Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 14:12:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7el9_31177/04_2023/7el9_31177.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7el9_31177/04_2023/7el9_31177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7el9_31177/04_2023/7el9_31177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7el9_31177/04_2023/7el9_31177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7el9_31177/04_2023/7el9_31177.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7el9_31177/04_2023/7el9_31177.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 8 6.06 5 P 14 5.49 5 S 182 5.16 5 C 17856 2.51 5 N 4736 2.21 5 O 5330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A ASP 370": "OD1" <-> "OD2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ASP 585": "OD1" <-> "OD2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A ASP 608": "OD1" <-> "OD2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 712": "OD1" <-> "OD2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ASP 716": "OD1" <-> "OD2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A ASP 747": "OD1" <-> "OD2" Residue "A ASP 750": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A ARG 804": "NH1" <-> "NH2" Residue "A GLU 1104": "OE1" <-> "OE2" Residue "A TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A TYR 1132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1135": "OD1" <-> "OD2" Residue "A ASP 1147": "OD1" <-> "OD2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A ARG 1169": "NH1" <-> "NH2" Residue "A ASP 1173": "OD1" <-> "OD2" Residue "A ARG 1216": "NH1" <-> "NH2" Residue "A GLU 1268": "OE1" <-> "OE2" Residue "A PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1307": "OE1" <-> "OE2" Residue "A ASP 1329": "OD1" <-> "OD2" Residue "A GLU 1359": "OE1" <-> "OE2" Residue "A PHE 1386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1424": "OD1" <-> "OD2" Residue "A ARG 1438": "NH1" <-> "NH2" Residue "A ARG 1442": "NH1" <-> "NH2" Residue "A ASP 1462": "OD1" <-> "OD2" Residue "A ARG 1473": "NH1" <-> "NH2" Residue "A ARG 1479": "NH1" <-> "NH2" Residue "A PHE 1485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1507": "NH1" <-> "NH2" Residue "A GLU 1512": "OE1" <-> "OE2" Residue "A ASP 1524": "OD1" <-> "OD2" Residue "A GLU 1525": "OE1" <-> "OE2" Residue "A TYR 1533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1538": "OE1" <-> "OE2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A GLU 1576": "OE1" <-> "OE2" Residue "A GLU 1577": "OE1" <-> "OE2" Residue "A ARG 1631": "NH1" <-> "NH2" Residue "A GLU 1642": "OE1" <-> "OE2" Residue "A TYR 1644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1692": "OE1" <-> "OE2" Residue "A GLU 1695": "OE1" <-> "OE2" Residue "A GLU 1703": "OE1" <-> "OE2" Residue "A ARG 1725": "NH1" <-> "NH2" Residue "A ASP 1729": "OD1" <-> "OD2" Residue "A ARG 1742": "NH1" <-> "NH2" Residue "A GLU 1750": "OE1" <-> "OE2" Residue "A PHE 1755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1769": "NH1" <-> "NH2" Residue "A ASP 1774": "OD1" <-> "OD2" Residue "A ARG 1796": "NH1" <-> "NH2" Residue "A ASP 1797": "OD1" <-> "OD2" Residue "A PHE 1857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1862": "OE1" <-> "OE2" Residue "A ASP 1869": "OD1" <-> "OD2" Residue "A GLU 1876": "OE1" <-> "OE2" Residue "A ASP 1879": "OD1" <-> "OD2" Residue "A PHE 1961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1974": "OE1" <-> "OE2" Residue "A ASP 1978": "OD1" <-> "OD2" Residue "A ASP 2009": "OD1" <-> "OD2" Residue "A PHE 2020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2027": "OD1" <-> "OD2" Residue "A PHE 2056": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2066": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2091": "NH1" <-> "NH2" Residue "A TYR 2095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2112": "OE1" <-> "OE2" Residue "A ASP 2113": "OD1" <-> "OD2" Residue "A GLU 2115": "OE1" <-> "OE2" Residue "A TYR 2127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2140": "OE1" <-> "OE2" Residue "A ASP 2147": "OD1" <-> "OD2" Residue "A GLU 