Starting phenix.real_space_refine on Fri Jul 26 15:19:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reu_4857/07_2024/6reu_4857_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reu_4857/07_2024/6reu_4857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reu_4857/07_2024/6reu_4857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reu_4857/07_2024/6reu_4857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reu_4857/07_2024/6reu_4857_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reu_4857/07_2024/6reu_4857_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21545 2.51 5 N 5796 2.21 5 O 6424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 91": "NH1" <-> "NH2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "P ASP 68": "OD1" <-> "OD2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 143": "OE1" <-> "OE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 33": "OE1" <-> "OE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 196": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 83": "OD1" <-> "OD2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S ASP 245": "OD1" <-> "OD2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 96": "NH1" <-> "NH2" Residue "T ASP 112": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T ASP 226": "OD1" <-> "OD2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 384": "OE1" <-> "OE2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 449": "OE1" <-> "OE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 510": "OD1" <-> "OD2" Residue "T GLU 522": "OE1" <-> "OE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 72": "OE1" <-> "OE2" Residue "U TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 135": "OD1" <-> "OD2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U GLU 221": "OE1" <-> "OE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 449": "OE1" <-> "OE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 467": "OD1" <-> "OD2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U GLU 521": "OE1" <-> "OE2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ASP 326": "OD1" <-> "OD2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V GLU 482": "OE1" <-> "OE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 521": "OE1" <-> "OE2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ASP 49": "OD1" <-> "OD2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X ASP 279": "OD1" <-> "OD2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X ASP 317": "OD1" <-> "OD2" Residue "X ARG 366": "NH1" <-> "NH2" Residue "X GLU 370": "OE1" <-> "OE2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ASP 500": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X GLU 536": "OE1" <-> "OE2" Residue "X GLU 541": "OE1" <-> "OE2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X GLU 564": "OE1" <-> "OE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y GLU 149": "OE1" <-> "OE2" Residue "Y ASP 168": "OD1" <-> "OD2" Residue "Y ARG 216": "NH1" <-> "NH2" Residue "Y GLU 229": "OE1" <-> "OE2" Residue "Y TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 289": "NH1" <-> "NH2" Residue "Y ASP 344": "OD1" <-> "OD2" Residue "Y ASP 345": "OD1" <-> "OD2" Residue "Y PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y ASP 409": "OD1" <-> "OD2" Residue "Y TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 428": "OE1" <-> "OE2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y ARG 437": "NH1" <-> "NH2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 465": "OD1" <-> "OD2" Residue "Y TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 483": "OE1" <-> "OE2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 53": "OD1" <-> "OD2" Residue "Z ASP 91": "OD1" <-> "OD2" Residue "Z ASP 104": "OD1" <-> "OD2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z ASP 139": "OD1" <-> "OD2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 218": "NH1" <-> "NH2" Residue "Z GLU 219": "OE1" <-> "OE2" Residue "Z ARG 225": "NH1" <-> "NH2" Residue "Z GLU 238": "OE1" <-> "OE2" Residue "Z ARG 239": "NH1" <-> "NH2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 483": "OE1" <-> "OE2" Residue "Z TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z GLU 511": "OE1" <-> "OE2" Residue "Z GLU 519": "OE1" <-> "OE2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z ASP 542": "OD1" <-> "OD2" Residue "Z ASP 548": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 33899 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.51, per 1000 atoms: 0.55 Number of scatterers: 33899 At special positions: 0 Unit cell: (163.08, 137.16, 209.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6424 8.00 N 5796 7.00 C 21545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.43 Conformation dependent library (CDL) restraints added in 6.3 seconds 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8162 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 0 sheets defined 50.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 54 through 68 removed outlier: 4.443A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 92 removed outlier: 4.004A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 119 removed outlier: 3.970A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.670A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.591A pdb=" N SER B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.923A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 117 removed outlier: 3.844A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 117 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.775A pdb=" N LEU B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 66 removed outlier: 4.627A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 90 removed outlier: 4.065A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 117 removed outlier: 4.248A pdb=" N VAL C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 124 removed outlier: 3.784A pdb=" N ILE C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 4.041A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.794A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 96 removed outlier: 3.725A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 96' Processing helix chain 'D' and resid 99 through 126 removed outlier: 4.231A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER D 117 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.386A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY E 65 " --> pdb=" O MET E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 91 removed outlier: 3.804A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 127 removed outlier: 3.691A pdb=" N VAL E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.514A pdb=" N LYS F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 92 removed outlier: 3.607A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.405A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY F 106 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 67 removed outlier: 3.660A pdb=" N LYS G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 92 removed outlier: 4.037A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 125 removed outlier: 4.370A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 118 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL G 120 " --> pdb=" O PHE G 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 64 removed outlier: 4.148A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 3.668A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.503A