269 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7264 (tmm) REVERT: z 383 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7111 (mp0) outliers start: 149 outliers final: 101 residues processed: 822 average time/residue: 1.8740 time to fit residues: 1996.7258 Evaluate side-chains 850 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 723 time to evaluate : 4.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 85 ARG Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 101 LYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 104 ARG Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 288 SER Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 14 VAL Chi-restraints excluded: chain j residue 36 ASN Chi-restraints excluded: chain k residue 49 LEU Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain k residue 147 ASP Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain k residue 236 LYS Chi-restraints excluded: chain k residue 419 GLU Chi-restraints excluded: chain z residue 158 VAL Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 251 MET Chi-restraints excluded: chain z residue 259 THR Chi-restraints excluded: chain z residue 269 MET Chi-restraints excluded: chain z residue 321 VAL Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 347 GLU Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain z residue 366 ASP Chi-restraints excluded: chain z residue 383 GLU Chi-restraints excluded: chain z residue 391 THR Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain z residue 424 VAL Chi-restraints excluded: chain z residue 430 ILE Chi-restraints excluded: chain z residue 540 GLU Chi-restraints excluded: chain z residue 545 LYS Chi-restraints excluded: chain z residue 550 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 418 optimal weight: 0.8980 chunk 674 optimal weight: 40.0000 chunk 411 optimal weight: 1.9990 chunk 319 optimal weight: 4.9990 chunk 468 optimal weight: 4.9990 chunk 707 optimal weight: 20.0000 chunk 651 optimal weight: 3.9990 chunk 563 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 435 optimal weight: 4.9990 chunk 345 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 186 ASN L 121 GLN P 32 GLN Q 48 GLN Q 97 GLN S 76 GLN S 105 ASN T 137 GLN X 39 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 415 GLN z 348 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 84638 Z= 0.316 Angle : 0.822 19.605 122113 Z= 0.421 Chirality : 0.043 0.381 14878 Planarity : 0.007 0.145 9400 Dihedral : 23.192 179.646 31891 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.91 % Allowed : 18.68 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 5506 helix: 0.68 (0.12), residues: 1795 sheet: -0.02 (0.16), residues: 972 loop : -0.50 (0.12), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP g 291 HIS 0.010 0.001 HIS z 273 PHE 0.030 0.002 PHE d 14 TYR 0.023 0.002 TYR T 65 ARG 0.020 0.001 ARG k 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 718 time to evaluate : 5.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6760 (tt0) REVERT: B 122 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7912 (mt-10) REVERT: B 217 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8164 (tpp) REVERT: C 105 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7299 (tp30) REVERT: C 167 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8665 (mtp180) REVERT: C 248 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: h 85 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7666 (ptp-170) REVERT: E 242 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8260 (mptt) REVERT: D 117 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6964 (ttm-80) REVERT: G 186 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: H 91 HIS cc_start: 0.8567 (m90) cc_final: 0.8265 (m-70) REVERT: J 18 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7436 (mtp85) REVERT: J 101 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7452 (ptpp) REVERT: F 62 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7558 (mtt180) REVERT: F 88 MET cc_start: 0.8743 (ttp) cc_final: 0.8015 (ttp) REVERT: O 67 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7810 (p0) REVERT: O 104 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7368 (mtm180) REVERT: O 124 MET cc_start: 0.8197 (mmt) cc_final: 0.7605 (mmt) REVERT: O 151 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6718 (pt) REVERT: M 52 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6671 (tt) REVERT: P 141 PHE cc_start: 0.8064 (m-80) cc_final: 0.7801 (m-80) REVERT: Q 32 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8398 (mm) REVERT: Q 45 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.6593 (mtp180) REVERT: Q 128 GLU cc_start: 0.8311 (tt0) cc_final: 0.7946 (tt0) REVERT: W 55 ASP cc_start: 0.8122 (p0) cc_final: 0.7857 (p0) REVERT: Y 48 TYR cc_start: 0.8492 (m-80) cc_final: 0.8186 (m-80) REVERT: Y 74 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7173 (mmm) REVERT: j 36 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.8002 (t0) REVERT: k 205 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7999 (mtpt) REVERT: k 236 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7075 (mttp) REVERT: k 419 GLU cc_start: 0.6006 (OUTLIER) cc_final: 0.5688 (tm-30) REVERT: z 231 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6235 (tpt170) REVERT: z 269 MET cc_start: 0.7729 (ttm) cc_final: 0.7297 (tmm) REVERT: z 383 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7100 (mp0) outliers start: 137 outliers final: 102 residues processed: 809 average time/residue: 1.9201 time to fit residues: 2021.9997 Evaluate side-chains 833 residues out of total 4870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 707 time to evaluate : 4.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 85 ARG Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 101 LYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 104 ARG Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 288 SER Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 14 VAL Chi-restraints excluded: chain j residue 36 ASN Chi-restraints excluded: chain k residue 49 LEU Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain k residue 147 ASP Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain k residue 236 LYS Chi-restraints excluded: chain k residue 419 GLU Chi-restraints excluded: chain z residue 158 VAL Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 251 MET Chi-restraints excluded: chain z residue 259 THR Chi-restraints excluded: chain z residue 321 VAL Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 347 GLU Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain z residue 366 ASP Chi-restraints excluded: chain z residue 383 GLU Chi-restraints excluded: chain z residue 391 THR Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain z residue 424 VAL Chi-restraints excluded: chain z residue 430 ILE Chi-restraints excluded: chain z residue 540 GLU Chi-restraints excluded: chain z residue 545 LYS Chi-restraints excluded: chain z residue 550 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 447 optimal weight: 4.9990 chunk 600 optimal weight: 0.0570 chunk 172 optimal weight: 0.9980 chunk 519 optimal weight: 0.0270 chunk 83 optimal weight: 5.9990 chunk 156 optimal weight: 30.0000 chunk 564 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 579 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 186 ASN F 203 ASN L 121 GLN P 32 GLN Q 48 GLN Q 97 GLN S 76 GLN S 105 ASN T 137 GLN X 39 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 25 GLN k 415 GLN z 348 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.165205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.142524 restraints weight = 77067.512| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 0.50 r_work: 0.3333 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 84638 Z= 0.171 Angle : 0.740 18.831 122113 Z= 0.386 Chirality : 0.038 0.351 14878 Planarity : 0.006 0.135 9400 Dihedral : 23.084 179.651 31891 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.49 % Allowed : 19.21 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.11), residues: 5506 helix: 0.92 (0.12), residues: 1801 sheet: 0.04 (0.16), residues: 982 loop : -0.41 (0.12), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP g 291 HIS 0.007 0.001 HIS z 273 PHE 0.017 0.001 PHE P 141 TYR 0.022 0.001 TYR T 65 ARG 0.021 0.000 ARG k 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27816.96 seconds wall clock time: 484 minutes 19.17 seconds (29059.17 seconds total)