2158": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D GLU 41": "OE1" <-> "OE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D ARG 264": "NH1" <-> "NH2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D ASP 278": "OD1" <-> "OD2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 366": "OD1" <-> "OD2" Residue "D ASP 370": "OD1" <-> "OD2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D ARG 376": "NH1" <-> "NH2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D ASP 395": "OD1" <-> "OD2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D ARG 423": "NH1" <-> "NH2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "D GLU 477": "OE1" <-> "OE2" Residue "D PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 508": "NH1" <-> "NH2" Residue "D PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 550": "OE1" <-> "OE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 574": "OD1" <-> "OD2" Residue "D ARG 577": "NH1" <-> "NH2" Residue "D ASP 585": "OD1" <-> "OD2" Residue "D GLU 586": "OE1" <-> "OE2" Residue "D ASP 608": "OD1" <-> "OD2" Residue "D PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 650": "OD1" <-> "OD2" Residue "D ARG 669": "NH1" <-> "NH2" Residue "D PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 684": "OD1" <-> "OD2" Residue "D PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 691": "NH1" <-> "NH2" Residue "D ARG 692": "NH1" <-> "NH2" Residue "D TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 712": "OD1" <-> "OD2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "D ASP 716": "OD1" <-> "OD2" Residue "D GLU 726": "OE1" <-> "OE2" Residue "D ASP 747": "OD1" <-> "OD2" Residue "D ASP 750": "OD1" <-> "OD2" Residue "D PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 768": "OE1" <-> "OE2" Residue "D ARG 804": "NH1" <-> "NH2" Residue "D GLU 1104": "OE1" <-> "OE2" Residue "D TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1129": "NH1" <-> "NH2" Residue "D TYR 1132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1135": "OD1" <-> "OD2" Residue "D ASP 1147": "OD1" <-> "OD2" Residue "D GLU 1150": "OE1" <-> "OE2" Residue "D ARG 1169": "NH1" <-> "NH2" Residue "D ASP 1173": "OD1" <-> "OD2" Residue "D ARG 1216": "NH1" <-> "NH2" Residue "D GLU 1268": "OE1" <-> "OE2" Residue "D PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1307": "OE1" <-> "OE2" Residue "D ASP 1329": "OD1" <-> "OD2" Residue "D GLU 1359": "OE1" <-> "OE2" Residue "D PHE 1386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1424": "OD1" <-> "OD2" Residue "D ARG 1438": "NH1" <-> "NH2" Residue "D ARG 1442": "NH1" <-> "NH2" Residue "D ASP 1462": "OD1" <-> "OD2" Residue "D ARG 1473": "NH1" <-> "NH2" Residue "D ARG 1479": "NH1" <-> "NH2" Residue "D PHE 1485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1507": "NH1" <-> "NH2" Residue "D GLU 1512": "OE1" <-> "OE2" Residue "D ASP 1524": "OD1" <-> "OD2" Residue "D GLU 1525": "OE1" <-> "OE2" Residue "D TYR 1533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1538": "OE1" <-> "OE2" Residue "D ARG 1559": "NH1" <-> "NH2" Residue "D GLU 1576": "OE1" <-> "OE2" Residue "D GLU 1577": "OE1" <-> "OE2" Residue "D ARG 1631": "NH1" <-> "NH2" Residue "D GLU 1642": "OE1" <-> "OE2" Residue "D TYR 1644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1692": "OE1" <-> "OE2" Residue "D GLU 1695": "OE1" <-> "OE2" Residue "D GLU 1703": "OE1" <-> "OE2" Residue "D ARG 1725": "NH1" <-> "NH2" Residue "D ASP 1729": "OD1" <-> "OD2" Residue "D ARG 1742": "NH1" <-> "NH2" Residue "D GLU 1750": "OE1" <-> "OE2" Residue "D PHE 1755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1769": "NH1" <-> "NH2" Residue "D ASP 1774": "OD1" <-> "OD2" Residue "D ARG 1796": "NH1" <-> "NH2" Residue "D ASP 1797": "OD1" <-> "OD2" Residue "D PHE 1857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1862": "OE1" <-> "OE2" Residue "D ASP 1869": "OD1" <-> "OD2" Residue "D GLU 1876": "OE1" <-> "OE2" Residue "D ASP 1879": "OD1" <-> "OD2" Residue "D PHE 1961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1974": "OE1" <-> "OE2" Residue "D ASP 1978": "OD1" <-> "OD2" Residue "D ASP 2009": "OD1" <-> "OD2" Residue "D PHE 