pdb=" N VAL H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.858A pdb=" N SER I 59 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 90 removed outlier: 3.994A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN I 87 " --> pdb=" O GLY I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 3.848A pdb=" N LEU I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE I 124 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.618A pdb=" N GLY J 63 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.096A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU J 85 " --> pdb=" O MET J 81 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN J 92 " --> pdb=" O GLY J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 124 removed outlier: 4.160A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 65 removed outlier: 4.295A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 83 removed outlier: 4.269A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR P 75 " --> pdb=" O GLN P 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 90 removed outlier: 3.697A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 109 removed outlier: 3.712A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 128 removed outlier: 3.585A pdb=" N ALA P 126 " --> pdb=" O PHE P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 132 removed outlier: 4.358A pdb=" N SER P 132 " --> pdb=" O GLY P 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 129 through 132' Processing helix chain 'P' and resid 133 through 147 removed outlier: 4.336A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 3.752A pdb=" N ALA Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 28 removed outlier: 3.729A pdb=" N LEU Q 27 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 31 No H-bonds generated for 'chain 'Q' and resid 29 through 31' Processing helix chain 'Q' and resid 32 through 36 Processing helix chain 'R' and resid 29 through 41 removed outlier: 3.748A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 54 Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.724A pdb=" N VAL R 155 " --> pdb=" O LEU R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 168 removed outlier: 4.194A pdb=" N VAL R 160 " --> pdb=" O ASP R 156 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS R 161 " --> pdb=" O PRO R 157 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA R 165 " --> pdb=" O LYS R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 193 removed outlier: 3.889A pdb=" N GLN R 178 " --> pdb=" O ASP R 174 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 70 removed outlier: 3.715A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE S 53 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 79 removed outlier: 3.550A pdb=" N VAL S 75 " --> pdb=" O ALA S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 90 removed outlier: 3.603A pdb=" N ARG S 87 " --> pdb=" O ASP S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 128 removed outlier: 3.940A pdb=" N ILE S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA S 128 " --> pdb=" O ARG S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 150 removed outlier: 3.566A pdb=" N LEU S 150 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 181 removed outlier: 3.704A pdb=" N ALA S 175 " --> pdb=" O THR S 171 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER S 176 " --> pdb=" O PHE S 172 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU S 177 " --> pdb=" O GLY S 173 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE S 178 " --> pdb=" O GLN S 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 221 removed outlier: 5.361A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 231 removed outlier: 4.063A pdb=" N ALA S 230 " --> pdb=" O ASN S 226 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR S 231 " --> pdb=" O SER S 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 226 through 231' Processing helix chain 'S' and resid 238 through 312 removed outlier: 3.566A pdb=" N VAL S 242 " --> pdb=" O GLU S 238 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR S 256 " --> pdb=" O GLY S 252 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA S 268 " --> pdb=" O CYS S 264 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS S 295 " --> pdb=" O ASP S 291 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA S 298 " --> pdb=" O ARG S 294 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU S 306 " --> pdb=" O THR S 302 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) Processing helix chain 'S' and resid 313 through 315 No H-bonds generated for 'chain 'S' and resid 313 through 315' Processing helix chain 'T' and resid 156 through 160 removed outlier: 3.677A pdb=" N THR T 159 " --> pdb=" O GLY T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 211 Processing helix chain 'T' and resid 230 through 247 removed outlier: 4.037A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 267 through 279 Processing helix chain 'T' and resid 280 through 284 removed outlier: 3.519A pdb=" N ARG T 283 " --> pdb=" O GLY T 280 " (cutoff:3.500A) Processing helix chain 'T' and resid 295 through 316 removed outlier: 3.966A pdb=" N GLN T 299 " --> pdb=" O ALA T 295 " (cutoff:3.500A) Proline residue: T 303 - end of helix removed outlier: 3.669A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR T 316 " --> pdb=" O TYR T 312 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 341 removed outlier: 3.739A pdb=" N GLN T 330 " --> pdb=" O ASP T 326 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER T 338 " --> pdb=" O TYR T 334 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 352 No H-bonds generated for 'chain 'T' and resid 351 through 352' Processing helix chain 'T' and resid 353 through 363 removed outlier: 4.140A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 410 through 416 removed outlier: 3.590A pdb=" N TYR T 414 " --> pdb=" O GLU T 411 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY T 416 " --> pdb=" O PHE T 413 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.973A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 455 removed outlier: 4.483A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 456 through 460 removed outlier: 3.704A pdb=" N ALA T 460 " --> pdb=" O ALA T 457 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 479 Processing helix chain 'T' and resid 495 through 506 removed outlier: 3.795A pdb=" N VAL T 499 " --> pdb=" O GLU T 495 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL T 501 " --> pdb=" O GLN T 497 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS T 506 " --> pdb=" O TYR T 502 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 522 removed outlier: 4.384A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 522 through 527 Processing helix chain 'T' and resid 530 through 540 removed outlier: 3.807A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA T 538 " --> pdb=" O LYS T 534 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY T 540 " --> pdb=" O LEU T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 546 through 556 Processing helix chain 'U' and resid 41 through 50 removed outlier: 3.570A pdb=" N LYS U 50 " --> pdb=" O ASP U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 63 Processing helix chain 'U' and resid 65 through 73 Processing helix chain 'U' and resid 74 through 77 Processing helix chain 'U' and resid 191 through 195 Processing helix chain 'U' and resid 206 through 211 removed