Starting phenix.real_space_refine on Sat Feb 17 13:33:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csp_26966/02_2024/8csp_26966_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csp_26966/02_2024/8csp_26966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csp_26966/02_2024/8csp_26966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csp_26966/02_2024/8csp_26966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csp_26966/02_2024/8csp_26966_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csp_26966/02_2024/8csp_26966_neut_updated.pdb" } resolution = 2.66 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= 0.045 sd= 1.467 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 4 8.98 5 Fe 8 7.16 5 Zn 1 6.06 5 P 742 5.49 5 Mg 28 5.21 5 S 265 5.16 5 C 41157 2.51 5 N 12380 2.21 5 O 14717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 13": "OE1" <-> "OE2" Residue "0 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 127": "OE1" <-> "OE2" Residue "0 TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 132": "OE1" <-> "OE2" Residue "1 ASP 138": "OD1" <-> "OD2" Residue "1 GLU 144": "OE1" <-> "OE2" Residue "1 GLU 150": "OE1" <-> "OE2" Residue "1 ASP 155": "OD1" <-> "OD2" Residue "1 GLU 291": "OE1" <-> "OE2" Residue "4 ASP 66": "OD1" <-> "OD2" Residue "4 ASP 92": "OD1" <-> "OD2" Residue "4 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 200": "OD1" <-> "OD2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 310": "OE1" <-> "OE2" Residue "4 GLU 399": "OE1" <-> "OE2" Residue "4 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 443": "OD1" <-> "OD2" Residue "4 ASP 451": "OD1" <-> "OD2" Residue "4 ASP 480": "OD1" <-> "OD2" Residue "5 GLU 275": "OE1" <-> "OE2" Residue "7 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 213": "OE1" <-> "OE2" Residue "7 GLU 228": "OE1" <-> "OE2" Residue "7 TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 318": "OE1" <-> "OE2" Residue "7 GLU 366": "OE1" <-> "OE2" Residue "8 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 234": "OD1" <-> "OD2" Residue "8 GLU 275": "OE1" <-> "OE2" Residue "8 PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 222": "OD1" <-> "OD2" Residue "9 ASP 256": "OD1" <-> "OD2" Residue "9 GLU 266": "OE1" <-> "OE2" Residue "9 GLU 326": "OE1" <-> "OE2" Residue "9 ASP 373": "OD1" <-> "OD2" Residue "9 GLU 512": "OE1" <-> "OE2" Residue "9 GLU 595": "OE1" <-> "OE2" Residue "9 ASP 607": "OD1" <-> "OD2" Residue "9 ASP 639": "OD1" <-> "OD2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 138": "OE1" <-> "OE2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F ASP 225": "OD1" <-> "OD2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 263": "OD1" <-> "OD2" Residue "G GLU 264": "OE1" <-> "OE2" Residue "G TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 321": "OD1" <-> "OD2" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 171": "OE1" <-> "OE2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 116": "OD1" <-> "OD2" Residue "L ASP 65": "OD1" <-> "OD2" Residue "L ASP 75": "OD1" <-> "OD2" Residue "L ASP 86": "OD1" <-> "OD2" Residue "L GLU 140": "OE1" <-> "OE2" Residue "L ASP 161": "OD1" <-> "OD2" Residue "M PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 80": "OE1" <-> "OE2" Residue "N ASP 93": "OD1" <-> "OD2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 53": "OD1" <-> "OD2" Residue "O GLU 63": "OE1" <-> "OE2" Residue "O TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 76": "OD1" <-> "OD2" Residue "O PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 210": "OE1" <-> "OE2" Residue "P ASP 73": "OD1" <-> "OD2" Residue "R TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 113": "OE1" <-> "OE2" Residue "R ASP 226": "OD1" <-> "OD2" Residue "R ASP 282": "OD1" <-> "OD2" Residue "R ASP 292": "OD1" <-> "OD2" Residue "S GLU 43": "OE1" <-> "OE2" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 86": "OD1" <-> "OD2" Residue "S GLU 114": "OE1" <-> "OE2" Residue "T TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 100": "OE1" <-> "OE2" Residue "T GLU 115": "OE1" <-> "OE2" Residue "T GLU 119": "OE1" <-> "OE2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 98": "OD1" <-> "OD2" Residue "U GLU 104": "OE1" <-> "OE2" Residue "U GLU 132": "OE1" <-> "OE2" Residue "U GLU 156": "OE1" <-> "OE2" Residue "U GLU 162": "OE1" <-> "OE2" Residue "U ASP 182": "OD1" <-> "OD2" Residue "U TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "V PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 171": "OE1" <-> "OE2" Residue "V PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 281": "OD1" <-> "OD2" Residue "V GLU 323": "OE1" <-> "OE2" Residue "V GLU 348": "OE1" <-> "OE2" Residue "W PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 111": "OD1" <-> "OD2" Residue "W TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 159": "OD1" <-> "OD2" Residue "X ASP 61": "OD1" <-> "OD2" Residue "X PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 263": "OD1" <-> "OD2" Residue "X TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 260": "OD1" <-> "OD2" Residue "Y ASP 279": "OD1" <-> "OD2" Residue "Y ASP 322": "OD1" <-> "OD2" Residue "Y PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 69302 Number of models: 1 Model: "" Number of chains: 40 Chain: "0" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1754 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "1" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2195 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "4" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4585 Classifications: {'peptide': 566} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 539} Chain breaks: 3 Chain: "5" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2568 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 23, 'TRANS': 295} Chain: "7" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3145 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 366} Chain breaks: 1 Chain: "8" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2543 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 18, 'TRANS': 307} Chain: "9" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3558 Classifications: {'peptide': 446} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 411} Chain breaks: 3 Chain: "A" Number of atoms: 15655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 15655 Classifications: {'RNA': 737} Modifications used: {'rna2p_pur': 66, 'rna2p_pyr': 55, 'rna3p_pur': 319, 'rna3p_pyr': 297} Link IDs: {'rna2p': 120, 'rna3p': 616} Chain breaks: 10 Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1789 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 10, 'TRANS': 209} Chain: "C" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1042 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 1 Chain: "D" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1838 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 839 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1724 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Chain: "G" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2395 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain breaks: 1 Chain: "H" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1045 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain breaks: 1 Chain: "J" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 839 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 97} Chain: "K" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 283 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain breaks: 2 Chain: "L" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1091 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "M" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 913 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1570 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 21, 'TRANS': 168} Chain: "P" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 731 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 7, 'TRANS': 84} Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 49 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "R" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2382 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain: "S" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1100 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "T" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1344 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain: "U" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1468 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain: "V" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2946 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 9, 'TRANS': 349} Chain breaks: 1 Chain: "W" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "X" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2849 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 332} Chain: "Y" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1043 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "Z" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain breaks: 1 Chain: "a" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1785 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "7" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'SF4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Unusual residues: {' K': 4, ' MG': 26} Classifications: {'undetermined': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13955 SG CYS 7 404 103.800 107.113 162.091 1.00 19.15 S ATOM 13476 SG CYS 7 347 107.604 102.804 158.325 1.00 21.64 S ATOM 13371 SG CYS 7 333 101.532 105.232 156.913 1.00 21.41 S ATOM 13418 SG CYS 7 339 106.934 108.394 156.771 1.00 17.22 S ATOM 41502 SG CYS E 105 121.431 74.068 47.737 1.00 62.84 S ATOM 52658 SG CYS P 100 120.981 71.746 51.293 1.00 45.38 S ATOM 52407 SG CYS P 68 125.132 70.663 46.031 1.00 49.31 S ATOM 51067 SG CYS O 94 111.543 159.763 99.764 1.00 33.91 S ATOM 51153 SG CYS O 105 114.435 160.302 97.614 1.00 31.13 S ATOM 51174 SG CYS O 108 113.443 163.172 99.444 1.00 33.64 S ATOM 51462 SG CYS O 143 110.983 161.803 96.642 1.00 27.23 S ATOM 49012 SG CYS M 26 90.632 170.806 77.118 1.00 30.16 S ATOM 57710 SG CYS T 149 94.046 170.946 78.053 1.00 30.67 S ATOM 57638 SG CYS T 139 93.456 172.025 71.615 1.00 29.36 S ATOM 57652 SG CYS T 141 96.186 171.853 74.307 1.00 28.65 S Time building chain proxies: 28.63, per 1000 atoms: 0.41 Number of scatterers: 69302 At special positions: 0 Unit cell: (223.02, 244.26, 221.958, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 8 26.01 K 4 19.00 S 265 16.00 P 742 15.00 Mg 28 11.99 O 14717 8.00 N 12380 7.00 C 41157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.25 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS P 68 " pdb="FE1 FES E 201 " - pdb=" SG CYS P 100 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 105 " pdb=" FES T 201 " pdb="FE1 FES T 201 " - pdb=" SG CYS M 26 " pdb="FE1 FES T 201 " - pdb=" SG CYS T 149 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 141 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 139 " pdb=" SF4 7 501 " pdb="FE3 SF4 7 501 " - pdb=" SG CYS 7 333 " pdb="FE4 SF4 7 501 " - pdb=" SG CYS 7 339 " pdb="FE2 SF4 7 501 " - pdb=" SG CYS 7 347 " pdb="FE1 SF4 7 501 " - pdb=" SG CYS 7 404 " Number of angles added : 23 Zn2+ tetrahedral coordination pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 105 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 108 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 143 " Number of angles added : 6 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 284 helices and 41 sheets defined 44.6% alpha, 10.3% beta 211 base pairs and 363 stacking pairs defined. Time for finding SS restraints: 23.67 Creating SS restraints... Processing helix chain '0' and resid 10 through 25 Processing helix chain '0' and resid 30 through 33 No H-bonds generated for 'chain '0' and resid 30 through 33' Processing helix chain '0' and resid 52 through 59 removed outlier: 4.604A pdb=" N ALA 0 56 " --> pdb=" O VAL 0 52 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASP 0 57 " --> pdb=" O ARG 0 53 " (cutoff:3.500A) Processing helix chain '0' and resid 64 through 70 removed outlier: 4.809A pdb=" N ARG 0 70 " --> pdb=" O GLN 0 66 " (cutoff:3.500A) Processing helix chain '0' and resid 72 through 75 Processing helix chain '0' and resid 83 through 88 Processing helix chain '0' and resid 147 through 151 Processing helix chain '0' and resid 168 through 180 Processing helix chain '1' and resid 56 through 59 Processing helix chain '1' and resid 66 through 69 No H-bonds generated for 'chain '1' and resid 66 through 69' Processing helix chain '1' and resid 103 through 107 Processing helix chain '1' and resid 116 through 129 removed outlier: 3.558A pdb=" N ALA 1 125 " --> pdb=" O LYS 1 121 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS 1 127 " --> pdb=" O CYS 1 123 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASP 1 128 " --> pdb=" O GLU 1 124 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE 1 129 " --> pdb=" O ALA 1 125 " (cutoff:3.500A) Processing helix chain '1' and resid 140 through 146 removed outlier: 3.773A pdb=" N LYS 1 145 " --> pdb=" O GLU 1 141 " (cutoff:3.500A) Processing helix chain '1' and resid 166 through 169 removed outlier: 3.791A pdb=" N ARG 1 169 " --> pdb=" O PRO 1 166 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 166 through 169' Processing helix chain '1' and resid 177 through 179 No H-bonds generated for 'chain '1' and resid 177 through 179' Processing helix chain '1' and resid 184 through 197 removed outlier: 6.716A pdb=" N GLU 1 196 " --> pdb=" O LYS 1 192 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG 1 197 " --> pdb=" O LEU 1 193 " (cutoff:3.500A) Processing helix chain '1' and resid 215 through 234 Processing helix chain '1' and resid 240 through 242 No H-bonds generated for 'chain '1' and resid 240 through 242' Processing helix chain '1' and resid 257 through 273 Processing helix chain '1' and resid 287 through 301 Processing helix chain '1' and resid 306 through 320 Processing helix chain '4' and resid 69 through 77 Processing helix chain '4' and resid 100 through 123 Processing helix chain '4' and resid 125 through 127 No H-bonds generated for 'chain '4' and resid 125 through 127' Processing helix chain '4' and resid 138 through 140 No H-bonds generated for 'chain '4' and resid 138 through 140' Processing helix chain '4' and resid 154 through 162 Processing helix chain '4' and resid 166 through 178 Processing helix chain '4' and resid 185 through 198 Processing helix chain '4' and resid 243 through 250 Processing helix chain '4' and resid 256 through 268 Processing helix chain '4' and resid 272 through 284 Processing helix chain '4' and resid 291 through 303 Processing helix chain '4' and resid 309 through 325 Processing helix chain '4' and resid 332 through 363 removed outlier: 4.230A pdb=" N ARG 4 344 " --> pdb=" O LYS 4 340 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE 4 345 " --> pdb=" O CYS 4 341 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS 4 346 " --> pdb=" O LEU 4 342 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL 4 347 " --> pdb=" O ARG 4 343 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE 4 348 " --> pdb=" O ARG 4 344 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA 4 349 " --> pdb=" O PHE 4 345 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG 4 350 " --> pdb=" O HIS 4 346 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N SER 4 351 " --> pdb=" O VAL 4 347 " (cutoff:3.500A) Proline residue: 4 352 - end of helix Processing helix chain '4' and resid 369 through 379 Processing helix chain '4' and resid 392 through 400 Processing helix chain '4' and resid 412 through 426 removed outlier: 4.583A pdb=" N PHE 4 416 " --> pdb=" O ASP 4 413 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN 4 417 " --> pdb=" O LYS 4 414 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU 4 426 " --> pdb=" O CYS 4 423 " (cutoff:3.500A) Processing helix chain '4' and resid 429 through 439 Processing helix chain '4' and resid 444 through 448 Processing helix chain '4' and resid 451 through 468 Processing helix chain '4' and resid 471 through 481 Processing helix chain '4' and resid 490 through 503 Processing helix chain '4' and resid 506 through 518 Proline residue: 4 510 - end of helix Processing helix chain '4' and resid 525 through 536 Processing helix chain '4' and resid 542 through 560 Processing helix chain '4' and resid 573 through 585 Processing helix chain '4' and resid 589 through 602 removed outlier: 3.688A pdb=" N GLY 4 597 " --> pdb=" O TRP 4 593 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU 4 598 " --> pdb=" O LYS 4 594 " (cutoff:3.500A) Processing helix chain '4' and resid 608 through 621 Processing helix chain '4' and resid 624 through 637 Processing helix chain '4' and resid 642 through 652 Processing helix chain '4' and resid 657 through 666 Processing helix chain '5' and resid 18 through 25 Processing helix chain '5' and resid 41 through 50 Processing helix chain '5' and resid 68 through 75 Processing helix chain '5' and resid 91 through 100 Processing helix chain '5' and resid 117 through 119 No H-bonds generated for 'chain '5' and resid 117 through 119' Processing helix chain '5' and resid 123 through 125 No H-bonds generated for 'chain '5' and resid 123 through 125' Processing helix chain '5' and resid 144 through 160 removed outlier: 3.955A pdb=" N THR 5 148 " --> pdb=" O PHE 5 144 " (cutoff:3.500A) Proline residue: 5 149 - end of helix Processing helix chain '5' and resid 163 through 166 Processing helix chain '5' and resid 178 through 184 Processing helix chain '5' and resid 195 through 201 Processing helix chain '5' and resid 214 through 216 No H-bonds generated for 'chain '5' and resid 214 through 216' Processing helix chain '5' and resid 242 through 253 Processing helix chain '5' and resid 260 through 267 removed outlier: 4.795A pdb=" N MET 5 266 " --> pdb=" O ARG 5 262 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU 5 267 " --> pdb=" O GLY 5 263 " (cutoff:3.500A) Processing helix chain '5' and resid 270 through 283 removed outlier: 5.447A pdb=" N LEU 5 274 " --> pdb=" O ALA 5 271 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU 5 275 " --> pdb=" O GLN 5 272 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER 5 276 " --> pdb=" O ARG 5 273 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR 5 277 " --> pdb=" O LEU 5 274 " (cutoff:3.500A) Processing helix chain '5' and resid 292 through 294 No H-bonds generated for 'chain '5' and resid 292 through 294' Processing helix chain '5' and resid 297 through 312 Processing helix chain '5' and resid 315 through 319 removed outlier: 3.997A pdb=" N PHE 5 318 " --> pdb=" O PRO 5 315 " (cutoff:3.500A) Processing helix chain '5' and resid 322 through 326 Processing helix chain '7' and resid 43 through 46 No H-bonds generated for 'chain '7' and resid 43 through 46' Processing helix chain '7' and resid 49 through 51 No H-bonds generated for 'chain '7' and resid 49 through 51' Processing helix chain '7' and resid 65 through 75 Processing helix chain '7' and resid 81 through 96 Processing helix chain '7' and resid 103 through 115 Processing helix chain '7' and resid 134 through 141 Processing helix chain '7' and resid 152 through 180 removed outlier: 6.219A pdb=" N ASP 7 164 " --> pdb=" O ALA 7 160 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLY 7 165 " --> pdb=" O ALA 7 161 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE 7 177 " --> pdb=" O ALA 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 198 through 207 Processing helix chain '7' and resid 221 through 231 Processing helix chain '7' and resid 268 through 270 No H-bonds generated for 'chain '7' and resid 268 through 270' Processing helix chain '7' and resid 274 through 287 Processing helix chain '7' and resid 300 through 314 Processing helix chain '7' and resid 417 through 420 No H-bonds generated for 'chain '7' and resid 417 through 420' Processing helix chain '7' and resid 422 through 430 Processing helix chain '8' and resid 87 through 98 Processing helix chain '8' and resid 102 through 107 Processing helix chain '8' and resid 117 through 138 removed outlier: 3.850A pdb=" N GLN 8 121 " --> pdb=" O THR 8 117 " (cutoff:3.500A) Proline residue: 8 122 - end of helix Processing helix chain '8' and resid 140 through 144 Processing helix chain '8' and resid 155 through 162 Processing helix chain '8' and resid 168 through 188 Processing helix chain '8' and resid 204 through 218 removed outlier: 3.972A pdb=" N CYS 8 215 " --> pdb=" O ALA 8 211 " (cutoff:3.500A) Processing helix chain '8' and resid 242 through 250 Processing helix chain '8' and resid 252 through 255 No H-bonds generated for 'chain '8' and resid 252 through 255' Processing helix chain '8' and resid 272 through 287 Proline residue: 8 276 - end of helix removed outlier: 3.945A pdb=" N GLU 8 279 " --> pdb=" O PRO 8 276 " (cutoff:3.500A) Proline residue: 8 280 - end of helix removed outlier: 4.190A pdb=" N ALA 8 287 " --> pdb=" O ALA 8 284 " (cutoff:3.500A) Processing helix chain '8' and resid 309 through 321 removed outlier: 3.616A pdb=" N ILE 8 312 " --> pdb=" O PRO 8 309 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N HIS 8 313 " --> pdb=" O GLY 8 310 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU 8 316 " --> pdb=" O HIS 8 313 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN 8 319 " --> pdb=" O LEU 8 316 " (cutoff:3.500A) Processing helix chain '8' and resid 326 through 334 Processing helix chain '8' and resid 353 through 361 Processing helix chain '8' and resid 363 through 368 removed outlier: 4.267A pdb=" N SER 8 368 " --> pdb=" O GLN 8 364 " (cutoff:3.500A) Processing helix chain '9' and resid 75 through 77 No H-bonds generated for 'chain '9' and resid 75 through 77' Processing helix chain '9' and resid 87 through 114 Processing helix chain '9' and resid 180 through 192 Processing helix chain '9' and resid 198 through 204 Processing helix chain '9' and resid 206 through 210 Processing helix chain '9' and resid 231 through 237 Proline residue: 9 235 - end of helix Processing helix chain '9' and resid 260 through 274 Processing helix chain '9' and resid 324 through 331 Processing helix chain '9' and resid 347 through 349 No H-bonds generated for 'chain '9' and resid 347 through 349' Processing helix chain '9' and resid 351 through 359 Processing helix chain '9' and resid 371 through 374 No H-bonds generated for 'chain '9' and resid 371 through 374' Processing helix chain '9' and resid 396 through 400 removed outlier: 4.073A pdb=" N MET 9 400 " --> pdb=" O PRO 9 397 " (cutoff:3.500A) Processing helix chain '9' and resid 506 through 509 No H-bonds generated for 'chain '9' and resid 506 through 509' Processing helix chain '9' and resid 512 through 518 Processing helix chain '9' and resid 571 through 581 removed outlier: 4.425A pdb=" N ASP 9 575 " --> pdb=" O LEU 9 571 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA 9 576 " --> pdb=" O ASP 9 572 " (cutoff:3.500A) Processing helix chain '9' and resid 593 through 599 removed outlier: 3.564A pdb=" N MET 9 597 " --> pdb=" O GLY 9 593 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY 9 599 " --> pdb=" O GLU 9 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 65 through 68 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 100 through 105 Proline residue: B 104 - end of helix Processing helix chain 'B' and resid 118 through 137 removed outlier: 3.588A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 161 removed outlier: 5.419A pdb=" N TYR B 153 " --> pdb=" O GLN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 182 No H-bonds generated for 'chain 'B' and resid 179 through 182' Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 243 through 273 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 53 through 56 No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 129 through 147 Processing helix chain 'D' and resid 264 through 277 removed outlier: 3.823A pdb=" N HIS D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 318 through 327 Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 408 through 415 Processing helix chain 'E' and resid 15 through 31 Processing helix chain 'E' and resid 72 through 84 removed outlier: 4.027A pdb=" N GLU E 76 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 60 through 71 removed outlier: 3.541A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'F' and resid 104 through 127 Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 176 through 191 Processing helix chain 'F' and resid 201 through 214 removed outlier: 3.622A pdb=" N HIS F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 231 Processing helix chain 'G' and resid 71 through 92 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 101 through 111 Processing helix chain 'G' and resid 119 through 121 No H-bonds generated for 'chain 'G' and resid 119 through 121' Processing helix chain 'G' and resid 128 through 131 No H-bonds generated for 'chain 'G' and resid 128 through 131' Processing helix chain 'G' and resid 151 through 153 No H-bonds generated for 'chain 'G' and resid 151 through 153' Processing helix chain 'G' and resid 156 through 174 Processing helix chain 'G' and resid 202 through 209 Processing helix chain 'G' and resid 215 through 230 Processing helix chain 'G' and resid 235 through 244 removed outlier: 3.845A pdb=" N PHE G 244 " --> pdb=" O PHE G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 303 No H-bonds generated for 'chain 'G' and resid 300 through 303' Processing helix chain 'G' and resid 307 through 319 Proline residue: G 316 - end of helix Processing helix chain 'G' and resid 337 through 354 removed outlier: 4.630A pdb=" N SER G 354 " --> pdb=" O LYS