2020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2027": "OD1" <-> "OD2" Residue "D PHE 2056": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2066": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2091": "NH1" <-> "NH2" Residue "D TYR 2095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2112": "OE1" <-> "OE2" Residue "D ASP 2113": "OD1" <-> "OD2" Residue "D GLU 2115": "OE1" <-> "OE2" Residue "D TYR 2127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2140": "OE1" <-> "OE2" Residue "D ASP 2147": "OD1" <-> "OD2" Residue "D GLU 2158": "OE1" <-> "OE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 46": "OD1" <-> "OD2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E GLU 70": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 28128 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 13503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1731, 13503 Classifications: {'peptide': 1731} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 46, 'TRANS': 1684} Chain breaks: 16 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 219 Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 4} Chain: "D" Number of atoms: 13503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1731, 13503 Classifications: {'peptide': 1731} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 46, 'TRANS': 1684} Chain breaks: 16 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 219 Chain: "E" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "F" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1875 SG CYS A 284 35.729 33.354 67.843 1.00 61.94 S ATOM 1899 SG CYS A 287 34.333 31.102 64.822 1.00 59.21 S ATOM 3239 SG CYS A 470 33.068 30.588 68.474 1.00 73.81 S ATOM 9797 SG CYS A1650 89.122 41.313 75.762 1.00 91.26 S ATOM 9810 SG CYS A1652 89.365 41.871 79.157 1.00 89.97 S ATOM 9829 SG CYS A1655 86.187 43.199 75.829 1.00 72.73 S ATOM 9901 SG CYS A1664 88.952 44.493 77.184 1.00 68.67 S ATOM 13564 SG CYS B 39 30.423 64.423 92.321 1.00 81.52 S ATOM 13585 SG CYS B 42 28.292 63.007 89.412 1.00 71.41 S ATOM 13719 SG CYS B 58 27.710 63.091 93.927 1.00 94.45 S ATOM 13744 SG CYS B 61 29.997 60.964 92.428 1.00 99.69 S ATOM 13667 SG CYS B 52 38.069 66.220 98.466 1.00104.91 S ATOM 13834 SG CYS B 72 38.709 63.943 96.025 1.00 92.56 S ATOM 13858 SG CYS B 75 40.828 66.570 96.387 1.00 88.59 S ATOM 15934 SG CYS D 284 140.290 134.640 67.846 1.00 61.74 S ATOM 15958 SG CYS D 287 141.685 136.893 64.826 1.00 59.06 S ATOM 17298 SG CYS D 470 142.950 137.407 68.478 1.00 74.13 S ATOM 23856 SG CYS D1650 86.899 126.658 75.757 1.00 90.95 S ATOM 23869 SG CYS D1652 86.656 126.099 79.151 1.00 90.00 S ATOM 23888 SG CYS D1655 89.835 124.773 75.823 1.00 72.84 S ATOM 23960 SG CYS D1664 87.070 123.478 77.178 1.00 68.06 S ATOM 27623 SG CYS E 39 145.605 103.565 92.315 1.00 81.76 S ATOM 27644 SG CYS E 42 147.736 104.983 89.406 1.00 71.52 S ATOM 27778 SG CYS E 58 148.317 104.897 93.921 1.00 95.83 S ATOM 27803 SG CYS E 61 146.030 107.024 92.423 1.00 99.71 S ATOM 27726 SG CYS E 52 137.959 101.763 98.458 1.00105.38 S ATOM 27893 SG CYS E 72 137.318 104.041 96.018 1.00 92.74 S ATOM 27917 SG CYS E 75 135.200 101.413 96.379 1.00 88.75 S Time building chain proxies: 15.22, per 1000 atoms: 0.54 Number of scatterers: 28128 At special positions: 0 Unit cell: (177, 169, 134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 Mn 2 24.99 S 182 16.00 P 14 15.00 O 5330 8.00 N 4736 7.00 C 17856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS D1691 " - pdb=" SG CYS D1776 " distance=2.03 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: 11.44 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A 472 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 284 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 287 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 470 " pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1650 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1664 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1652 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1655 " pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 58 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 