outlier: 3.659A pdb=" N ALA U 211 " --> pdb=" O LYS U 207 " (cutoff:3.500A) Processing helix chain 'U' and resid 230 through 245 Processing helix chain 'U' and resid 265 through 278 Processing helix chain 'U' and resid 280 through 283 Processing helix chain 'U' and resid 295 through 316 removed outlier: 3.603A pdb=" N GLN U 299 " --> pdb=" O ALA U 295 " (cutoff:3.500A) Proline residue: U 303 - end of helix removed outlier: 3.804A pdb=" N ALA U 310 " --> pdb=" O GLY U 306 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 removed outlier: 4.066A pdb=" N MET U 337 " --> pdb=" O ALA U 333 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 362 Processing helix chain 'U' and resid 369 through 373 removed outlier: 3.709A pdb=" N LEU U 372 " --> pdb=" O SER U 369 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY U 373 " --> pdb=" O LYS U 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 369 through 373' Processing helix chain 'U' and resid 392 through 402 removed outlier: 3.681A pdb=" N ASN U 397 " --> pdb=" O TYR U 393 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER U 400 " --> pdb=" O THR U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 457 removed outlier: 3.504A pdb=" N GLN U 441 " --> pdb=" O PRO U 437 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU U 449 " --> pdb=" O THR U 445 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) Processing helix chain 'U' and resid 465 through 469 removed outlier: 4.557A pdb=" N ALA U 468 " --> pdb=" O ASP U 465 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 484 removed outlier: 3.748A pdb=" N ARG U 479 " --> pdb=" O GLU U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 501 removed outlier: 3.701A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) Processing helix chain 'U' and resid 501 through 506 removed outlier: 3.595A pdb=" N THR U 505 " --> pdb=" O VAL U 501 " (cutoff:3.500A) Processing helix chain 'U' and resid 520 through 528 removed outlier: 3.825A pdb=" N VAL U 528 " --> pdb=" O VAL U 524 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 540 removed outlier: 3.702A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 557 removed outlier: 3.635A pdb=" N ALA U 548 " --> pdb=" O PRO U 544 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA U 552 " --> pdb=" O ALA U 548 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU U 554 " --> pdb=" O LEU U 550 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG U 555 " --> pdb=" O LYS U 551 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 64 removed outlier: 3.852A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 4.244A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 213 removed outlier: 3.566A pdb=" N ALA V 211 " --> pdb=" O LYS V 207 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU V 212 " --> pdb=" O ALA V 208 " (cutoff:3.500A) Processing helix chain 'V' and resid 230 through 246 Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 280 through 285 removed outlier: 3.803A pdb=" N ARG V 283 " --> pdb=" O GLY V 280 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR V 285 " --> pdb=" O MET V 282 " (cutoff:3.500A) Processing helix chain 'V' and resid 297 through 310 Proline residue: V 303 - end of helix Processing helix chain 'V' and resid 310 through 316 removed outlier: 3.580A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 removed outlier: 3.685A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.723A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 394 through 400 removed outlier: 3.528A pdb=" N ILE V 399 " --> pdb=" O ALA V 395 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER V 400 " --> pdb=" O THR V 396 " (cutoff:3.500A) Processing helix chain 'V' and resid 409 through 414 Processing helix chain 'V' and resid 438 through 453 removed outlier: 4.715A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU V 446 " --> pdb=" O VAL V 442 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 484 removed outlier: 4.416A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 4.093A pdb=" N VAL V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR V 505 " --> pdb=" O VAL V 501 " (cutoff:3.500A) Processing helix chain 'V' and resid 516 through 528 removed outlier: 3.968A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.771A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS V 537 " --> pdb=" O PHE V 533 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 556 removed outlier: 3.994A pdb=" N ALA V 548 " --> pdb=" O PRO V 544 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS V 556 " --> pdb=" O ALA V 552 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.540A pdb=" N LEU X 118 " --> pdb=" O ARG X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 166 through 171 Processing helix chain 'X' and resid 189 through 201 removed outlier: 3.555A pdb=" N GLU X 195 " --> pdb=" O VAL X 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 229 removed outlier: 3.911A pdb=" N LEU X 223 " --> pdb=" O GLU X 219 " (cutoff:3.500A) Processing helix chain 'X' and resid 238 through 242 removed outlier: 3.723A pdb=" N ASN X 241 " --> pdb=" O GLU X 238 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER X 242 " --> pdb=" O ARG X 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 238 through 242' Processing helix chain 'X' and resid 256 through 275 removed outlier: 3.517A pdb=" N ARG X 260 " --> pdb=" O GLY X 256 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA X 262 " --> pdb=" O ARG X 258 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU X 263 " --> pdb=" O ALA X 259 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL X 268 " --> pdb=" O THR X 264 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA X 269 " --> pdb=" O GLY X 265 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP X 274 " --> pdb=" O GLU X 270 " (cutoff:3.500A) Processing helix chain 'X' and resid 286 through 299 removed outlier: 4.146A pdb=" N VAL X 297 " --> pdb=" O ALA X 293 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 348 through 353 Processing helix chain 'X' and resid 354 through 358 removed outlier: 4.091A pdb=" N LEU X 358 " --> pdb=" O PHE X 355 " (cutoff:3.500A) Processing helix chain 'X' and resid 365 through 371 removed outlier: 3.677A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 393 through 415 removed outlier: 4.255A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA X 400 " --> pdb=" O HIS X 396 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 416 through 421 Processing helix chain 'X' and resid 433 through 440 removed outlier: 3.504A pdb=" N GLN X 440 " --> pdb=" O ALA X 436 " (cutoff:3.500A) Processing helix chain 'X' and resid 450 through 455 Processing helix chain 'X' and resid 463 through 476 removed outlier: 3.988A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY X 469 " --> pdb=" O ASP X 465 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 483 through 487 removed outlier: 3.632A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 508 removed outlier: 3.613A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS X 501 " --> pdb=" O GLU X 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 530 through 534 Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 164 through 170 Processing helix chain 'Y' and resid 188 through 203 Processing helix chain 'Y' and resid 216 through 230 removed outlier: 3.654A pdb=" N GLU Y 226 " --> pdb=" O ASP Y 222 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.943A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER Y 242 " --> pdb=" O ARG Y 239 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 260 through 275 removed outlier: 3.579A pdb=" N THR Y 264 " --> pdb=" O ARG Y 260 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 301 removed outlier: 3.569A pdb=" N ALA Y 299 " --> pdb=" O SER Y 295 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU Y 301 " --> pdb=" O VAL Y 297 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 removed outlier: 3.875A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 341 through 345 removed outlier: 3.645A pdb=" N ASP Y 344 " --> pdb=" O VAL Y 341 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.532A pdb=" N THR Y 353 " --> pdb=" O PRO Y 349 " (cutoff:3.500A) Processing helix chain 'Y' and resid 365 through 370 removed outlier: 3.524A pdb=" N ALA Y 369 " --> pdb=" O SER Y 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 392 through 420 removed outlier: 4.172A pdb=" N HIS Y 396 " --> pdb=" O ILE Y 392 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR Y 397 " --> pdb=" O GLY Y 393 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR Y 410 " --> pdb=" O VAL Y 406 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS Y 411 " --> pdb=" O LEU Y 407 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 427 through 443 removed outlier: 4.337A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG Y 441 " --> pdb=" O ARG Y 437 " (cutoff:3.500A) Processing helix chain 'Y' and resid 463 through 476 removed outlier: 3.529A pdb=" N GLY Y 472 " --> pdb=" O SER Y 468 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 482 through 486 Processing helix chain 'Y' and resid 491 through 494 Processing helix chain 'Y' and resid 495 through 504 Processing helix chain 'Y' and resid 505 through 508 Processing helix chain 'Y' and resid 518 through 523 removed outlier: 3.806A pdb=" N LYS Y 522 " --> pdb=" O SER Y 518 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP Y 523 " --> pdb=" O GLU Y 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 518 through 523' Processing helix chain 'Y' and resid 526 through 531 Processing helix chain 'Y' and resid 545 through 552 removed outlier: 3.558A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Y' and resid 553 through 555 No H-bonds generated for 'chain 'Y' and resid 553 through 555' Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 149 through 153 removed outlier: 3.655A pdb=" N GLU Z 152 " --> pdb=" O GLU Z 149 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 171 Processing helix chain 'Z' and resid 190 through 204 removed outlier: 3.530A pdb=" N ILE Z 197 " --> pdb=" O ILE Z 193 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LYS Z 202 " --> pdb=" O ASN Z 198 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA Z 203 " --> pdb=" O ASN Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 216 through 230 removed outlier: 3.647A pdb=" N LEU Z 223 " --> pdb=" O GLU Z 219 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE Z 228 " --> pdb=" O TYR Z 224 " (cutoff:3.500A) Processing helix chain 'Z' and resid 238 through 242 removed outlier: 3.759A pdb=" N ASN Z 241 " --> pdb=" O GLU Z 238 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 4.887A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 298 removed outlier: 3.686A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 348 through 353 Processing helix chain 'Z' and resid 367 through 372 Processing helix chain 'Z' and resid 393 through 413 removed outlier: 3.970A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 421 removed outlier: 3.893A pdb=" N ILE Z 419 " --> pdb=" O ASP Z 415 " (cutoff:3.500A) Processing helix chain 'Z' and resid 429 through 443 removed outlier: 3.635A pdb=" N ALA Z 434 " --> pdb=" O LYS Z 430 " (cutoff:3.500A) Processing helix chain 'Z' and resid 450 through 455 removed outlier: 3.547A pdb=" N GLY Z 455 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.675A pdb=" N THR Z 466 " --> pdb=" O ASP Z 462 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU Z 474 " --> pdb=" O PHE Z 470 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 487 removed outlier: 3.739A pdb=" N PHE Z 486 " --> pdb=" O GLU Z 483 " (cutoff:3.500A) Processing helix chain 'Z' and resid 493 through 508 removed outlier: 4.066A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS Z 498 " --> pdb=" O GLU Z 494 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA Z 499 " --> pdb=" O VAL Z 495 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 530 through 534 removed outlier: 3.654A pdb=" N GLU Z 533 " --> pdb=" O LEU Z 530 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE Z 534 " --> pdb=" O VAL Z 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 530 through 534' 1248 hydrogen bonds defined for protein. 3591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.63 Time building geometry restraints manager: 13.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10445 1.34 - 1.46: 5376 1.46 - 1.58: 18378 1.58 - 1.70: 21 1.70 - 1.82: 200 Bond restraints: 34420 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.37e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.12e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.29e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.15e+01 ... (remaining 34415 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.48: 904 106.48 - 113.92: 19929 113.92 - 121.36: 17674 121.36 - 128.80: 8030 128.80 - 136.24: 112 Bond angle restraints: 46649 Sorted by residual: angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 119.82 20.05 1.00e+00 1.00e+00 4.02e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 116.87 19.96 1.00e+00 1.00e+00 3.99e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 120.19 19.68 1.00e+00 1.00e+00 3.87e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 121.50 18.37 1.00e+00 1.00e+00 3.37e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 121.00 15.83 1.00e+00 1.00e+00 2.51e+02 ... (remaining 46644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.30: 19821 26.30 - 52.59: 886 52.59 - 78.89: 94 78.89 - 105.18: 25 105.18 - 131.48: 2 Dihedral angle restraints: 20828 sinusoidal: 8068 harmonic: 12760 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual 180.00 -125.55 -54.45 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -131.64 -48.36 0 5.00e+00 4.00e-02 9.36e+01 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -140.03 -39.97 0 5.00e+00 4.00e-02 6.39e+01 ... (remaining 20825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4552 0.073 - 0.147: 864 0.147 - 0.220: 93 0.220 - 0.294: 9 0.294 - 0.367: 2 Chirality restraints: 5520 Sorted by residual: chirality pdb=" CB ILE T 417 " pdb=" CA ILE T 417 " pdb=" CG1 ILE T 417 " pdb=" CG2 ILE T 417 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB ILE V 542 " pdb=" CA ILE V 542 " pdb=" CG1 ILE V 542 " pdb=" CG2 ILE V 542 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB VAL T 456 " pdb=" CA VAL T 456 " pdb=" CG1 VAL T 456 " pdb=" CG2 VAL T 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 5517 not shown) Planarity restraints: 5999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS P 148 " 0.031 2.00e-02 2.50e+03 6.38e-02 4.07e+01 pdb=" C HIS P 148 " -0.110 2.00e-02 2.50e+03 pdb=" O HIS P 148 " 0.042 2.00e-02 2.50e+03 pdb=" N LYS P 149 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA Z 350 " -0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO Z 351 