G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 366 Processing helix chain 'H' and resid 85 through 101 Processing helix chain 'H' and resid 150 through 162 Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'J' and resid 33 through 39 Processing helix chain 'K' and resid 49 through 57 Processing helix chain 'K' and resid 112 through 116 Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'L' and resid 87 through 92 Processing helix chain 'L' and resid 95 through 97 No H-bonds generated for 'chain 'L' and resid 95 through 97' Processing helix chain 'L' and resid 100 through 115 Processing helix chain 'L' and resid 125 through 143 Processing helix chain 'L' and resid 150 through 173 Processing helix chain 'L' and resid 175 through 184 Processing helix chain 'M' and resid 70 through 78 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 101 through 123 Processing helix chain 'N' and resid 109 through 111 No H-bonds generated for 'chain 'N' and resid 109 through 111' Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 62 through 68 Processing helix chain 'O' and resid 120 through 126 removed outlier: 3.894A pdb=" N GLN O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 140 No H-bonds generated for 'chain 'O' and resid 137 through 140' Processing helix chain 'O' and resid 144 through 159 Processing helix chain 'O' and resid 191 through 195 Processing helix chain 'O' and resid 201 through 203 No H-bonds generated for 'chain 'O' and resid 201 through 203' Processing helix chain 'O' and resid 210 through 219 Processing helix chain 'P' and resid 77 through 83 removed outlier: 4.105A pdb=" N PHE P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 97 No H-bonds generated for 'chain 'P' and resid 94 through 97' Processing helix chain 'P' and resid 101 through 116 Processing helix chain 'P' and resid 127 through 129 No H-bonds generated for 'chain 'P' and resid 127 through 129' Processing helix chain 'R' and resid 73 through 83 Processing helix chain 'R' and resid 87 through 90 No H-bonds generated for 'chain 'R' and resid 87 through 90' Processing helix chain 'R' and resid 108 through 125 Processing helix chain 'R' and resid 146 through 148 No H-bonds generated for 'chain 'R' and resid 146 through 148' Processing helix chain 'R' and resid 167 through 169 No H-bonds generated for 'chain 'R' and resid 167 through 169' Processing helix chain 'R' and resid 186 through 196 Processing helix chain 'R' and resid 208 through 210 No H-bonds generated for 'chain 'R' and resid 208 through 210' Processing helix chain 'R' and resid 212 through 220 Processing helix chain 'R' and resid 224 through 234 Processing helix chain 'R' and resid 240 through 256 Processing helix chain 'R' and resid 259 through 261 No H-bonds generated for 'chain 'R' and resid 259 through 261' Processing helix chain 'R' and resid 268 through 278 Processing helix chain 'R' and resid 282 through 290 Processing helix chain 'R' and resid 294 through 307 Processing helix chain 'R' and resid 312 through 320 Processing helix chain 'R' and resid 324 through 334 Processing helix chain 'R' and resid 339 through 355 Processing helix chain 'S' and resid 12 through 22 Processing helix chain 'S' and resid 32 through 37 Processing helix chain 'S' and resid 66 through 77 removed outlier: 3.911A pdb=" N ILE S 70 " --> pdb=" O HIS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 108 Processing helix chain 'S' and resid 114 through 128 Processing helix chain 'T' and resid 8 through 11 Processing helix chain 'T' and resid 13 through 18 Processing helix chain 'T' and resid 39 through 50 removed outlier: 4.907A pdb=" N GLY T 43 " --> pdb=" O LEU T 40 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE T 50 " --> pdb=" O PHE T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 58 Processing helix chain 'T' and resid 95 through 106 Processing helix chain 'T' and resid 110 through 123 removed outlier: 4.010A pdb=" N LEU T 123 " --> pdb=" O GLU T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 142 No H-bonds generated for 'chain 'T' and resid 140 through 142' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 161 through 164 No H-bonds generated for 'chain 'T' and resid 161 through 164' Processing helix chain 'U' and resid 36 through 38 No H-bonds generated for 'chain 'U' and resid 36 through 38' Processing helix chain 'U' and resid 50 through 86 Processing helix chain 'U' and resid 89 through 166 removed outlier: 4.245A pdb=" N LYS U 165 " --> pdb=" O GLN U 161 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN U 166 " --> pdb=" O GLU U 162 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 181 Processing helix chain 'V' and resid 32 through 35 No H-bonds generated for 'chain 'V' and resid 32 through 35' Processing helix chain 'V' and resid 38 through 41 No H-bonds generated for 'chain 'V' and resid 38 through 41' Processing helix chain 'V' and resid 50 through 62 Processing helix chain 'V' and resid 69 through 78 Processing helix chain 'V' and resid 82 through 96 removed outlier: 3.560A pdb=" N ASP V 86 " --> pdb=" O ARG V 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 103 No H-bonds generated for 'chain 'V' and resid 101 through 103' Processing helix chain 'V' and resid 106 through 118 Processing helix chain 'V' and resid 122 through 130 Processing helix chain 'V' and resid 132 through 135 No H-bonds generated for 'chain 'V' and resid 132 through 135' Processing helix chain 'V' and resid 141 through 153 Processing helix chain 'V' and resid 157 through 170 Processing helix chain 'V' and resid 176 through 190 Processing helix chain 'V' and resid 198 through 214 Proline residue: V 211 - end of helix removed outlier: 3.950A pdb=" N LYS V 214 " --> pdb=" O LEU V 210 " (cutoff:3.500A) Processing helix chain 'V' and resid 218 through 238 Processing helix chain 'V' and resid 240 through 244 Processing helix chain 'V' and resid 255 through 267 Processing helix chain 'V' and resid 277 through 290 Processing helix chain 'V' and resid 327 through 344 Processing helix chain 'V' and resid 352 through 405 removed outlier: 5.775A pdb=" N SER V 365 " --> pdb=" O LYS V 361 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N THR V 366 " --> pdb=" O GLU V 362 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 85 Processing helix chain 'W' and resid 88 through 92 Processing helix chain 'W' and resid 131 through 133 No H-bonds generated for 'chain 'W' and resid 131 through 133' Processing helix chain 'X' and resid 56 through 58 No H-bonds generated for 'chain 'X' and resid 56 through 58' Processing helix chain 'X' and resid 61 through 63 No H-bonds generated for 'chain 'X' and resid 61 through 63' Processing helix chain 'X' and resid 72 through 77 Processing helix chain 'X' and resid 85 through 94 removed outlier: 3.786A pdb=" N MET X 89 " --> pdb=" O PRO X 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN X 90 " --> pdb=" O ARG X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 113 Processing helix chain 'X' and resid 134 through 147 Processing helix chain 'X' and resid 158 through 162 Processing helix chain 'X' and resid 181 through 194 removed outlier: 3.771A pdb=" N ASN X 190 " --> pdb=" O THR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 198 through 201 No H-bonds generated for 'chain 'X' and resid 198 through 201' Processing helix chain 'X' and resid 222 through 231 Processing helix chain 'X' and resid 233 through 253 removed outlier: 4.930A pdb=" N THR X 237 " --> pdb=" O ARG X 234 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP X 238 " --> pdb=" O ASN X 235 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY X 241 " --> pdb=" O ASP X 238 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE X 242 " --> pdb=" O ALA X 239 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS X 248 " --> pdb=" O LYS X 245 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN X 250 " --> pdb=" O LEU X 247 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER X 251 " --> pdb=" O LYS X 248 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 267 No H-bonds generated for 'chain 'X' and resid 265 through 267' Processing helix chain 'X' and resid 284 through 286 No H-bonds generated for 'chain 'X' and resid 284 through 286' Processing helix chain 'X' and resid 288 through 297 removed outlier: 3.521A pdb=" N LEU X 293 " --> pdb=" O LEU X 289 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS X 295 " --> pdb=" O HIS X 291 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET X 297 " --> pdb=" O LEU X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 325 through 337 removed outlier: 6.927A pdb=" N LYS X 331 " --> pdb=" O GLU X 327 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLU X 332 " --> pdb=" O LEU X 328 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY X 333 " --> pdb=" O LEU X 329 " (cutoff:3.500A) Processing helix chain 'X' and resid 350 through 362 Processing helix chain 'X' and resid 374 through 384 Processing helix chain 'X' and resid 388 through 396 Processing helix chain 'Y' and resid 277 through 290 removed outlier: 3.529A pdb=" N THR Y 288 " --> pdb=" O LYS Y 284 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL Y 289 " --> pdb=" O GLN Y 285 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN Y 290 " --> pdb=" O LEU Y 286 " (cutoff:3.500A) Processing helix chain 'Y' and resid 297 through 307 Processing helix chain 'Y' and resid 328 through 332 Processing helix chain 'Y' and resid 335 through 338 Processing helix chain 'Y' and resid 346 through 360 Processing helix chain 'Y' and resid 366 through 382 Processing helix chain 'Z' and resid 6 through 19 Processing helix chain 'Z' and resid 28 through 30 No H-bonds generated for 'chain 'Z' and resid 28 through 30' Processing helix chain 'Z' and resid 32 through 38 Processing helix chain 'Z' and resid 55 through 67 Processing helix chain 'a' and resid 126 through 134 Processing helix chain 'a' and resid 189 through 196 removed outlier: 3.913A pdb=" N SER a 196 " --> pdb=" O LYS a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 217 through 225 Processing helix chain 'a' and resid 238 through 240 No H-bonds generated for 'chain 'a' and resid 238 through 240' Processing helix chain 'a' and resid 244 through 254 Processing helix chain 'a' and resid 316 through 326 Processing helix chain 'a' and resid 344 through 359 Processing helix chain 'a' and resid 364 through 367 Processing helix chain 'a' and resid 394 through 401 Processing helix chain 'a' and resid 403 through 422 removed outlier: 6.282A pdb=" N VAL a 407 " --> pdb=" O LYS a 404 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE a 408 " --> pdb=" O GLY a 405 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '0' and resid 80 through 82 Processing sheet with id= B, first strand: chain '0' and resid 163 through 165 Processing sheet with id= C, first strand: chain '0' and resid 94 through 102 removed outlier: 6.649A pdb=" N TRP 0 115 " --> pdb=" O THR 0 98 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL 0 100 " --> pdb=" O LYS 0 113 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS 0 113 " --> pdb=" O VAL 0 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 150 through 153 Processing sheet with id= E, first strand: chain '5' and resid 204 through 212 removed outlier: 6.901A pdb=" N VAL 5 227 " --> pdb=" O ILE 5 209 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR 5 211 " --> pdb=" O VAL 5 225 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL 5 225 " --> pdb=" O THR 5 211 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN 5 171 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR 5 58 " --> pdb=" O HIS 5 137 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE 5 139 " --> pdb=" O TYR 5 58 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR 5 60 " --> pdb=" O ILE 5 139 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU 5 80 " --> pdb=" O VAL 5 59 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLU 5 61 " --> pdb=" O GLU 5 80 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU 5 82 " --> pdb=" O GLU 5 61 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '7' and resid 349 through 353 removed outlier: 4.468A pdb=" N ALA 7 265 " --> pdb=" O PHE 7 192 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '7' and resid 393 through 395 Processing sheet with id= H, first strand: chain '7' and resid 327 through 331 removed outlier: 6.804A pdb=" N ILE 7 373 " --> pdb=" O PHE 7 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '8' and resid 369 through 371 removed outlier: 5.960A pdb=" N THR 8 345 " --> pdb=" O SER 8 370 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU 8 65 " --> pdb=" O VAL 8 147 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA 8 149 " --> pdb=" O LEU 8 65 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE 8 67 " --> pdb=" O ALA 8 149 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY 8 151 " --> pdb=" O PHE 8 67 