39 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 55 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 72 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 52 " pdb=" ZN D2302 " pdb="ZN ZN D2302 " - pdb=" ND1 HIS D 472 " pdb="ZN ZN D2302 " - pdb=" SG CYS D 284 " pdb="ZN ZN D2302 " - pdb=" SG CYS D 287 " pdb="ZN ZN D2302 " - pdb=" SG CYS D 470 " pdb=" ZN D2303 " pdb="ZN ZN D2303 " - pdb=" SG CYS D1650 " pdb="ZN ZN D2303 " - pdb=" SG CYS D1664 " pdb="ZN ZN D2303 " - pdb=" SG CYS D1652 " pdb="ZN ZN D2303 " - pdb=" SG CYS D1655 " pdb=" ZN E 101 " pdb="ZN ZN E 101 " - pdb=" SG CYS E 61 " pdb="ZN ZN E 101 " - pdb=" SG CYS E 58 " pdb="ZN ZN E 101 " - pdb=" SG CYS E 39 " pdb="ZN ZN E 101 " - pdb=" SG CYS E 42 " pdb=" ZN E 102 " pdb="ZN ZN E 102 " - pdb=" NE2 HIS E 55 " pdb="ZN ZN E 102 " - pdb=" SG CYS E 75 " pdb="ZN ZN E 102 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 102 " - pdb=" SG CYS E 52 " Number of angles added : 36 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6744 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 24 sheets defined 49.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 37 through 56 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 108 through 131 removed outlier: 4.472A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.823A pdb=" N ARG A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 removed outlier: 4.135A pdb=" N ILE A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.753A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.768A pdb=" N ASP A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 412 through 423 removed outlier: 4.007A pdb=" N ASN A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 479 through 502 removed outlier: 3.668A pdb=" N GLN A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.504A pdb=" N ARG A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 604 through 623 Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 625 through 644 removed outlier: 3.564A pdb=" N ASN A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.872A pdb=" N VAL A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 removed outlier: 3.912A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 712 through 732 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 789 Processing helix chain 'A' and resid 1135 through 1156 Processing helix chain 'A' and resid 1163 through 1181 Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1197 through 1207 removed outlier: 4.344A pdb=" N MET A1207 " --> pdb=" O ALA A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 Processing helix chain 'A' and resid 1239 through 1248 removed outlier: 3.542A pdb=" N ILE A1248 " --> pdb=" O GLU A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1276 removed outlier: 4.562A pdb=" N GLN A1275 " --> pdb=" O HIS A1271 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1319 Processing helix chain 'A' and resid 1351 through 1365 Processing helix chain 'A' and resid 1395 through 1405 Processing helix chain 'A' and resid 1411 through 1429 removed outlier: 3.563A pdb=" N ASN A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1450 removed outlier: 3.699A pdb=" N THR A1437 " --> pdb=" O THR A1433 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1468 Processing helix chain 'A' and resid 1472 through 1485 Processing helix chain 'A' and resid 1490 through 1507 Processing helix chain 'A' and resid 1513 through 1520 Processing helix chain 'A' and resid 1523 through 1534 removed outlier: 3.508A pdb=" N TYR A1533 " --> pdb=" O GLY A1529 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A1534 " --> pdb=" O PHE A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1545 Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 3.625A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1625 Processing helix chain 'A' and resid 1639 through 1645 Processing helix chain 'A' and resid 1665 through 1669 removed outlier: 3.683A pdb=" N LEU A1668 " --> pdb=" O ASN A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1694 removed outlier: 3.517A pdb=" N GLY A1694 " --> pdb=" O ALA