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO Z 351 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Z 351 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 83 " 0.050 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO S 84 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO S 84 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO S 84 " 0.042 5.00e-02 4.00e+02 ... (remaining 5996 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 41 2.32 - 2.97: 15908 2.97 - 3.61: 51963 3.61 - 4.26: 81388 4.26 - 4.90: 130641 Nonbonded interactions: 279941 Sorted by model distance: nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 1.681 2.170 nonbonded pdb=" O3B ADP X 601 " pdb="MG MG X 602 " model vdw 1.956 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.012 2.170 nonbonded pdb=" O LYS X 498 " pdb=" CG MET X 502 " model vdw 2.034 3.440 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.066 2.170 ... (remaining 279936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.270 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 83.220 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 34420 Z= 0.420 Angle : 0.987 20.046 46649 Z= 0.576 Chirality : 0.058 0.367 5520 Planarity : 0.007 0.088 5999 Dihedral : 15.155 131.480 12666 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.74 % Favored : 94.13 % Rotamer: Outliers : 0.42 % Allowed : 8.42 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.88 (0.09), residues: 4462 helix: -4.07 (0.06), residues: 1933 sheet: -2.33 (0.20), residues: 526 loop : -2.44 (0.12), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP Z 141 HIS 0.010 0.001 HIS S 250 PHE 0.024 0.003 PHE P 122 TYR 0.020 0.002 TYR X 310 ARG 0.008 0.001 ARG V 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 495 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 110 THR cc_start: 0.4215 (OUTLIER) cc_final: 0.3682 (p) REVERT: E 81 MET cc_start: -0.0306 (ttp) cc_final: -0.0758 (tmm) REVERT: J 122 PHE cc_start: 0.3151 (m-10) cc_final: 0.2120 (t80) REVERT: P 44 LEU cc_start: 0.1064 (pp) cc_final: 0.0377 (mm) REVERT: S 274 MET cc_start: -0.1972 (mmp) cc_final: -0.2469 (mmt) REVERT: T 322 ILE cc_start: 0.3972 (tp) cc_final: 0.3751 (tt) REVERT: U 476 ARG cc_start: 0.1799 (tpp80) cc_final: 0.1271 (ptm160) REVERT: V 163 VAL cc_start: -0.4921 (OUTLIER) cc_final: -0.5737 (t) REVERT: V 309 MET cc_start: -0.0722 (mtt) cc_final: -0.1021 (tpp) REVERT: X 97 VAL cc_start: -0.3088 (OUTLIER) cc_final: -0.3431 (m) REVERT: X 115 ARG cc_start: 0.3904 (mmt90) cc_final: 0.2065 (mpt180) REVERT: X 194 MET cc_start: 0.4600 (tpt) cc_final: 0.2762 (ttp) REVERT: X 358 LEU cc_start: 0.3787 (mt) cc_final: 0.2738 (mp) REVERT: X 405 LYS cc_start: 0.2767 (mmtm) cc_final: 0.1488 (mtmt) REVERT: Y 340 TYR cc_start: 0.2780 (t80) cc_final: 0.2067 (m-10) REVERT: Z 91 ASP cc_start: 0.2015 (m-30) cc_final: 0.1251 (m-30) REVERT: Z 556 SER cc_start: 0.2904 (p) cc_final: 0.2567 (m) outliers start: 15 outliers final: 4 residues processed: 507 average time/residue: 0.5056 time to fit residues: 403.5908 Evaluate side-chains 257 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 250 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 6.9990 chunk 335 optimal weight: 0.9980 chunk 185 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 346 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 401 optimal weight: 10.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 87 ASN E 87 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN I 92 ASN P 52 GLN R 53 ASN R 73 ASN R 83 GLN S 52 ASN S 195 ASN S 257 ASN ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 241 HIS T 386 GLN T 405 GLN T 422 ASN ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 527 GLN U 140 GLN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 242 GLN U 264 GLN U 319 HIS U 330 GLN U 358 HIS U 549 HIS V 123 GLN ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 422 ASN ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 79 HIS ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN X 390 ASN Y 79 HIS Y 174 GLN Y 198 ASN Y 199 ASN Y 278 GLN ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 79 HIS ** Z 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 199 ASN Z 294 ASN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 388 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0789 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34420 Z= 0.223 Angle : 0.692 11.174 46649 Z= 0.355 Chirality : 0.046 0.264 5520 Planarity : 0.006 0.068 5999 Dihedral : 7.186 100.330 4919 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.24 (0.11), residues: 4462 helix: -2.31 (0.09), residues: 2041 sheet: -1.55 (0.22), residues: 501 loop : -1.95 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 141 HIS 0.007 0.001 HIS R 66 PHE 0.043 0.002 PHE V 489 TYR 0.036 0.002 TYR Y 173 ARG 0.007 0.001 ARG T 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 302 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 MET cc_start: -0.0471 (ttp) cc_final: -0.0807 (tmm) REVERT: J 122 PHE cc_start: 0.3695 (m-10) cc_final: 0.2448 (t80) REVERT: S 60 MET cc_start: 0.1025 (mpp) cc_final: 0.0820 (mmt) REVERT: S 267 HIS cc_start: 0.1072 (m-70) cc_final: 0.0523 (m-70) REVERT: S 274 MET cc_start: -0.1721 (mmp) cc_final: -0.2238 (mmt) REVERT: U 476 ARG cc_start: 0.2591 (tpp80) cc_final: 0.1452 (ptm160) REVERT: U 546 LEU cc_start: 0.6741 (mp) cc_final: 0.5766 (tt) REVERT: V 309 MET cc_start: -0.0697 (mtt) cc_final: -0.1092 (tpp) REVERT: V 398 VAL cc_start: 0.0542 (t) cc_final: 0.0218 (t) REVERT: X 90 MET cc_start: -0.0256 (mmm) cc_final: -0.2277 (tpt) REVERT: X 115 ARG cc_start: 0.3951 (mmt90) cc_final: 0.2200 (mpt180) REVERT: X 189 LYS cc_start: 0.4238 (mtmm) cc_final: 0.3509 (ttpt) REVERT: X 194 MET cc_start: 0.4509 (tpt) cc_final: 0.2103 (ptp) REVERT: X 285 ASP cc_start: 0.3808 (t0) cc_final: 0.3472 (m-30) REVERT: X 405 LYS cc_start: 0.3143 (mmtm) cc_final: 0.2022 (mtmt) REVERT: X 484 MET cc_start: 0.0877 (mmt) cc_final: 0.0559 (tpp) REVERT: Y 340 TYR cc_start: 0.3313 (t80) cc_final: 0.2258 (m-10) REVERT: Y 422 MET cc_start: -0.2572 (ttp) cc_final: -0.2817 (ttp) REVERT: Z 80 MET cc_start: 0.2396 (ttp) cc_final: 0.1655 (ptm) outliers start: 3 outliers final: 0 residues processed: 305 average time/residue: 0.4643 time to fit residues: 230.5679 Evaluate side-chains 220 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 334 optimal weight: 0.8980 chunk 273 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 402 optimal weight: 6.9990 chunk 434 optimal weight: 7.9990 chunk 358 optimal weight: 7.9990 chunk 398 optimal weight: 4.9990 chunk 137 optimal weight: 0.0270 chunk 322 optimal weight: 0.2980 overall best weight: 2.