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER 8 296 " --> pdb=" O ALA 8 149 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLY 8 151 " --> pdb=" O SER 8 296 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR 8 298 " --> pdb=" O GLY 8 151 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '8' and resid 257 through 262 removed outlier: 6.862A pdb=" N LEU 8 197 " --> pdb=" O ARG 8 258 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR 8 260 " --> pdb=" O SER 8 195 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER 8 195 " --> pdb=" O THR 8 260 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N MET 8 262 " --> pdb=" O MET 8 193 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N MET 8 193 " --> pdb=" O MET 8 262 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N SER 8 239 " --> pdb=" O VAL 8 227 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL 8 227 " --> pdb=" O SER 8 239 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '9' and resid 309 through 315 removed outlier: 7.558A pdb=" N VAL 9 245 " --> pdb=" O ARG 9 311 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL 9 313 " --> pdb=" O VAL 9 245 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY 9 247 " --> pdb=" O VAL 9 313 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU 9 315 " --> pdb=" O GLY 9 247 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER 9 215 " --> pdb=" O GLN 9 242 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE 9 244 " --> pdb=" O SER 9 215 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL 9 217 " --> pdb=" O ILE 9 244 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU 9 246 " --> pdb=" O VAL 9 217 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR 9 219 " --> pdb=" O LEU 9 246 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASN 9 248 " --> pdb=" O TYR 9 219 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL 9 221 " --> pdb=" O ASN 9 248 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP 9 340 " --> pdb=" O LEU 9 216 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU 9 218 " --> pdb=" O ASP 9 340 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR 9 342 " --> pdb=" O LEU 9 218 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N MET 9 220 " --> pdb=" O TYR 9 342 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '9' and resid 376 through 379 Processing sheet with id= M, first strand: chain '9' and resid 527 through 531 removed outlier: 3.746A pdb=" N ALA 9 621 " --> pdb=" O VAL 9 633 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '9' and resid 566 through 570 Processing sheet with id= O, first strand: chain 'B' and resid 165 through 167 removed outlier: 6.662A pdb=" N LEU B 192 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE B 145 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 194 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE B 195 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 220 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR B 234 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL B 223 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL B 236 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 106 through 110 removed outlier: 6.811A pdb=" N ILE B 115 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER B 109 " --> pdb=" O HIS B 113 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N HIS B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 109 through 113 Processing sheet with id= R, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.109A pdb=" N GLN C 156 " --> pdb=" O VAL C 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 254 through 261 removed outlier: 6.343A pdb=" N ALA D 246 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE D 222 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLY D 248 " --> pdb=" O THR D 220 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR D 220 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 294 through 298 Processing sheet with id= U, first strand: chain 'D' and resid 370 through 372 removed outlier: 3.521A pdb=" N ALA D 385 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU D 372 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL D 383 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 43 through 46 removed outlier: 3.525A pdb=" N GLY E 43 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS E 11 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL E 88 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 51 through 53 Processing sheet with id= X, first strand: chain 'E' and resid 35 through 41 removed outlier: 6.790A pdb=" N ASP E 67 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU E 39 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU E 65 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 156 through 163 removed outlier: 3.897A pdb=" N LYS F 163 " --> pdb=" O ARG F 166 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 197 through 199 Processing sheet with id= AA, first strand: chain 'G' and resid 269 through 276 Processing sheet with id= AB, first strand: chain 'H' and resid 105 through 109 removed outlier: 4.208A pdb=" N SER H 105 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR H 175 " --> pdb=" O LYS H 74 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU H 76 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR H 173 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL H 78 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU H 171 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL H 80 " --> pdb=" O ALA H 169 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA H 169 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 114 through 118 Processing sheet with id= AD, first strand: chain 'J' and resid 107 through 111 removed outlier: 6.763A pdb=" N ARG J 82 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N THR J 65 " --> pdb=" O CYS J 80 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS J 80 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR J 67 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 17 through 26 removed outlier: 6.556A pdb=" N ALA M 36 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLN M 50 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU M 65 " --> pdb=" O ASP M 55 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 12 through 16 removed outlier: 8.758A pdb=" N LYS N 78 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N PHE N 50 " --> pdb=" O LYS N 78 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU N 80 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N HIS N 52 " --> pdb=" O GLU N 80 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG N 29 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL N 17 " --> pdb=" O ARG N 29 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 63 through 65 removed outlier: 6.453A pdb=" N LEU N 65 " --> pdb=" O ILE N 84 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE N 84 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'R' and resid 156 through 159 removed outlier: 6.539A pdb=" N LYS R 183 " --> pdb=" O VAL R 141 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL R 141 " --> pdb=" O LYS R 183 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'T' and resid 63 through 68 removed outlier: 6.731A pdb=" N TYR T 79 " --> pdb=" O LYS T 28 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET T 30 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG T 77 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL T 32 " --> pdb=" O PHE T 75 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE T 75 " --> pdb=" O VAL T 32 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'U' and resid 189 through 191 Processing sheet with id= AK, first strand: chain 'W' and resid 122 through 125 removed outlier: 3.726A pdb=" N HIS W 106 " --> pdb=" O TYR W 113 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP W 115 " --> pdb=" O ILE W 104 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE W 104 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS W 98 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY W 171 " --> pdb=" O ARG W 141 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG W 143 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU W 169 " --> pdb=" O ARG W 143 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'X' and resid 67 through 70 removed outlier: 4.496A pdb=" N ALA X 97 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 341 through 345 removed outlier: 9.025A pdb=" N TYR X 124 " --> pdb=" O GLY X 304 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE X 306 " --> pdb=" O TYR X 124 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU X 126 " --> pdb=" O ILE X 306 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER X 308 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLY X 128 " --> pdb=" O SER X 308 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU X 258 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL X 307 " --> pdb=" O LEU X 258 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL X 260 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA X 309 " --> pdb=" O VAL X 260 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL X 262 " --> pdb=" O ALA X 309 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU X 151 " --> pdb=" O LEU X 259 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA X 261 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU X 153 " --> pdb=" O ALA X 261 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASP X 263 " --> pdb=" O LEU X 153 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE X 155 " --> pdb=" O ASP X 263 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'a' and resid 302 through 307 removed outlier: 7.922A pdb=" N SER a 231 " --> pdb=" O LYS a 303 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE a 305 " --> pdb=" O SER a 231 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU a 233 " --> pdb=" O ILE a 305 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N MET a 307 " --> pdb=" O LEU a 233 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N MET a 235 " --> pdb=" O MET a 307 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'a' and resid 427 through 435 removed outlier: 6.511A pdb=" N LEU a 383 " --> pdb=" O ASP a 428 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG a 430 " --> pdb=" O LEU a 383 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE a 385 " --> pdb=" O ARG a 430 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N SER a 432 " --> pdb=" O ILE a 385 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN a 387 " --> pdb=" O SER a 432 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LYS a 434 " --> pdb=" O GLN a 387 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU a 389 " --> pdb=" O LYS a 434 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS a 388 " --> pdb=" O THR a 372 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR a 372 " --> pdb=" O LYS a 388 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU a 390 " --> pdb=" O GLN a 370 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLN a 370 " --> pdb=" O LEU a 390 " (cutoff:3.500A) 2140 hydrogen bonds defined for protein. 5946 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 521 hydrogen bonds 942 hydrogen bond angles 0 basepair planarities 211 basepair parallelities 363 stacking parallelities Total time for adding SS restraints: 36.65 Time building geometry restraints manager: 26.