A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1698 Processing helix chain 'A' and resid 1732 through 1744 Processing helix chain 'A' and resid 1744 through 1750 removed outlier: 3.548A pdb=" N GLU A1750 " --> pdb=" O VAL A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1764 removed outlier: 3.662A pdb=" N SER A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1783 removed outlier: 4.220A pdb=" N ASP A1780 " --> pdb=" O CYS A1776 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1793 Processing helix chain 'A' and resid 1805 through 1809 Processing helix chain 'A' and resid 1826 through 1843 removed outlier: 3.669A pdb=" N ILE A1830 " --> pdb=" O SER A1826 " (cutoff:3.500A) Processing helix chain 'A' and resid 1851 through 1856 Processing helix chain 'A' and resid 1860 through 1864 removed outlier: 4.168A pdb=" N VAL A1863 " --> pdb=" O PHE A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1875 through 1884 Processing helix chain 'A' and resid 1919 through 1924 removed outlier: 4.384A pdb=" N LEU A1924 " --> pdb=" O ASP A1920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1940 Processing helix chain 'A' and resid 2003 through 2015 Processing helix chain 'A' and resid 2031 through 2037 Processing helix chain 'A' and resid 2101 through 2110 removed outlier: 3.788A pdb=" N ALA A2110 " --> pdb=" O LYS A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2123 removed outlier: 3.590A pdb=" N VAL A2117 " --> pdb=" O ASP A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2129 removed outlier: 3.603A pdb=" N TYR A2127 " --> pdb=" O GLN A2123 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2146 Processing helix chain 'A' and resid 2150 through 2155 Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.723A pdb=" N ASN B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 12 Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 37 through 56 Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 108 through 131 removed outlier: 4.473A pdb=" N LEU D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP D 129 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 171 removed outlier: 3.823A pdb=" N ARG D 161 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 removed outlier: 4.135A pdb=" N ILE D 188 " --> pdb=" O TYR D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 221 Processing helix chain 'D' and resid 231 through 250 removed outlier: 3.753A pdb=" N VAL D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 274 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 289 through 303 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 345 through 366 removed outlier: 3.769A pdb=" N ASP D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 405 Processing helix chain 'D' and resid 412 through 423 removed outlier: 4.006A pdb=" N ASN D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 421 " --> pdb=" O CYS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 451 Processing helix chain 'D' and resid 474 through 478 Processing helix chain 'D' and resid 479 through 502 removed outlier: 3.668A pdb=" N GLN D 483 " --> pdb=" O SER D 479 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET D 484 " --> pdb=" O SER D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 578 removed outlier: 3.504A pdb=" N ARG D 577 " --> pdb=" O ASP D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 598 Processing helix chain 'D' and resid 604 through 623 Proline residue: D 611 - end of helix Processing helix chain 'D' and resid 625 through 644 removed outlier: 3.564A pdb=" N ASN D 644 " --> pdb=" O MET D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 656 removed outlier: 3.872A pdb=" N VAL D 656 " --> pdb=" O THR D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 680 removed outlier: 3.911A pdb=" N VAL D 667 " --> pdb=" O SER D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 702 Processing helix chain 'D' and resid 703 through 706 Processing helix chain 'D' and resid 712 through 732 Proline residue: D 727 - end of helix Processing helix chain 'D' and resid 745 through 760 Processing helix chain 'D' and resid 776 through 789 