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN E 87 ASN F 87 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN S 267 HIS ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 HIS ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 358 HIS U 441 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN V 253 GLN ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 GLN X 221 ASN X 252 ASN Y 294 ASN Y 388 ASN Z 144 HIS ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0910 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34420 Z= 0.180 Angle : 0.612 10.585 46649 Z= 0.311 Chirality : 0.044 0.212 5520 Planarity : 0.004 0.056 5999 Dihedral : 6.638 79.386 4919 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.24 % Favored : 95.63 % Rotamer: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.12), residues: 4462 helix: -1.34 (0.11), residues: 2044 sheet: -1.16 (0.23), residues: 488 loop : -1.66 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 37 HIS 0.007 0.001 HIS R 104 PHE 0.021 0.002 PHE E 116 TYR 0.026 0.001 TYR Y 173 ARG 0.008 0.000 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 276 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 81 MET cc_start: 0.0719 (ptm) cc_final: -0.1311 (tmm) REVERT: J 122 PHE cc_start: 0.3918 (m-10) cc_final: 0.2702 (t80) REVERT: J 126 PHE cc_start: 0.2488 (m-80) cc_final: 0.1297 (t80) REVERT: S 62 MET cc_start: -0.0506 (mmp) cc_final: -0.2099 (ttm) REVERT: S 169 ARG cc_start: 0.1520 (mpt90) cc_final: -0.1029 (tpt90) REVERT: S 267 HIS cc_start: 0.1276 (m90) cc_final: 0.1070 (m90) REVERT: S 274 MET cc_start: -0.1818 (mmp) cc_final: -0.2345 (mmt) REVERT: U 265 LYS cc_start: 0.1155 (pttt) cc_final: 0.0424 (pttt) REVERT: U 476 ARG cc_start: 0.2510 (tpp80) cc_final: 0.1351 (ptm160) REVERT: V 309 MET cc_start: -0.0396 (mtt) cc_final: -0.1534 (tmm) REVERT: X 115 ARG cc_start: 0.3775 (mmt90) cc_final: 0.1712 (mpp-170) REVERT: X 189 LYS cc_start: 0.4161 (mtmm) cc_final: 0.3475 (tmmt) REVERT: X 194 MET cc_start: 0.4677 (tpt) cc_final: 0.2067 (ptt) REVERT: X 285 ASP cc_start: 0.4124 (t0) cc_final: 0.3447 (m-30) outliers start: 4 outliers final: 0 residues processed: 279 average time/residue: 0.4542 time to fit residues: 208.1115 Evaluate side-chains 211 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 20.0000 chunk 302 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 chunk 403 optimal weight: 30.0000 chunk 427 optimal weight: 0.9980 chunk 210 optimal weight: 4.9990 chunk 382 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN Q 74 ASN ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 196 GLN ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 486 GLN U 123 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 299 GLN U 461 GLN V 139 HIS ** V 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN V 264 GLN V 386 GLN V 397 ASN V 422 ASN ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 471 GLN X 221 ASN Y 83 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 HIS ** Z 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1329 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 34420 Z= 0.255 Angle : 0.705 9.009 46649 Z= 0.359 Chirality : 0.046 0.368 5520 Planarity : 0.005 0.064 5999 Dihedral : 6.911 89.400 4919 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.33 % Favored : 94.53 % Rotamer: Outliers : 0.14 % Allowed : 5.72 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.12), residues: 4462 helix: -1.10 (0.11), residues: 2036 sheet: -0.95 (0.24), residues: 453 loop : -1.54 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP Y 141 HIS 0.011 0.002 HIS Y 79 PHE 0.041 0.003 PHE E 82 TYR 0.028 0.002 TYR Y 271 ARG 0.014 0.001 ARG Z 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 277 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 MET cc_start: -0.1402 (ttm) cc_final: -0.2214 (mmt) REVERT: I 81 MET cc_start: 0.1472 (ptm) cc_final: -0.1152 (tmm) REVERT: J 122 PHE cc_start: 0.4140 (m-10) cc_final: 0.2922 (t80) REVERT: J 126 PHE cc_start: 0.2613 (m-80) cc_final: 0.1255 (t80) REVERT: S 274 MET cc_start: -0.1748 (mmp) cc_final: -0.2344 (mmt) REVERT: U 265 LYS cc_start: 0.1452 (pttt) cc_final: 0.0495 (pttt) REVERT: U 439 MET cc_start: -0.2015 (tpt) cc_final: -0.2348 (tpt) REVERT: U 476 ARG cc_start: 0.2659 (tpp80) cc_final: 0.1206 (ptm160) REVERT: U 509 LEU cc_start: 0.4832 (pt) cc_final: 0.4472 (mm) REVERT: V 309 MET cc_start: -0.0745 (mtt) cc_final: -0.1483 (tpp) REVERT: V 513 ARG cc_start: 0.3387 (ttt90) cc_final: 0.1657 (mtm180) REVERT: X 90 MET cc_start: 0.0072 (mmm) cc_final: -0.2262 (tpt) REVERT: X 115 ARG cc_start: 0.4144 (mmt90) cc_final: 0.3681 (tpp-160) REVERT: X 285 ASP cc_start: 0.4973 (t0) cc_final: 0.4117 (m-30) outliers start: 5 outliers final: 1 residues processed: 282 average time/residue: 0.4567 time to fit residues: 212.0325 Evaluate side-chains 208 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 3.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 0.9990 chunk 242 optimal weight: 9.9990 chunk 6 optimal weight: 0.0970 chunk 318 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 364 optimal weight: 7.9990 chunk 295 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 218 optimal weight: 0.2980 chunk 383 optimal weight: 0.0030 chunk 107 optimal weight: 5.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 ASN Q 21 ASN S 174 GLN S 185 HIS ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 228 GLN ** U 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 140 GLN V 169 GLN ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 GLN X 221 ASN Y 221 ASN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1126 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 34420 Z= 0.155 Angle : 0.573 9.559 46649 Z= 0.290 Chirality : 0.043 0.232 5520 Planarity : 0.004 0.065 5999 Dihedral : 6.319 85.721 4919 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.97 % Favored : 95.90 % Rotamer: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.12), residues: 4462 helix: -0.59 (0.11), residues: 2063 sheet: -0.79 (0.24), residues: 477 loop : -1.42 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP P 58 HIS 0.010 0.001 HIS V 126 PHE 0.026 0.002 PHE E 116 TYR 0.022 0.001 TYR Y 248 ARG 0.005 0.000 ARG V 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 266 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 LEU cc_start: 0.2688 (pp) cc_final: 0.2453 (tt) REVERT: E 61 MET cc_start: -0.0971 (ttm) cc_final: -0.1824 (ppp) REVERT: G 110 THR cc_start: 0.7001 (p) cc_final: 0.6796 (t) REVERT: G 121 VAL cc_start: 0.1626 (t) cc_final: 0.1120 (p) REVERT: I 81 MET cc_start: 0.0998 (ptm) cc_final: -0.0724 (tmm) REVERT: J 122 PHE cc_start: 0.4098 (m-10) cc_final: 0.2901 (t80) REVERT: J 126 PHE cc_start: 0.2796 (m-80) cc_final: 0.1340 (t80) REVERT: S 62 MET cc_start: -0.0606 (mmp) cc_final: -0.2011 (ttm) REVERT: S 267 HIS cc_start: 0.0701 (m90) cc_final: 0.0030 (m90) REVERT: S 274 MET cc_start: -0.2106 (mmp) cc_final: -0.2789 (mmt) REVERT: U 265 LYS cc_start: 0.1731 (pttt) cc_final: 0.0951 (pttt) REVERT: U 476 ARG cc_start: 0.2515 (tpp80) cc_final: 0.1185 (ptm160) REVERT: U 546 LEU cc_start: 0.3292 (tt) cc_final: 0.3041 (mt) REVERT: V 309 MET cc_start: -0.0426 (mtt) cc_final: -0.1211 (mmm) REVERT: V 513 ARG cc_start: 0.3411 (ttt90) cc_final: 0.1713 (mtm180) REVERT: X 115 ARG cc_start: 0.3846 (mmt90) cc_final: 0.3560 (tpp-160) REVERT: X 194 MET cc_start: 0.3784 (tpt) cc_final: 0.2222 (mtt) REVERT: X 285 ASP cc_start: 0.4617 (t0) cc_final: 0.3863 (m-30) REVERT: X 451 GLU cc_start: 0.2559 (pm20) cc_final: 0.2294 (pm20) outliers start: 2 outliers final: 0 residues processed: 268 average time/residue: 0.4572 time to fit residues: 201.4147 Evaluate side-chains 213 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 0.6980 chunk 384 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 250 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 427 optimal weight: 1.9990 chunk 355 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 chunk 141 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 228 GLN U 461 GLN V 140 GLN ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN Y 322 GLN Y 337 GLN Z 68 HIS ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1208 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 