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 32970 1.43 - 1.65: 38923 1.65 - 1.87: 409 1.87 - 2.09: 0 2.09 - 2.31: 20 Bond restraints: 72322 Sorted by residual: bond pdb=" N1 GDP X 503 " pdb=" C2 GDP X 503 " ideal model delta sigma weight residual 1.337 1.556 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C6 GDP X 503 " pdb=" O6 GDP X 503 " ideal model delta sigma weight residual 1.250 1.417 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" C5 GDP X 503 " pdb=" C4 GDP X 503 " ideal model delta sigma weight residual 1.490 1.350 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C2 GDP X 503 " pdb=" N3 GDP X 503 " ideal model delta sigma weight residual 1.350 1.454 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C2 GDP X 503 " pdb=" N2 GDP X 503 " ideal model delta sigma weight residual 1.355 1.458 -0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 72317 not shown) Histogram of bond angle deviations from ideal: 71.51 - 85.20: 16 85.20 - 98.90: 0 98.90 - 112.60: 43298 112.60 - 126.29: 54901 126.29 - 139.99: 3099 Bond angle restraints: 101314 Sorted by residual: angle pdb=" CA PRO V 270 " pdb=" N PRO V 270 " pdb=" CD PRO V 270 " ideal model delta sigma weight residual 112.00 105.61 6.39 1.40e+00 5.10e-01 2.08e+01 angle pdb=" C HIS 9 584 " pdb=" CA HIS 9 584 " pdb=" CB HIS 9 584 " ideal model delta sigma weight residual 116.34 111.27 5.07 1.40e+00 5.10e-01 1.31e+01 angle pdb=" C3' C A1330 " pdb=" O3' C A1330 " pdb=" P A A1331 " ideal model delta sigma weight residual 120.20 125.55 -5.35 1.50e+00 4.44e-01 1.27e+01 angle pdb=" N GLY X 82 " pdb=" CA GLY X 82 " pdb=" C GLY X 82 " ideal model delta sigma weight residual 112.77 117.21 -4.44 1.28e+00 6.10e-01 1.21e+01 angle pdb=" N GLN V 402 " pdb=" CA GLN V 402 " pdb=" CB GLN V 402 " ideal model delta sigma weight residual 110.16 115.25 -5.09 1.48e+00 4.57e-01 1.18e+01 ... (remaining 101309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 42271 35.56 - 71.13: 2023 71.13 - 106.69: 310 106.69 - 142.26: 6 142.26 - 177.82: 8 Dihedral angle restraints: 44618 sinusoidal: 25199 harmonic: 19419 Sorted by residual: dihedral pdb=" CA LYS J 72 " pdb=" C LYS J 72 " pdb=" N PRO J 73 " pdb=" CA PRO J 73 " ideal model delta harmonic sigma weight residual 180.00 122.87 57.13 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" O4' C A 870 " pdb=" C1' C A 870 " pdb=" N1 C A 870 " pdb=" C2 C A 870 " ideal model delta sinusoidal sigma weight residual 200.00 28.95 171.05 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' C A 739 " pdb=" C1' C A 739 " pdb=" N1 C A 739 " pdb=" C2 C A 739 " ideal model delta sinusoidal sigma weight residual 200.00 45.83 154.17 1 1.50e+01 4.44e-03 8.11e+01 ... (remaining 44615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.192: 11779 4.192 - 8.385: 0 8.385 - 12.577: 0 12.577 - 16.769: 0 16.769 - 20.961: 4 Chirality restraints: 11783 Sorted by residual: chirality pdb="FE1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S3 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False -10.55 10.41 -20.96 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE2 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S3 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.36 20.92 2.00e-01 2.50e+01 1.09e+04 chirality pdb="FE3 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False -10.55 10.32 -20.88 2.00e-01 2.50e+01 1.09e+04 ... (remaining 11780 not shown) Planarity restraints: 10261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER V 269 " 0.080 5.00e-02 4.00e+02 1.17e-01 2.21e+01 pdb=" N PRO V 270 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO V 270 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO V 270 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG 0 195 " -0.316 9.50e-02 1.11e+02 1.42e-01 1.29e+01 pdb=" NE ARG 0 195 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG 0 195 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG 0 195 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG 0 195 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 47 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO E 48 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO E 48 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 48 " 0.049 5.00e-02 4.00e+02 ... (remaining 10258 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.59: 583 2.59 - 3.23: 64404 3.23 - 3.87: 144547 3.87 - 4.50: 198855 4.50 - 5.14: 292349 Nonbonded interactions: 700738 Sorted by model distance: nonbonded pdb=" OH TYR 1 198 " pdb=" OD1 ASP 1 203 " model vdw 1.957 2.440 nonbonded pdb=" OG1 THR 5 17 " pdb=" OE1 GLU 5 20 " model vdw 1.963 2.440 nonbonded pdb=" OP1 C A 828 " pdb="MG MG A1714 " model vdw 1.968 2.170 nonbonded pdb=" OP1 A A 801 " pdb="MG MG A1710 " model vdw 1.968 2.170 nonbonded pdb=" OP2 A A 940 " pdb="MG MG A1707 " model vdw 1.982 2.170 ... (remaining 700733 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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 15.700 Check model and map are aligned: 0.960 Set scattering table: 0.660 Process input model: 189.060 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.220 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:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 222.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.004 0.219 72322 Z= 0.259 Angle : 0.646 10.608 101314 Z= 0.343 Chirality : 0.387 20.961 11783 Planarity : 0.006 0.142 10261 Dihedral : 18.402 177.822 32018 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.10), residues: 6541 helix: 1.20 (0.09), residues: 3020 sheet: -0.23 (0.18), residues: 730 loop : 0.04 (0.12), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Y 375 HIS 0.014 0.001 HIS X 81 PHE 0.025 0.002 PHE 8 232 TYR 0.032 0.002 TYR 4 486 ARG 0.037 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1062 time to evaluate : 5.076 Fit side-chains REVERT: 8 363 MET cc_start: 0.7015 (tpp) cc_final: 0.6812 (mmm) REVERT: D 342 MET cc_start: 0.8422 (tpp) cc_final: 0.7753 (tpp) REVERT: D 360 GLN cc_start: 0.8719 (tp40) cc_final: 0.8488 (tp40) REVERT: G 200 LEU cc_start: 0.7590 (tp) cc_final: 0.7028 (tp) REVERT: G 314 MET cc_start: 0.8911 (ttp) cc_final: 0.8700 (ttm) REVERT: G 348 MET cc_start: 0.8478 (mtm) cc_final: 0.8231 (mtm) REVERT: J 68 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7047 (mtt180) REVERT: J 116 GLN cc_start: 0.7182 (mp10) cc_final: 0.6648 (mp10) REVERT: N 36 ASP cc_start: 0.8529 (t0) cc_final: 0.8148 (t0) REVERT: O 65 GLN cc_start: 0.7133 (mm110) cc_final: 0.6751 (mm-40) REVERT: R 271 MET cc_start: 0.8521 (ttp) cc_final: 0.8276 (ttm) REVERT: S 123 LYS cc_start: 0.7579 (ttpp) cc_final: 0.7330 (ttpt) REVERT: T 3 MET cc_start: 0.7892 (mtp) cc_final: 0.7468 (mtt) REVERT: T 57 TYR cc_start: 0.8499 (t80) cc_final: 0.8180 (t80) REVERT: T 132 ARG cc_start: 0.7342 (tpp-160) cc_final: 0.6797 (tpt90) REVERT: T 138 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7164 (mp0) REVERT: V 169 MET cc_start: 0.8529 (mmm) cc_final: 0.8120 (mmt) REVERT: X 167 ASP cc_start: 0.7135 (p0) cc_final: 0.6916 (t0) REVERT: X 296 MET cc_start: 0.8537 (mmm) cc_final: 0.8166 (mmm) REVERT: Y 378 ASN cc_start: 0.6307 (m110) cc_final: 0.5925 (m-40) REVERT: Z 17 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7406 (ttt180) outliers start: 0 outliers final: 2 residues processed: 1062 average time/residue: 1.7746 time to fit residues: 2383.9444 Evaluate side-chains 711 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 709 time to evaluate : 5.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain Y residue 249 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 610 optimal weight: 0.5980 chunk 548 optimal weight: 0.9980 chunk 304 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 369 optimal weight: 4.9990 chunk 292 optimal weight: 20.0000 chunk 566 optimal weight: 0.0670 chunk 219 optimal weight: 1.9990 chunk 344 optimal weight: 9.9990 chunk 421 optimal weight: 0.7980 chunk 656 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 231 HIS 4 346 HIS 4 545 GLN ** 4 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 229 HIS 5 272 GLN 7 69 ASN 7 85 ASN 7 98 HIS ** 7 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 70 GLN 8 145 ASN 8 222 ASN 8 249 GLN 8 313 HIS 9 188 HIS 9 283 HIS 9 551 ASN 9 584 HIS B 167 HIS C 57 HIS D 341 ASN D 369 HIS ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN F 72 GLN F 147 GLN G 90 ASN J 35 GLN J 106 GLN K 55 ASN O 98 ASN P 78 GLN R 277 ASN R 299 ASN R 308 HIS S 47 GLN S 61 GLN U 62 HIS U 110 GLN X 67 HIS X 81 HIS X 110 HIS X 159 HIS Y 290 ASN ** a 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 301 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 72322 Z= 0.238 Angle : 0.771 50.452 101314 Z= 0.463 Chirality : 0.127 6.774 11783 Planarity : 0.004 0.078 10261 Dihedral : 19.404 177.239 18472 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.94 % Allowed : 8.85 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.10), residues: 6541 helix: 1.53 (0.09), residues: 3041 sheet: 0.11 (0.18), residues: 753 loop : 0.15 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 9 183 HIS 0.016 0.001 HIS 9 187 PHE 0.028 0.001 PHE 8 232 TYR 0.022 0.001 TYR a 322 ARG 0.011 0.000 ARG 9 573 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 764 time to evaluate : 5.584 Fit side-chains revert: symmetry clash REVERT: 0 107 GLN cc_start: 0.7384 (tp-100) cc_final: 0.7175 (tp-100) REVERT: 8 166 MET cc_start: 0.7891 (mtp) cc_final: 0.7656 (mtp) REVERT: 9 549 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: 9 637 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6744 (m-80) REVERT: D 342 MET cc_start: 0.8484 (tpp) cc_final: 0.8027 (tpp) REVERT: D 360 GLN cc_start: 0.8721 (tp40) cc_final: 0.8517 (tp40) REVERT: E 13 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6333 (mtm) REVERT: E 85 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6779 (m-30) REVERT: F 225 ASP cc_start: 0.6860 (m-30) cc_final: 0.6660 (m-30) REVERT: J 116 GLN cc_start: 0.7099 (mp10) cc_final: 0.6510 (mp10) REVERT: K 58 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.5909 (mmp-170) REVERT: L 148 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6967 (pttm) REVERT: N 36 ASP cc_start: 0.8205 (t0) cc_final: 0.7867 (t0) REVERT: N 67 ARG cc_start: 0.8255 (ttm110) cc_final: 0.8024 (ttp80) REVERT: O 65 GLN cc_start: 0.7152 (mm110) cc_final: 0.6764 (mm-40) REVERT: O 233 GLU cc_start: 0.6852 (tt0) cc_final: 0.6452 (tt0) REVERT: S 7 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: S 101 GLU cc_start: 0.6506 (mt-10) cc_final: 0.6202 (mt-10) REVERT: T 3 MET cc_start: 0.7905 (mtp) cc_final: 0.7369 (mtt) REVERT: T 57 TYR cc_start: 0.8504 (t80) cc_final: 0.8125 (t80) REVERT: T 132 ARG cc_start: 0.7327 (tpp-160) cc_final: 0.6952 (tpt90) REVERT: T 138 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7160 (mp0) REVERT: U 114 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5398 (mtp180) REVERT: V 169 MET cc_start: 0.8514 (mmm) cc_final: 0.8083 (mmt) REVERT: V 392 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7489 (ttp80) REVERT: W 111 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7082 (t0) REVERT: W 172 ILE cc_start: 0.8596 (mm) cc_final: 0.8296 (mm) REVERT: X 296 MET cc_start: 0.8402 (mmm) cc_final: 0.8129 (mmm) REVERT: Y 351 MET cc_start: 0.7669 (mpp) cc_final: 0.7403 (tpp) REVERT: Y 378 ASN cc_start: 0.6443 (m110) cc_final: 0.6017 (m-40) REVERT: Z 17 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7279 (ttt180) REVERT: Z 21 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: Z 32 LYS cc_start: 0.5423 (ttpt) cc_final: 0.4919 (ttpp) outliers start: 112 outliers final: 29 residues processed: 829 average time/residue: 1.6287 time to fit residues: 1733.3698 Evaluate side-chains 718 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 679 time to evaluate : 5.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 4 residue 253 GLU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 362 ASP Chi-restraints excluded: chain 9 residue 549 GLN Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 148 LYS Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain a residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 364 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 546 optimal weight: 10.0000 chunk 447 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 chunk 657 optimal weight: 0.0870 chunk 710 optimal weight: 10.0000 chunk 585 optimal weight: 9.9990 chunk 652 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 527 optimal weight: 2.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 111 HIS 4 346 HIS ** 4 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 85 ASN 7 107 GLN 7 282 GLN ** 7 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 400 HIS 8 70 GLN 8 145 ASN 8 222 ASN 8 313 HIS 9 92 GLN 9 96 GLN B 201 ASN ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN G 90 ASN J 106 GLN K 55 ASN L 146 HIS L 162 GLN O 98 ASN R 214 ASN R 299 ASN S 47 GLN S 61 GLN U 110 GLN U 166 ASN V 329 GLN W 135 GLN X 81 HIS Y 290 ASN ** a 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.238 72322 Z= 0.342 Angle : 0.809 50.563 101314 Z= 0.480 Chirality : 0.125 6.475 11783 Planarity : 0.005 0.060 10261 Dihedral : 19.333 177.167 18468 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.56 % Allowed : 10.79 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.10), residues: 6541 helix: 1.36 (0.09), residues: 3044 sheet: 0.10 (0.18), residues: 736 loop : 0.09 (0.12), residues: 2761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 9 183 HIS 0.019 0.001 HIS 9 187 PHE 0.039 0.002 PHE 8 206 TYR 0.020 0.002 TYR a 226 ARG 0.007 0.001 ARG U 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 688 time to evaluate : 5.