Processing helix chain 'D' and resid 1135 through 1156 Processing helix chain 'D' and resid 1163 through 1181 Processing helix chain 'D' and resid 1191 through 1196 Processing helix chain 'D' and resid 1197 through 1207 removed outlier: 4.344A pdb=" N MET D1207 " --> pdb=" O ALA D1203 " (cutoff:3.500A) Processing helix chain 'D' and resid 1221 through 1233 Processing helix chain 'D' and resid 1239 through 1248 removed outlier: 3.542A pdb=" N ILE D1248 " --> pdb=" O GLU D1244 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1276 removed outlier: 4.562A pdb=" N GLN D1275 " --> pdb=" O HIS D1271 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D1276 " --> pdb=" O GLN D1272 " (cutoff:3.500A) Processing helix chain 'D' and resid 1295 through 1319 Processing helix chain 'D' and resid 1351 through 1365 Processing helix chain 'D' and resid 1395 through 1405 Processing helix chain 'D' and resid 1411 through 1429 removed outlier: 3.563A pdb=" N ASN D1429 " --> pdb=" O GLN D1425 " (cutoff:3.500A) Processing helix chain 'D' and resid 1433 through 1450 removed outlier: 3.699A pdb=" N THR D1437 " --> pdb=" O THR D1433 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D1438 " --> pdb=" O LYS D1434 " (cutoff:3.500A) Processing helix chain 'D' and resid 1464 through 1468 Processing helix chain 'D' and resid 1472 through 1485 Processing helix chain 'D' and resid 1490 through 1507 Processing helix chain 'D' and resid 1513 through 1520 Processing helix chain 'D' and resid 1523 through 1534 removed outlier: 3.508A pdb=" N TYR D1533 " --> pdb=" O GLY D1529 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA D1534 " --> pdb=" O PHE D1530 " (cutoff:3.500A) Processing helix chain 'D' and resid 1539 through 1545 Processing helix chain 'D' and resid 1579 through 1590 removed outlier: 3.625A pdb=" N LYS D1583 " --> pdb=" O PRO D1579 " (cutoff:3.500A) Processing helix chain 'D' and resid 1613 through 1625 Processing helix chain 'D' and resid 1639 through 1645 Processing helix chain 'D' and resid 1665 through 1669 removed outlier: 3.684A pdb=" N LEU D1668 " --> pdb=" O ASN D1665 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1694 removed outlier: 3.516A pdb=" N GLY D1694 " --> pdb=" O ALA D1690 " (cutoff:3.500A) Processing helix chain 'D' and resid 1695 through 1698 Processing helix chain 'D' and resid 1732 through 1744 Processing helix chain 'D' and resid 1744 through 1750 removed outlier: 3.548A pdb=" N GLU D1750 " --> pdb=" O VAL D1746 " (cutoff:3.500A) Processing helix chain 'D' and resid 1758 through 1764 removed outlier: 3.662A pdb=" N SER D1762 " --> pdb=" O ASP D1758 " (cutoff:3.500A) Processing helix chain 'D' and resid 1774 through 1783 removed outlier: 4.221A pdb=" N ASP D1780 " --> pdb=" O CYS D1776 " (cutoff:3.500A) Processing helix chain 'D' and resid 1788 through 1793 Processing helix chain 'D' and resid 1805 through 1809 Processing helix chain 'D' and resid 1826 through 1843 removed outlier: 3.669A pdb=" N ILE D1830 " --> pdb=" O SER D1826 " (cutoff:3.500A) Processing helix chain 'D' and resid 1851 through 1856 Processing helix chain 'D' and resid 1860 through 1864 removed outlier: 4.168A pdb=" N VAL D1863 " --> pdb=" O PHE D1860 " (cutoff:3.500A) Processing helix chain 'D' and resid 1875 through 1884 Processing helix chain 'D' and resid 1919 through 1924 removed outlier: 4.384A pdb=" N LEU D1924 " --> pdb=" O ASP D1920 " (cutoff:3.500A) Processing helix chain 'D' and resid 1933 through 1940 Processing helix chain 'D' and resid 2003 through 2015 Processing helix chain 'D' and resid 2031 through 2037 Processing helix chain 'D' and resid 2101 through 2110 removed outlier: 3.788A pdb=" N ALA D2110 " --> pdb=" O LYS D2106 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2123 removed outlier: 3.590A pdb=" N VAL D2117 " --> pdb=" O ASP D2113 " (cutoff:3.500A) Processing helix chain 'D' and resid 2123 through 2129 removed outlier: 3.603A pdb=" N TYR D2127 " --> pdb=" O GLN D2123 " (cutoff:3.500A) Processing helix chain 'D' and resid 2139 through 2146 Processing helix chain 'D' and resid 2150 through 2155 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.724A