34420 Z= 0.160 Angle : 0.576 9.635 46649 Z= 0.290 Chirality : 0.043 0.194 5520 Planarity : 0.004 0.050 5999 Dihedral : 6.161 78.704 4919 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.73 % Favored : 95.14 % Rotamer: Outliers : 0.03 % Allowed : 1.91 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4462 helix: -0.37 (0.12), residues: 2054 sheet: -0.70 (0.25), residues: 448 loop : -1.30 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 58 HIS 0.007 0.001 HIS T 549 PHE 0.024 0.001 PHE E 116 TYR 0.018 0.001 TYR Y 173 ARG 0.006 0.000 ARG Y 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 LEU cc_start: 0.2988 (pp) cc_final: 0.2744 (tt) REVERT: D 61 MET cc_start: 0.4386 (mmt) cc_final: 0.4113 (mmt) REVERT: G 110 THR cc_start: 0.7165 (p) cc_final: 0.6881 (t) REVERT: G 121 VAL cc_start: 0.1722 (t) cc_final: 0.1205 (p) REVERT: I 81 MET cc_start: 0.1515 (ptm) cc_final: -0.0492 (tmm) REVERT: J 122 PHE cc_start: 0.4130 (m-10) cc_final: 0.2886 (t80) REVERT: J 126 PHE cc_start: 0.2754 (m-80) cc_final: 0.1367 (t80) REVERT: S 62 MET cc_start: -0.0121 (mmp) cc_final: -0.1838 (ttm) REVERT: S 267 HIS cc_start: 0.0745 (m90) cc_final: 0.0204 (m90) REVERT: S 274 MET cc_start: -0.2099 (mmp) cc_final: -0.2837 (mmt) REVERT: U 265 LYS cc_start: 0.1909 (pttt) cc_final: 0.1130 (pttt) REVERT: U 476 ARG cc_start: 0.2467 (tpp80) cc_final: 0.0914 (ptm160) REVERT: V 223 ILE cc_start: 0.1508 (tp) cc_final: 0.1275 (tp) REVERT: V 309 MET cc_start: -0.0379 (mtt) cc_final: -0.1243 (mmm) REVERT: V 439 MET cc_start: -0.4208 (tpt) cc_final: -0.5457 (tpt) REVERT: V 513 ARG cc_start: 0.3200 (ttt90) cc_final: 0.1726 (ptt-90) REVERT: X 90 MET cc_start: 0.0246 (mmm) cc_final: -0.3270 (tpt) REVERT: X 194 MET cc_start: 0.3628 (tpt) cc_final: 0.1970 (mtm) REVERT: X 451 GLU cc_start: 0.2636 (pm20) cc_final: 0.2367 (pm20) REVERT: Y 488 MET cc_start: 0.4478 (ppp) cc_final: 0.4269 (ppp) REVERT: Y 489 VAL cc_start: 0.3704 (t) cc_final: 0.3227 (p) REVERT: Z 82 ASP cc_start: 0.2285 (t0) cc_final: 0.1995 (t0) outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.4538 time to fit residues: 198.1555 Evaluate side-chains 213 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 243 optimal weight: 0.6980 chunk 312 optimal weight: 0.0070 chunk 241 optimal weight: 7.9990 chunk 359 optimal weight: 10.0000 chunk 238 optimal weight: 0.9990 chunk 426 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 276 ASN ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 264 GLN U 461 GLN ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN Y 221 ASN Y 311 GLN Y 357 HIS Z 157 GLN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 448 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1271 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34420 Z= 0.170 Angle : 0.582 8.783 46649 Z= 0.293 Chirality : 0.043 0.218 5520 Planarity : 0.004 0.119 5999 Dihedral : 6.126 73.823 4919 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.73 % Favored : 95.14 % Rotamer: Outliers : 0.03 % Allowed : 1.35 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4462 helix: -0.29 (0.12), residues: 2053 sheet: -0.70 (0.26), residues: 438 loop : -1.28 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 58 HIS 0.005 0.001 HIS S 267 PHE 0.036 0.002 PHE D 82 TYR 0.018 0.001 TYR V 259 ARG 0.017 0.000 ARG Y 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 3.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 LEU cc_start: 0.3503 (pp) cc_final: 0.3232 (tt) REVERT: D 61 MET cc_start: 0.4475 (mmt) cc_final: 0.4273 (mmt) REVERT: E 61 MET cc_start: -0.1121 (ttt) cc_final: -0.1478 (ppp) REVERT: G 61 MET cc_start: -0.0616 (mmp) cc_final: -0.0846 (mmp) REVERT: G 110 THR cc_start: 0.7022 (p) cc_final: 0.6778 (t) REVERT: G 121 VAL cc_start: 0.1673 (t) cc_final: 0.1179 (p) REVERT: I 81 MET cc_start: 0.1261 (ptm) cc_final: -0.0426 (tmm) REVERT: J 122 PHE cc_start: 0.4288 (m-10) cc_final: 0.3015 (t80) REVERT: J 126 PHE cc_start: 0.2852 (m-80) cc_final: 0.1381 (t80) REVERT: S 267 HIS cc_start: 0.0564 (m90) cc_final: 0.0162 (m90) REVERT: S 274 MET cc_start: -0.2104 (mmp) cc_final: -0.2944 (mmt) REVERT: U 265 LYS cc_start: 0.1970 (pttt) cc_final: 0.1185 (pttt) REVERT: U 476 ARG cc_start: 0.2605 (tpp80) cc_final: 0.0875 (ptm160) REVERT: V 439 MET cc_start: -0.4235 (tpt) cc_final: -0.5435 (tpt) REVERT: V 513 ARG cc_start: 0.3204 (ttt90) cc_final: 0.1501 (mtm110) REVERT: X 90 MET cc_start: 0.0503 (mmm) cc_final: -0.3221 (tpt) REVERT: X 194 MET cc_start: 0.3742 (tpt) cc_final: 0.2115 (mtt) REVERT: X 451 GLU cc_start: 0.2883 (pm20) cc_final: 0.2549 (pm20) REVERT: Y 251 MET cc_start: 0.4585 (mmt) cc_final: 0.4339 (mmt) REVERT: Y 340 TYR cc_start: 0.3482 (t80) cc_final: 0.2039 (m-10) REVERT: Y 488 MET cc_start: 0.4568 (ppp) cc_final: 0.4350 (ppp) REVERT: Y 489 VAL cc_start: 0.3808 (t) cc_final: 0.3335 (p) REVERT: Z 82 ASP cc_start: 0.2453 (t0) cc_final: 0.2206 (t0) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.4483 time to fit residues: 194.9893 Evaluate side-chains 213 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 290 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 334 optimal weight: 0.0060 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 486 GLN U 140 GLN ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN V 330 GLN ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 ASN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN X 252 ASN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1304 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 34420 Z= 0.161 Angle : 0.578 7.831 46649 Z= 0.289 Chirality : 0.043 0.184 5520 Planarity : 0.004 0.073 5999 Dihedral : 6.040 69.193 4919 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.11 % Rotamer: Outliers : 0.06 % Allowed : 1.37 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4462 helix: -0.18 (0.12), residues: 2072 sheet: -0.61 (0.26), residues: 421 loop : -1.26 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 141 HIS 0.004 0.001 HIS S 267 PHE 0.029 0.002 PHE D 82 TYR 0.017 0.001 TYR V 334 ARG 0.008 0.000 ARG T 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 255 time to evaluate : 3.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.4612 (mmp) cc_final: 0.4303 (mmm) REVERT: B 115 LEU cc_start: 0.3586 (pp) cc_final: 0.3301 (tt) REVERT: E 61 MET cc_start: -0.0749 (ttt) cc_final: -0.1333 (ppp) REVERT: G 110 THR cc_start: 0.7225 (p) cc_final: 0.6982 (t) REVERT: G 121 VAL cc_start: 0.1650 (t) cc_final: 0.1185 (p) REVERT: I 81 MET cc_start: 0.0946 (ptm) cc_final: -0.0454 (tmm) REVERT: I 97 LYS cc_start: 0.3750 (tppt) cc_final: 0.2715 (tmtt) REVERT: J 122 PHE cc_start: 0.4187 (m-10) cc_final: 0.3092 (t80) REVERT: J 126 PHE cc_start: 0.2808 (m-80) cc_final: 0.1385 (t80) REVERT: S 62 MET cc_start: 0.0219 (mmp) cc_final: -0.1672 (ttm) REVERT: S 267 HIS cc_start: 0.0462 (m90) cc_final: 0.0222 (m90) REVERT: S 271 MET cc_start: 0.3469 (mmm) cc_final: 0.3249 (mmm) REVERT: S 274 MET cc_start: -0.2212 (mmp) cc_final: -0.3128 (mmt) REVERT: U 265 LYS cc_start: 0.2036 (pttt) cc_final: 0.1184 (pttt) REVERT: U 476 ARG cc_start: 0.2579 (tpp80) cc_final: 0.0951 (ptm160) REVERT: V 226 ASP cc_start: 0.6748 (m-30) cc_final: 0.6180 (t70) REVERT: V 439 MET cc_start: -0.4274 (tpt) cc_final: -0.5431 (tpt) REVERT: V 513 ARG cc_start: 0.3258 (ttt90) cc_final: 0.1925 (ptt180) REVERT: X 90 MET cc_start: 0.0054 (mmm) cc_final: -0.3289 (tpt) REVERT: X 194 MET cc_start: 0.3730 (tpt) cc_final: 0.2244 (mtm) REVERT: X 451 GLU