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 107 GLN cc_start: 0.7332 (tp-100) cc_final: 0.7121 (tp-100) REVERT: 7 307 MET cc_start: 0.8590 (mmp) cc_final: 0.8251 (mmp) REVERT: 8 166 MET cc_start: 0.8102 (mtp) cc_final: 0.7813 (mtp) REVERT: 9 637 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: C 118 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6799 (mt-10) REVERT: D 342 MET cc_start: 0.8615 (tpp) cc_final: 0.8329 (tpp) REVERT: E 85 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6889 (m-30) REVERT: F 72 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7753 (mt0) REVERT: F 234 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.5768 (ttm-80) REVERT: G 82 ASN cc_start: 0.7675 (m-40) cc_final: 0.7374 (m-40) REVERT: G 273 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: J 116 GLN cc_start: 0.7075 (mp10) cc_final: 0.6685 (mp10) REVERT: L 148 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6836 (pttm) REVERT: N 36 ASP cc_start: 0.8339 (t0) cc_final: 0.7993 (t0) REVERT: O 65 GLN cc_start: 0.7156 (mm110) cc_final: 0.6914 (mm-40) REVERT: O 109 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.6737 (ptm160) REVERT: O 233 GLU cc_start: 0.6866 (tt0) cc_final: 0.6471 (tt0) REVERT: R 282 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6395 (m-30) REVERT: S 7 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: T 3 MET cc_start: 0.8069 (mtp) cc_final: 0.7349 (mtt) REVERT: T 57 TYR cc_start: 0.8557 (t80) cc_final: 0.8258 (t80) REVERT: T 111 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6028 (tm-30) REVERT: T 122 GLN cc_start: 0.7538 (tt0) cc_final: 0.7317 (tt0) REVERT: T 132 ARG cc_start: 0.7555 (tpp-160) cc_final: 0.7138 (tpt170) REVERT: U 114 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5401 (mtp180) REVERT: V 169 MET cc_start: 0.8520 (mmm) cc_final: 0.8129 (mmt) REVERT: V 376 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: V 394 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6821 (tp40) REVERT: W 111 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7104 (t0) REVERT: X 81 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7144 (p90) REVERT: X 217 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: Z 21 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: Z 32 LYS cc_start: 0.5664 (OUTLIER) cc_final: 0.5122 (ttpp) outliers start: 148 outliers final: 59 residues processed: 774 average time/residue: 1.6189 time to fit residues: 1613.6773 Evaluate side-chains 729 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 651 time to evaluate : 5.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 4 residue 101 LEU Chi-restraints excluded: chain 4 residue 175 GLN Chi-restraints excluded: chain 4 residue 253 GLU Chi-restraints excluded: chain 4 residue 319 LEU Chi-restraints excluded: chain 4 residue 328 VAL Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 7 residue 74 LEU Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 223 MET Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 262 MET Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 362 ASP Chi-restraints excluded: chain 9 residue 535 MET Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 228 LYS Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 148 LYS Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain O residue 109 ARG Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain V residue 158 LYS Chi-restraints excluded: chain V residue 376 GLU Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 32 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 649 optimal weight: 0.6980 chunk 494 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 313 optimal weight: 10.0000 chunk 441 optimal weight: 4.9990 chunk 660 optimal weight: 0.9980 chunk 698 optimal weight: 4.9990 chunk 344 optimal weight: 0.8980 chunk 625 optimal weight: 0.5980 chunk 188 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 181 ASN 4 346 HIS 7 85 ASN 7 107 GLN 7 112 HIS ** 7 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 70 GLN 8 145 ASN 8 222 ASN 8 229 ASN 8 311 HIS 8 313 HIS 9 92 GLN B 265 GLN J 106 GLN K 55 ASN O 152 GLN R 299 ASN R 312 GLN S 47 GLN S 61 GLN U 110 GLN V 399 GLN X 81 HIS X 190 ASN ** a 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 72322 Z= 0.239 Angle : 0.757 50.585 101314 Z= 0.458 Chirality : 0.122 6.359 11783 Planarity : 0.004 0.053 10261 Dihedral : 19.234 177.090 18468 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.27 % Allowed : 12.44 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.10), residues: 6541 helix: 1.57 (0.09), residues: 3048 sheet: 0.28 (0.18), residues: 762 loop : 0.19 (0.12), residues: 2731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 9 183 HIS 0.023 0.001 HIS X 81 PHE 0.032 0.001 PHE 8 206 TYR 0.021 0.001 TYR F 50 ARG 0.007 0.000 ARG a 267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 701 time to evaluate : 5.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 25 LEU cc_start: 0.8733 (mt) cc_final: 0.8470 (mm) REVERT: 0 107 GLN cc_start: 0.7276 (tp-100) cc_final: 0.7054 (tp-100) REVERT: 7 307 MET cc_start: 0.8541 (mmp) cc_final: 0.8120 (mmp) REVERT: 8 166 MET cc_start: 0.8038 (mtp) cc_final: 0.7655 (mtp) REVERT: 9 637 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: D 342 MET cc_start: 0.8606 (tpp) cc_final: 0.8338 (tpp) REVERT: E 56 GLN cc_start: 0.6941 (tm-30) cc_final: 0.6669 (tm-30) REVERT: F 72 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: F 234 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.5707 (ttm-80) REVERT: G 273 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7063 (pm20) REVERT: J 116 GLN cc_start: 0.7084 (mp10) cc_final: 0.6543 (mp10) REVERT: N 36 ASP cc_start: 0.8228 (t0) cc_final: 0.7855 (t0) REVERT: O 65 GLN cc_start: 0.7216 (mm110) cc_final: 0.6926 (mm-40) REVERT: O 109 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.6917 (ptm160) REVERT: O 233 GLU cc_start: 0.6863 (tt0) cc_final: 0.6482 (tt0) REVERT: S 7 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7690 (pm20) REVERT: S 106 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7625 (mp) REVERT: S 112 THR cc_start: 0.7484 (OUTLIER) cc_final: 0.7275 (t) REVERT: T 3 MET cc_start: 0.8034 (mtp) cc_final: 0.7466 (mtt) REVERT: T 57 TYR cc_start: 0.8528 (t80) cc_final: 0.8167 (t80) REVERT: T 66 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8064 (mmt) REVERT: T 132 ARG cc_start: 0.7486 (tpp-160) cc_final: 0.6993 (tpt170) REVERT: T 138 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7208 (mp0) REVERT: U 112 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7267 (tp30) REVERT: U 114 ARG cc_start: 0.6316 (OUTLIER) cc_final: 0.5366 (mtp180) REVERT: U 116 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7840 (mp) REVERT: U 146 VAL cc_start: 0.8323 (t) cc_final: 0.8075 (m) REVERT: V 84 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: V 169 MET cc_start: 0.8494 (mmm) cc_final: 0.8058 (mmt) REVERT: V 315 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7005 (tp30) REVERT: V 376 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: V 394 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6847 (tp40) REVERT: W 111 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7072 (t0) REVERT: X 217 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: Y 351 MET cc_start: 0.7573 (tpp) cc_final: 0.7351 (mmm) REVERT: Y 367 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7207 (mtpp) REVERT: Z 21 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: Z 32 LYS cc_start: 0.5805 (OUTLIER) cc_final: 0.5266 (ttpp) outliers start: 131 outliers final: 47 residues processed: 780 average time/residue: 1.6000 time to fit residues: 1611.8609 Evaluate side-chains 718 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 650 time to evaluate : 5.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 253 GLU Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 7 residue 74 LEU Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 282 THR Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 270 GLU Chi-restraints excluded: chain 9 residue 362 ASP Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 109 ARG Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 84 GLU Chi-restraints excluded: chain V residue 315 GLU Chi-restraints excluded: chain V residue 376 GLU Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 32 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 582 optimal weight: 3.9990 chunk 396 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 520 optimal weight: 4.9990 chunk 288 optimal weight: 10.0000 chunk 596 optimal weight: 5.9990 chunk 483 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 356 optimal weight: 0.9980 chunk 627 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 181 ASN 4 346 HIS 7 72 GLN 7 85 ASN 7 107 GLN 7 112 HIS 7 144 HIS ** 7 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 70 GLN 8 121 GLN 8 145 ASN 8 222 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 311 HIS 9 92 GLN B 124 HIS E 58 HIS ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN J 106 GLN K 55 ASN O 152 GLN P 104 GLN R 299 ASN R 312 GLN S 47 GLN S 61 GLN W 135 GLN X 81 HIS X 190 ASN Y 381 ASN ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.237 72322 Z= 0.476 Angle : 0.866 50.646 101314 Z= 0.504 Chirality : 0.126 6.473 11783 Planarity : 0.005 0.059 10261 Dihedral : 19.320 176.134 18468 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.22 % Allowed : 12.73 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 6541 helix: 1.04 (0.09), residues: 3051 sheet: 0.06 (0.19), residues: 710 loop : -0.11 (0.12), residues: 2780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Y 375 HIS 0.017 0.002 HIS 9 187 PHE 0.037 0.002 PHE 8 206 TYR 0.022 0.002 TYR O 136 ARG 0.007 0.001 ARG K 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 671 time to evaluate : 5.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 307 MET cc_start: 0.8633 (mmp) cc_final: 0.8091 (mmp) REVERT: 8 166 MET cc_start: 0.8180 (mtp) cc_final: 0.7881 (mtp) REVERT: 9 637 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6790 (m-80) REVERT: C 19 ARG cc_start: 0.5387 (OUTLIER) cc_final: 0.4358 (mmp80) REVERT: E 11 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8011 (ttpp) REVERT: E 85 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6916 (m-30) REVERT: E 100 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6585 (mm110) REVERT: F 72 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: F 234 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.5698 (ttm-80) REVERT: G 82 ASN cc_start: 0.7777 (m-40) cc_final: 0.7431 (m-40) REVERT: G 97 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7636 (mt-10) REVERT: G 273 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: J 116 GLN cc_start: 0.7149 (mp10) cc_final: 0.6704 (mp10) REVERT: N 36 ASP cc_start: 0.8426 (t0) cc_final: 0.8131 (t0) REVERT: O 65 GLN cc_start: 0.7289 (mm110) cc_final: 0.6996 (mm-40) REVERT: O 233 GLU cc_start: 0.6877 (tt0) cc_final: 0.6482 (tt0) REVERT: R 192 MET cc_start: 0.9156 (mmp) cc_final: 0.8947 (mmp) REVERT: S 7 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: S 106 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7769 (mp) REVERT: T 3 MET cc_start: 0.8044 (mtp) cc_final: 0.7593 (mtt) REVERT: T 57 TYR cc_start: 0.8550 (t80) cc_final: 0.8213 (t80) REVERT: T 111 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.6035 (tm-30) REVERT: T 132 ARG cc_start: 0.7564 (tpp-160) cc_final: 0.7200 (tpt170) REVERT: U 112 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7299 (tp30) REVERT: U 114 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5435 (mtp180) REVERT: U 116 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7847 (mp) REVERT: V 84 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: V 169 MET cc_start: 0.8491 (mmm) cc_final: 0.8187 (mmt) REVERT: V 315 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6968 (tp30) REVERT: V 376 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: V 394 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6787 (tp40) REVERT: W 111 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7154 (t0) REVERT: X 217 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: Z 13 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6886 (ttm170) REVERT: Z 21 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: Z 32 LYS cc_start: 0.5773 (OUTLIER) cc_final: 0.5218 (ttpp) REVERT: Z 39 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7268 (pm20) outliers start: 186 outliers final: 82 residues processed: 788 average time/residue: 1.6218 time to fit residues: 1650.4517 Evaluate side-chains 755 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 648 time to evaluate : 5.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 154 THR Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 101 LEU Chi-restraints excluded: chain 4 residue 253 GLU Chi-restraints excluded: chain 4 residue 319 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 328 VAL Chi-restraints excluded: chain 4 residue 363 ILE Chi-restraints excluded: chain 4 residue 392 ILE Chi-restraints excluded: chain 4 residue 502 VAL Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 5 residue 228 VAL Chi-restraints excluded: chain 5 residue 283 LEU Chi-restraints excluded: chain 7 residue 43 PHE Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 223 MET Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 262 MET Chi-restraints excluded: chain 8 residue 282 THR Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 225 ASP Chi-restraints excluded: chain 9 residue 362 ASP Chi-restraints excluded: chain 9 residue 383 THR Chi-restraints excluded: chain 9 residue 530 VAL Chi-restraints excluded: chain 9 residue 588 GLN Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 228 LYS Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 84 GLU Chi-restraints excluded: chain V residue 315 GLU Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 376 GLU Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain Z residue 13 ARG Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain a residue 255 THR Chi-restraints excluded: chain a residue 326 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 235 optimal weight: 2.9990 chunk 629 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 410 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 699 optimal weight: 4.9990 chunk 580 optimal weight: 9.9990 chunk 323 optimal weight: 4.9990 chunk 58 optimal weight: 0.0570 chunk 231 optimal weight: 3.9990 chunk 367 optimal weight: 6.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 181 ASN 4 346 HIS 7 85 ASN 7 107 GLN 7 112 HIS 7 398 HIS 8 222 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 311 HIS 9 92 GLN B 265 GLN ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 GLN K 55 ASN O 152 GLN R 299 ASN S 47 GLN S 61 GLN T 122 GLN V 399 GLN Y 381 ASN ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 123 ASN a 295 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 72322 Z= 0.269 Angle : 0.778 50.613 101314 Z= 0.466 Chirality : 0.122 6.371 11783 Planarity : 0.004 0.063 10261 Dihedral : 19.235 176.672 18468 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.41 % Allowed : 14.20 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.10), residues: 6541 helix: 1.32 (0.09), residues: 3048 sheet: 0.26 (0.19), residues: 729 loop : -0.01 (0.12), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 375 HIS 0.020 0.001 HIS 9 187 PHE 0.030 0.001 PHE 8 206 TYR 0.023 0.001 TYR F 50 ARG 0.015 0.000 ARG 9 573 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 664 time to evaluate : 5.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 323 MET cc_start: 0.8171 (ttm) cc_final: 0.7968 (ttp) REVERT: 8 166 MET cc_start: 0.8136 (mtp) cc_final: 0.7739 (mtp) REVERT: 9 637 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6749 (m-80) REVERT: C 153 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8367 (tt) REVERT: F 72 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7747 (mt0) REVERT: G 273 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: J 116 GLN cc_start: 0.7095 (mp10) cc_final: 0.6583 (mp10) REVERT: L 148 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7119 (pttt) REVERT: N 36 ASP cc_start: 0.8424 (t0) cc_final: 0.8109 (t0) REVERT: O 65 GLN cc_start: 0.7320 (mm110) cc_final: 0.6942 (mm-40) REVERT: O 109 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.6934 (ptm160) REVERT: O 197 ASP cc_start: 0.7726 (m-30) cc_final: 0.7509 (m-30) REVERT: O 233 GLU cc_start: 0.6839 (tt0) cc_final: 0.6411 (tt0) REVERT: P 88 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7509 (m) REVERT: R 192 MET cc_start: 0.9143 (mmp) cc_final: 0.8873 (mmp) REVERT: S 7 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: S 106 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7730 (mp) REVERT: T 3 MET cc_start: 0.8078 (mtp) cc_final: 0.7590 (mtt) REVERT: T 57 TYR cc_start: 0.8560 (t80) cc_final: 0.8236 (t80) REVERT: T 132 ARG cc_start: 0.7528 (tpp-160) cc_final: 0.7164 (tpt170) REVERT: U 112 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7234 (tp30) REVERT: U 114 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.5414 (mtp180) REVERT: U 116 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7883 (mp) REVERT: U 146 VAL cc_start: 0.8363 (t) cc_final: 0.8134 (m) REVERT: V 84 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: V 169 MET cc_start: 0.8506 (mmm) cc_final: 0.8129 (mmt) REVERT: V 315 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6978 (tp30) REVERT: V 376 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: V 394 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6888 (tp40) REVERT: W 111 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7105 (t0) REVERT: X 217 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: Y 367 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7223 (mtpp) REVERT: Z 10 ARG cc_start: 0.7026 (ttm-80) cc_final: 0.6796 (ttm-80) REVERT: Z 21 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: Z 32 LYS cc_start: 0.5693 (OUTLIER) cc_final: 0.5128 (ttpp) outliers start: 139 outliers final: 62 residues processed: 753 average time/residue: 1.6104 time to fit residues: 1567.4627 Evaluate side-chains 723 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 640 time to evaluate : 5.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 253 GLU Chi-restraints excluded: chain 4 residue 319 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 5 residue 228 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 270 GLU Chi-restraints excluded: chain 9 residue 362 ASP Chi-restraints excluded: chain 9 residue 383 THR Chi-restraints excluded: chain 9 residue 530 VAL Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 148 LYS Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 109 ARG Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 57 MET Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 64 LYS Chi-restraints excluded: chain V residue 84 GLU Chi-restraints excluded: chain V residue 315 GLU Chi-restraints excluded: chain V residue 376 GLU Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 200 ASN Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain a residue 255 THR Chi-restraints excluded: chain a residue 326 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 674 optimal weight: 0.0970 chunk 78 optimal weight: 1.9990 chunk 398 optimal weight: 3.9990 chunk 510 optimal weight: 2.9990 chunk 395 optimal weight: 2.9990 chunk 588 optimal weight: 0.9980 chunk 390 optimal weight: 0.3980 chunk 696 optimal weight: 6.9990 chunk 436 optimal weight: 2.9990 chunk 424 optimal weight: 0.0010 chunk 321 optimal weight: 9.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 107 GLN 0 181 ASN 4 346 HIS 7 85 ASN 7 107 GLN 8 70 GLN 8 222 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 311 HIS 9 92 GLN 9 522 GLN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN H 183 HIS J 106 GLN K 55 ASN O 152 GLN P 104 GLN R 299 ASN R 312 GLN S 47 GLN S 61 GLN T 101 HIS U 186 ASN V 399 GLN W 135 GLN Y 381 ASN ** a 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 72322 Z= 0.229 Angle : 0.751 50.569 101314 Z= 0.455 Chirality : 0.121 6.330 11783 Planarity : 0.004 0.049 10261 Dihedral : 19.077 177.476 18468 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.06 % Allowed : 14.79 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.10), residues: 6541 helix: 1.62 (0.10), residues: 3040 sheet: 0.49 (0.19), residues: 739 loop : 0.15 (0.12), residues: 2762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Y 375 HIS 0.008 0.001 HIS 9 187 PHE 0.028 0.001 PHE 8 232 TYR 0.023 0.001 TYR F 50 ARG 0.011 0.000 ARG 0 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 683 time to evaluate : 5.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 97 MET cc_start: 0.7174 (mtm) cc_final: 0.6919 (mtp) REVERT: 1 267 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8234 (mm) REVERT: 4 323 MET cc_start: 0.8166 (ttm) cc_final: 0.7965 (ttp) REVERT: 9 637 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: B 135 MET cc_start: 0.8971 (mmm) cc_final: 0.8749 (mmm) REVERT: F 72 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: F 234 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.5178 (ttm-80) REVERT: J 116 GLN cc_start: 0.6921 (mp10) cc_final: 0.6484 (mp10) REVERT: N 36 ASP cc_start: 0.8318 (t0) cc_final: 0.8005 (t0) REVERT: O 65 GLN cc_start: 0.7306 (mm110) cc_final: 0.6842 (mm-40) REVERT: O 109 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.6814 (ptm160) REVERT: O 233 GLU cc_start: 0.6890 (tt0) cc_final: 0.6494 (tt0) REVERT: P 88 THR cc_start: 0.7840 (p) cc_final: 0.7548 (m) REVERT: R 192 MET cc_start: 0.9126 (mmp) cc_final: 0.8895 (mmp) REVERT: R 255 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7943 (ttpp) REVERT: S 102 LYS cc_start: 0.8163 (tppt) cc_final: 0.7749 (tppt) REVERT: S 106 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7753 (mp) REVERT: S 119 VAL cc_start: 0.8566 (m) cc_final: 0.8340 (m) REVERT: T 3 MET cc_start: 0.8030 (mtp) cc_final: 0.7573 (mtt) REVERT: T 57 TYR cc_start: 0.8535 (t80) cc_final: 0.8218 (t80) REVERT: T 132 ARG cc_start: 0.7487 (tpp-160) cc_final: 0.7108 (tpt170) REVERT: U 112 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7216 (tp30) REVERT: U 114 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.5354 (mtp180) REVERT: U 116 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7876 (mp) REVERT: U 146 VAL cc_start: 0.8407 (t) cc_final: 0.8189 (m) REVERT: V 169 MET cc_start: 0.8486 (mmm) cc_final: 0.8131 (mmt) REVERT: V 315 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6968 (tp30) REVERT: V 394 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6893 (tp40) REVERT: X 217 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: Z 21 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: Z 32 LYS cc_start: 0.5734 (OUTLIER) cc_final: 0.5163 (ttpp) outliers start: 119 outliers final: 50 residues processed: 756 average time/residue: 1.5799 time to fit residues: 1543.2845 Evaluate side-chains 704 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 640 time to evaluate : 5.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 1 residue 267 LEU Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 534 LEU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 282 THR Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 9 residue 92 GLN Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 270 GLU Chi-restraints excluded: chain 9 residue 362 ASP Chi-restraints excluded: chain 9 residue 383 THR Chi-restraints excluded: chain 9 residue 530 VAL Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 109 ARG Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 122 VAL Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 315 GLU Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain a residue 160 GLU Chi-restraints excluded: chain a residue 255 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 431 optimal weight: 3.9990 chunk 278 optimal weight: 20.0000 chunk 416 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 443 optimal weight: 5.9990 chunk 474 optimal weight: 6.9990 chunk 344 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 547 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 107 GLN 0 181 ASN 4 346 HIS 7 85 ASN 7 107 GLN 8 70 GLN 8 222 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 311 HIS 9 92 GLN B 265 GLN ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN H 183 HIS J 106 GLN K 55 ASN O 152 GLN P 104 GLN R 299 ASN R 312 GLN S 47 GLN S 61 GLN T 101 HIS V 399 GLN Y 381 ASN ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 72322 Z= 0.336 Angle : 0.803 50.595 101314 Z= 0.476 Chirality : 0.123 6.411 11783 Planarity : 0.005 0.054 10261 Dihedral : 19.084 176.952 18468 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.10 % Allowed : 15.36 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.10), residues: 6541 helix: 1.41 (0.09), residues: 3053 sheet: 0.47 (0.19), residues: 719 loop : 0.05 (0.12), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Y 375 HIS 0.010 0.001 HIS 9 187 PHE 0.034 0.002 PHE 8 206 TYR 0.022 0.002 TYR F 50 ARG 0.010 0.001 ARG X 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 652 time to evaluate : 5.