cc_start: 0.2541 (pm20) cc_final: 0.2168 (pm20) REVERT: Y 251 MET cc_start: 0.4713 (mmt) cc_final: 0.4472 (mmm) REVERT: Y 489 VAL cc_start: 0.4015 (t) cc_final: 0.3528 (p) outliers start: 2 outliers final: 0 residues processed: 257 average time/residue: 0.4208 time to fit residues: 182.6362 Evaluate side-chains 213 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 0.8980 chunk 408 optimal weight: 9.9990 chunk 372 optimal weight: 7.9990 chunk 396 optimal weight: 0.9990 chunk 238 optimal weight: 20.0000 chunk 172 optimal weight: 0.9980 chunk 311 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 358 optimal weight: 2.9990 chunk 375 optimal weight: 1.9990 chunk 395 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 GLN ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN X 252 ASN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 408 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1343 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34420 Z= 0.161 Angle : 0.586 10.235 46649 Z= 0.292 Chirality : 0.043 0.241 5520 Planarity : 0.004 0.070 5999 Dihedral : 5.974 73.416 4919 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.18 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.03 (0.13), residues: 4462 helix: -0.13 (0.12), residues: 2070 sheet: -0.60 (0.27), residues: 406 loop : -1.21 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 58 HIS 0.005 0.001 HIS T 139 PHE 0.027 0.002 PHE F 116 TYR 0.017 0.001 TYR Y 248 ARG 0.007 0.000 ARG X 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 3.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.4520 (mmp) cc_final: 0.4248 (mmm) REVERT: B 115 LEU cc_start: 0.3772 (pp) cc_final: 0.3463 (tt) REVERT: E 61 MET cc_start: -0.1022 (ttt) cc_final: -0.1487 (ppp) REVERT: G 110 THR cc_start: 0.7009 (p) cc_final: 0.6619 (t) REVERT: G 121 VAL cc_start: 0.1778 (t) cc_final: 0.1301 (p) REVERT: I 81 MET cc_start: 0.0998 (ptm) cc_final: -0.0405 (tmm) REVERT: I 97 LYS cc_start: 0.2969 (tppt) cc_final: 0.2087 (tmtt) REVERT: J 122 PHE cc_start: 0.4265 (m-10) cc_final: 0.3140 (t80) REVERT: J 126 PHE cc_start: 0.2693 (m-80) cc_final: 0.1397 (t80) REVERT: S 267 HIS cc_start: 0.0392 (m90) cc_final: 0.0181 (m90) REVERT: S 274 MET cc_start: -0.2344 (mmp) cc_final: -0.3117 (mmt) REVERT: U 265 LYS cc_start: 0.2106 (pttt) cc_final: 0.1280 (pttt) REVERT: U 476 ARG cc_start: 0.2706 (tpp80) cc_final: 0.1180 (ptm160) REVERT: V 226 ASP cc_start: 0.6654 (m-30) cc_final: 0.6156 (t70) REVERT: V 439 MET cc_start: -0.4568 (tpt) cc_final: -0.5643 (tpt) REVERT: V 513 ARG cc_start: 0.3305 (ttt90) cc_final: 0.1959 (ptt180) REVERT: X 90 MET cc_start: 0.0146 (mmm) cc_final: -0.3299 (tpt) REVERT: X 194 MET cc_start: 0.3698 (tpt) cc_final: 0.2184 (mtm) REVERT: Y 488 MET cc_start: 0.4584 (ppp) cc_final: 0.3967 (ptm) REVERT: Y 489 VAL cc_start: 0.3926 (t) cc_final: 0.3455 (p) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.4521 time to fit residues: 195.7418 Evaluate side-chains 212 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 3.9990 chunk 419 optimal weight: 0.4980 chunk 256 optimal weight: 0.7980 chunk 199 optimal weight: 7.9990 chunk 291 optimal weight: 0.7980 chunk 440 optimal weight: 0.0770 chunk 405 optimal weight: 1.9990 chunk 350 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 270 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN V 104 GLN ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 GLN ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 GLN X 221 ASN X 252 ASN ** X 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 78 GLN Z 79 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1256 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34420 Z= 0.144 Angle : 0.563 9.860 46649 Z= 0.280 Chirality : 0.042 0.255 5520 Planarity : 0.004 0.049 5999 Dihedral : 5.751 78.960 4919 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 0.06 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.13), residues: 4462 helix: 0.00 (0.12), residues: 2078 sheet: -0.48 (0.27), residues: 405 loop : -1.12 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 58 HIS 0.011 0.001 HIS Z 79 PHE 0.028 0.001 PHE A 107 TYR 0.017 0.001 TYR Y 248 ARG 0.008 0.000 ARG T 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.4358 (mmp) cc_final: 0.4099 (mmm) REVERT: B 78 LEU cc_start: 0.5090 (tp) cc_final: 0.4872 (tp) REVERT: B 115 LEU cc_start: 0.4305 (pp) cc_final: 0.3972 (tt) REVERT: E 61 MET cc_start: -0.1150 (ttt) cc_final: -0.1469 (ppp) REVERT: G 110 THR cc_start: 0.6957 (p) cc_final: 0.6587 (t) REVERT: G 121 VAL cc_start: 0.1584 (t) cc_final: 0.1175 (p) REVERT: I 81 MET cc_start: 0.0615 (ptm) cc_final: -0.0448 (tmm) REVERT: I 97 LYS cc_start: 0.2746 (tppt) cc_final: 0.2003 (tmtt) REVERT: J 122 PHE cc_start: 0.4241 (m-10) cc_final: 0.2972 (t80) REVERT: J 126 PHE cc_start: 0.2661 (m-80) cc_final: 0.1383 (t80) REVERT: S 274 MET cc_start: -0.2408 (mmp) cc_final: -0.3117 (mmt) REVERT: T 282 MET cc_start: 0.2033 (ttt) cc_final: 0.1713 (ttt) REVERT: U 265 LYS cc_start: 0.2075 (pttt) cc_final: 0.1281 (pttt) REVERT: U 287 MET cc_start: 0.1433 (mpp) cc_final: 0.0978 (mmm) REVERT: U 476 ARG cc_start: 0.2667 (tpp80) cc_final: 0.1163 (ptm160) REVERT: V 226 ASP cc_start: 0.6607 (m-30) cc_final: 0.6184 (t70) REVERT: V 439 MET cc_start: -0.4841 (tpt) cc_final: -0.5773 (tpt) REVERT: V 551 LYS cc_start: -0.1227 (ptmt) cc_final: -0.2260 (mmtt) REVERT: X 90 MET cc_start: -0.0216 (mmm) cc_final: -0.3379 (tpt) REVERT: X 194 MET cc_start: 0.3670 (tpt) cc_final: 0.2262 (mtm) REVERT: Y 488 MET cc_start: 0.4741 (ppp) cc_final: 0.4254 (ptm) outliers start: 2 outliers final: 0 residues processed: 264 average time/residue: 0.4394 time to fit residues: 194.1355 Evaluate side-chains 220 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 2.9990 chunk 373 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 323 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 351 optimal weight: 0.5980 chunk 146 optimal weight: 0.0470 chunk 360 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 486 GLN ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN V 179 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 GLN ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN X 252 ASN ** X 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.227392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.219618 restraints weight = 103011.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.220345 restraints weight = 97726.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.221277 restraints weight = 68326.513| |-----------------------------------------------------------------------------| r_work (final): 0.4933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1366 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34420 Z= 0.155 Angle : 0.575 10.084 46649 Z= 0.287 Chirality : 0.043 0.250 5520 Planarity : 0.004 0.050 5999 Dihedral : 5.743 78.520 4919 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.50 % Favored : 95.36 % Rotamer: Outliers : 0.03 % Allowed : 0.22 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.79 (0.13), residues: 4462 helix: -0.01 (0.12), residues: 2086 sheet: -0.33 (0.28), residues: 388 loop : -1.03 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 58 HIS 0.014 0.001 HIS S 267 PHE 0.038 0.001 PHE E 116 TYR 0.014 0.001 TYR T 304 ARG 0.006 0.000 ARG T 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6112.15 seconds wall clock time: 111 minutes 38.52 seconds (6698.52 seconds total)