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 108 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6892 (p90) REVERT: 9 637 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: F 72 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7753 (mt0) REVERT: G 273 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: J 90 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7533 (tt0) REVERT: J 116 GLN cc_start: 0.7099 (mp10) cc_final: 0.6565 (mp10) REVERT: L 148 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7179 (pttt) REVERT: N 36 ASP cc_start: 0.8395 (t0) cc_final: 0.8096 (t0) REVERT: O 65 GLN cc_start: 0.7352 (mm110) cc_final: 0.6910 (mm-40) REVERT: O 109 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.6910 (ptm160) REVERT: O 197 ASP cc_start: 0.7717 (m-30) cc_final: 0.7510 (m-30) REVERT: O 233 GLU cc_start: 0.6868 (tt0) cc_final: 0.6456 (tt0) REVERT: P 88 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7573 (m) REVERT: R 192 MET cc_start: 0.9147 (mmp) cc_final: 0.8860 (mmp) REVERT: R 255 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7972 (ttpp) REVERT: S 93 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7784 (ttpp) REVERT: S 102 LYS cc_start: 0.8218 (tppt) cc_final: 0.7862 (tppt) REVERT: S 106 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7799 (mp) REVERT: T 3 MET cc_start: 0.8077 (mtp) cc_final: 0.7615 (mtt) REVERT: T 57 TYR cc_start: 0.8555 (t80) cc_final: 0.8224 (t80) REVERT: T 132 ARG cc_start: 0.7549 (tpp-160) cc_final: 0.7185 (tpt170) REVERT: U 112 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: U 114 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5429 (mtp180) REVERT: U 116 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7890 (mp) REVERT: U 146 VAL cc_start: 0.8375 (t) cc_final: 0.8150 (m) REVERT: V 169 MET cc_start: 0.8504 (mmm) cc_final: 0.8118 (mmt) REVERT: V 315 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6985 (tp30) REVERT: V 394 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6814 (tp40) REVERT: X 182 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7936 (tp) REVERT: X 217 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: Z 21 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: Z 32 LYS cc_start: 0.5782 (OUTLIER) cc_final: 0.5207 (ttpp) REVERT: Z 55 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.6373 (m90) outliers start: 121 outliers final: 62 residues processed: 730 average time/residue: 1.6338 time to fit residues: 1538.8554 Evaluate side-chains 719 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 639 time to evaluate : 4.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 319 LEU Chi-restraints excluded: chain 4 residue 392 ILE Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 108 HIS Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 262 MET Chi-restraints excluded: chain 8 residue 282 THR Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 92 GLN Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 270 GLU Chi-restraints excluded: chain 9 residue 362 ASP Chi-restraints excluded: chain 9 residue 383 THR Chi-restraints excluded: chain 9 residue 400 MET Chi-restraints excluded: chain 9 residue 530 VAL Chi-restraints excluded: chain 9 residue 588 GLN Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 148 LYS Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 109 ARG Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 122 VAL Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 315 GLU Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 200 ASN Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 633 optimal weight: 1.9990 chunk 667 optimal weight: 0.6980 chunk 609 optimal weight: 0.7980 chunk 649 optimal weight: 0.7980 chunk 390 optimal weight: 0.6980 chunk 282 optimal weight: 9.9990 chunk 509 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 586 optimal weight: 0.6980 chunk 614 optimal weight: 0.7980 chunk 647 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 107 GLN 0 181 ASN 4 346 HIS 7 85 ASN 7 107 GLN ** 7 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 222 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 311 HIS 9 92 GLN B 265 GLN ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS J 106 GLN K 55 ASN O 152 GLN R 312 GLN S 47 GLN S 61 GLN V 329 GLN V 399 GLN W 135 GLN X 81 HIS Y 381 ASN ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 72322 Z= 0.232 Angle : 0.759 50.582 101314 Z= 0.458 Chirality : 0.121 6.338 11783 Planarity : 0.004 0.052 10261 Dihedral : 19.020 177.224 18468 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.54 % Allowed : 16.02 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.10), residues: 6541 helix: 1.64 (0.10), residues: 3039 sheet: 0.59 (0.19), residues: 741 loop : 0.19 (0.12), residues: 2761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP Y 375 HIS 0.008 0.001 HIS 9 187 PHE 0.029 0.001 PHE 4 309 TYR 0.023 0.001 TYR F 50 ARG 0.008 0.000 ARG R 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 660 time to evaluate : 5.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 97 MET cc_start: 0.7208 (mtm) cc_final: 0.6958 (mtp) REVERT: 4 323 MET cc_start: 0.8183 (ttm) cc_final: 0.7900 (ttp) REVERT: 8 166 MET cc_start: 0.7964 (mtp) cc_final: 0.7666 (mtp) REVERT: 9 637 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: C 19 ARG cc_start: 0.5403 (OUTLIER) cc_final: 0.4537 (mmp80) REVERT: F 72 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7675 (mt0) REVERT: G 273 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6985 (pm20) REVERT: J 116 GLN cc_start: 0.6991 (mp10) cc_final: 0.6549 (mp10) REVERT: N 36 ASP cc_start: 0.8352 (t0) cc_final: 0.8014 (t0) REVERT: O 65 GLN cc_start: 0.7329 (mm110) cc_final: 0.6908 (mm-40) REVERT: O 109 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.6832 (ptm160) REVERT: O 233 GLU cc_start: 0.6893 (tt0) cc_final: 0.6493 (tt0) REVERT: P 88 THR cc_start: 0.7829 (p) cc_final: 0.7571 (m) REVERT: R 192 MET cc_start: 0.9136 (mmp) cc_final: 0.8871 (mmp) REVERT: R 255 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7955 (ttpp) REVERT: S 93 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7722 (ttpp) REVERT: S 119 VAL cc_start: 0.8588 (m) cc_final: 0.8350 (m) REVERT: T 3 MET cc_start: 0.8057 (mtp) cc_final: 0.7604 (mtt) REVERT: T 57 TYR cc_start: 0.8532 (t80) cc_final: 0.8217 (t80) REVERT: T 132 ARG cc_start: 0.7501 (tpp-160) cc_final: 0.7132 (tpt170) REVERT: U 112 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7243 (tp30) REVERT: U 114 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5362 (mtp180) REVERT: U 116 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7898 (mp) REVERT: U 146 VAL cc_start: 0.8367 (t) cc_final: 0.8154 (m) REVERT: V 169 MET cc_start: 0.8491 (mmm) cc_final: 0.8136 (mmt) REVERT: V 394 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6903 (tp40) REVERT: X 167 ASP cc_start: 0.7301 (p0) cc_final: 0.7048 (t0) REVERT: X 182 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7664 (tp) REVERT: X 217 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: Y 343 LYS cc_start: 0.7371 (mmmm) cc_final: 0.6993 (mmtt) REVERT: Z 21 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: Z 32 LYS cc_start: 0.5719 (OUTLIER) cc_final: 0.5150 (ttpp) REVERT: Z 55 HIS cc_start: 0.6584 (OUTLIER) cc_final: 0.6349 (m90) REVERT: a 239 ASP cc_start: 0.6190 (p0) cc_final: 0.5537 (p0) outliers start: 89 outliers final: 53 residues processed: 719 average time/residue: 1.6031 time to fit residues: 1494.0353 Evaluate side-chains 707 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 640 time to evaluate : 5.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 262 MET Chi-restraints excluded: chain 8 residue 282 THR Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 92 GLN Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 270 GLU Chi-restraints excluded: chain 9 residue 362 ASP Chi-restraints excluded: chain 9 residue 383 THR Chi-restraints excluded: chain 9 residue 400 MET Chi-restraints excluded: chain 9 residue 530 VAL Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 109 ARG Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 122 VAL Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 57 MET Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 200 ASN Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 426 optimal weight: 0.0010 chunk 686 optimal weight: 9.9990 chunk 419 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 chunk 477 optimal weight: 9.9990 chunk 720 optimal weight: 5.9990 chunk 662 optimal weight: 0.2980 chunk 573 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 443 optimal weight: 5.9990 chunk 351 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 181 ASN 4 346 HIS 5 141 ASN 7 85 ASN 7 107 GLN 7 290 HIS 8 222 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 311 HIS ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS J 106 GLN K 55 ASN O 152 GLN R 299 ASN R 312 GLN S 47 GLN T 122 GLN V 399 GLN Y 381 ASN ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 72322 Z= 0.227 Angle : 0.753 50.569 101314 Z= 0.455 Chirality : 0.121 6.334 11783 Planarity : 0.004 0.051 10261 Dihedral : 18.926 177.426 18468 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.28 % Allowed : 16.35 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.10), residues: 6541 helix: 1.73 (0.10), residues: 3039 sheet: 0.63 (0.19), residues: 758 loop : 0.24 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP Y 375 HIS 0.008 0.001 HIS 9 187 PHE 0.032 0.001 PHE 4 309 TYR 0.024 0.001 TYR F 50 ARG 0.009 0.000 ARG R 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 673 time to evaluate : 5.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 97 MET cc_start: 0.7126 (mtm) cc_final: 0.6880 (mtp) REVERT: 4 323 MET cc_start: 0.8164 (ttm) cc_final: 0.7904 (ttp) REVERT: 8 108 HIS cc_start: 0.7124 (OUTLIER) cc_final: 0.6862 (p90) REVERT: 8 166 MET cc_start: 0.7952 (mtp) cc_final: 0.7647 (mtp) REVERT: 9 392 ILE cc_start: 0.7741 (pt) cc_final: 0.7529 (pt) REVERT: C 19 ARG cc_start: 0.5412 (OUTLIER) cc_final: 0.4550 (mmp80) REVERT: E 56 GLN cc_start: 0.7203 (tm-30) cc_final: 0.6738 (tm-30) REVERT: J 116 GLN cc_start: 0.7014 (mp10) cc_final: 0.6573 (mp10) REVERT: N 36 ASP cc_start: 0.8350 (t0) cc_final: 0.7994 (t0) REVERT: O 65 GLN cc_start: 0.7309 (mm110) cc_final: 0.6878 (mm-40) REVERT: O 233 GLU cc_start: 0.6893 (tt0) cc_final: 0.6529 (tt0) REVERT: P 88 THR cc_start: 0.7843 (p) cc_final: 0.7586 (m) REVERT: R 192 MET cc_start: 0.9125 (mmp) cc_final: 0.8874 (mmp) REVERT: R 255 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7941 (ttpp) REVERT: S 93 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7733 (ttpp) REVERT: S 119 VAL cc_start: 0.8587 (m) cc_final: 0.8349 (m) REVERT: T 3 MET cc_start: 0.8043 (mtp) cc_final: 0.7598 (mtt) REVERT: T 57 TYR cc_start: 0.8537 (t80) cc_final: 0.8278 (t80) REVERT: T 132 ARG cc_start: 0.7481 (tpp-160) cc_final: 0.7114 (tpt170) REVERT: U 112 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7246 (tp30) REVERT: U 114 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.5358 (mtp180) REVERT: U 116 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7889 (mp) REVERT: V 169 MET cc_start: 0.8473 (mmm) cc_final: 0.8116 (mmt) REVERT: V 315 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6960 (tp30) REVERT: V 394 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6905 (tp40) REVERT: X 217 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: Y 343 LYS cc_start: 0.7402 (mmmm) cc_final: 0.6983 (mmtt) REVERT: Z 21 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: Z 32 LYS cc_start: 0.5806 (OUTLIER) cc_final: 0.5237 (ttpp) REVERT: a 239 ASP cc_start: 0.6314 (p0) cc_final: 0.5669 (p0) outliers start: 74 outliers final: 43 residues processed: 720 average time/residue: 1.6118 time to fit residues: 1504.8288 Evaluate side-chains 701 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 648 time to evaluate : 5.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 175 GLN Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 108 HIS Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 262 MET Chi-restraints excluded: chain 8 residue 282 THR Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 270 GLU Chi-restraints excluded: chain 9 residue 362 ASP Chi-restraints excluded: chain 9 residue 383 THR Chi-restraints excluded: chain 9 residue 530 VAL Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 122 VAL Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 315 GLU Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 200 ASN Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain a residue 266 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 455 optimal weight: 1.9990 chunk 610 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 528 optimal weight: 0.0370 chunk 84 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 574 optimal weight: 0.0970 chunk 240 optimal weight: 2.9990 chunk 589 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 181 ASN 4 346 HIS 7 85 ASN 7 107 GLN 8 199 GLN 8 222 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 311 HIS 9 92 GLN B 265 GLN ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 HIS H 183 HIS J 106 GLN K 55 ASN O 152 GLN R 277 ASN S 47 GLN S 61 GLN V 399 GLN Y 381 ASN ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.150063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116333 restraints weight = 106131.445| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.49 r_work: 0.3387 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 72322 Z= 0.250 Angle : 0.762 50.582 101314 Z= 0.458 Chirality : 0.122 6.356 11783 Planarity : 0.004 0.050 10261 Dihedral : 18.891 177.119 18468 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.28 % Allowed : 16.66 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.10), residues: 6541 helix: 1.72 (0.10), residues: 3037 sheet: 0.68 (0.19), residues: 748 loop : 0.27 (0.12), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP Y 375 HIS 0.008 0.001 HIS 9 187 PHE 0.033 0.001 PHE 4 309 TYR 0.027 0.001 TYR D 285 ARG 0.016 0.000 ARG U 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24686.40 seconds wall clock time: 428 minutes 57.47 seconds (25737.47 seconds total)