pdb=" N ASN E 68 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 69 " --> pdb=" O MET E 65 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.580A pdb=" N THR A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 387 removed outlier: 3.861A pdb=" N CYS A 528 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU A 559 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU A 567 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 735 through 736 removed outlier: 7.098A pdb=" N PHE A1117 " --> pdb=" O GLU A1237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1379 through 1382 Processing sheet with id=AA6, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA7, first strand: chain 'A' and resid 1630 through 1631 Processing sheet with id=AA8, first strand: chain 'A' and resid 1716 through 1719 Processing sheet with id=AA9, first strand: chain 'A' and resid 1847 through 1848 removed outlier: 6.674A pdb=" N PHE A2085 " --> pdb=" O LEU A2092 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1952 through 1961 removed outlier: 7.121A pdb=" N GLY A1980 " --> pdb=" O VAL A1992 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1952 through 1961 Processing sheet with id=AB3, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AB4, first strand: chain 'D' and resid 90 through 94 removed outlier: 3.580A pdb=" N THR D 97 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU D 98 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE D 140 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU D 100 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASP D 142 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU D 102 " --> pdb=" O ASP D 142 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ARG D 144 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE D 104 " --> pdb=" O ARG D 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 258 through 260 Processing sheet with id=AB6, first strand: chain 'D' and resid 385 through 387 removed outlier: 3.862A pdb=" N CYS D 528 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU D 559 " --> pdb=" O GLU D 567 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU D 567 " --> pdb=" O LEU D 559 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 735 through 736 removed outlier: 7.098A pdb=" N PHE D1117 " --> pdb=" O GLU D1237 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1379 through 1382 Processing sheet with id=AB9, first strand: chain 'D' and resid 1548 through 1549 Processing sheet with id=AC1, first strand: chain 'D' and resid 1630 through 1631 Processing sheet with id=AC2, first strand: chain 'D' and resid 1716 through 1719 Processing sheet with id=AC3, first strand: chain 'D' and resid 1847 through 1848 removed outlier: 6.675A pdb=" N PHE D2085 " --> pdb=" O LEU D2092 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1952 through 1961 removed outlier: 7.121A pdb=" N GLY D1980 " --> pdb=" O VAL D1992 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1952 through 1961 Processing sheet with id=AC6, first strand: chain 'E' and resid 50 through 51 1312 hydrogen bonds defined for protein. 3768 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: 11.49 Time building geometry restraints manager: 12.43 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: 8991 1.34 - 1.46: 3928 1.46 - 1.57: 15423 1.57 - 1.69: 26 1.69 - 1.81: 262 Bond restraints: 28630 Sorted by residual: bond pdb=" N ARG D1509 " pdb=" CA ARG D1509 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.03e+00 bond pdb=" N ARG A1509 " pdb=" CA ARG A1509 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.03e+00 bond pdb=" N ILE A1510 " pdb=" CA ILE A1510 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.97e+00 bond pdb=" N ILE D1510 " pdb=" CA ILE D1510 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.84e+00 bond pdb=" N CYS A 55 " pdb=" CA CYS A 55 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.31e-02 5.83e+03 6.76e+00 ... (remaining 28625 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 666 107.08 - 113.81: 16472 113.81 - 120.55: 11115 120.55 - 127.28: 10229 127.28 - 134.01: 250 Bond angle restraints: 38732 Sorted by residual: angle pdb=" N GLU A 56 " pdb=" CA GLU A 56 " pdb=" C GLU A 56 " ideal model delta sigma weight residual 112.54 106.86 5.68 1.22e+00 6.72e-01 2.17e+01 angle pdb=" N GLU D 56 " pdb=" CA GLU D 56 " pdb=" C GLU D 56 " ideal model delta sigma weight residual 112.54 106.89 5.65 1.22e+00 6.72e-01 2.14e+01 angle pdb=" N GLU D 427 " pdb=" CA GLU D 427 " pdb=" C GLU D 427 " ideal model delta sigma weight residual 114.56 108.91 5.65 1.27e+00 6.20e-01 1.98e+01 angle pdb=" N GLU A 427 " pdb=" CA GLU A 427 " pdb=" C GLU A 427 " ideal model delta sigma weight residual 114.56 108.91 5.65 1.27e+00 6.20e-01 1.98e+01 angle pdb=" N THR D1753 " pdb=" CA THR D1753 " pdb=" C THR D1753 " ideal model delta sigma weight residual 109.81 116.46 -6.65 2.21e+00 2.05e-01 9.06e+00 ... (remaining 38727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15591 17.97 - 35.94: 1296 35.94 - 53.92: 296 53.92 - 71.89: 65 71.89 - 89.86: 28 Dihedral angle restraints: 17276 sinusoidal: 6914 harmonic: 10362 Sorted by residual: dihedral pdb=" CA SER A 192 " pdb=" C SER A 192 " pdb=" N ASN A 193 " pdb=" CA ASN A 193 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA SER D 192 " pdb=" C SER D 192 " pdb=" N ASN D 193 " pdb=" CA ASN D 193 " ideal model delta harmonic sigma weight residual 180.00 150.44 29.56 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CB CYS A1691 " pdb=" SG CYS A1691 " pdb=" SG CYS A1776 " pdb=" CB CYS A1776 " ideal model delta sinusoidal sigma weight residual 93.00 142.20 -49.20 1 1.00e+01 1.00e-02 3.33e+01 ... (remaining 17273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3850 0.055 - 0.111: 605 0.111 - 0.166: 40 0.166 - 0.222: 6 0.222 - 0.277: 5 Chirality restraints: 4506 Sorted by residual: chirality pdb=" CA ARG D1509 " pdb=" N ARG D1509 " pdb=" C ARG D1509 " pdb=" CB ARG D1509 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ARG A1509 " pdb=" N ARG A1509 " pdb=" C ARG A1509 " pdb=" CB ARG A1509 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA THR D1753 " pdb=" N THR D1753 " pdb=" C THR D1753 " pdb=" CB THR D1753 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 4503 not shown) Planarity restraints: 4850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A2017 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO A2018 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A2018 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A2018 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D2017 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO D2018 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D2018 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D2018 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 789 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C ARG D 789 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG D 789 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY D 790 " -0.010 2.00e-02 2.50e+03 ... (remaining 4847 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2679 2.74 - 3.28: 29721 3.28 - 3.82: 47219 3.82 - 4.36: 56470 4.36 - 4.90: 94785 Nonbonded interactions: 230874 Sorted by model distance: nonbonded pdb=" OD1 ASP A 769 " pdb=" OG1 THR A 772 " model vdw 2.202 2.440 nonbonded pdb=" OD1 ASP D 769 " pdb=" OG1 THR D 772 " model vdw 2.203 2.440 nonbonded pdb=" OE1 GLU D1381 " pdb="MN MN D2301 " model vdw 2.208 2.320 nonbonded pdb=" OE1 GLU A1381 " pdb="MN MN A2301 " model vdw 2.208 2.320 nonbonded pdb=" OD1 ASP D1420 " pdb=" NH1 ARG D1476 " model vdw 2.218 2.520 ... (remaining 230869 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.430 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 77.140 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.160 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 : 0.003 0.037 28630 Z= 0.165 Angle : 0.583 9.565 38732 Z= 0.320 Chirality : 0.040 0.277 4506 Planarity : 0.003 0.069 4850 Dihedral : 14.558 89.859 10520 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.98 % Favored : 88.88 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: -3.18 (0.13), residues: 3488 helix: -0.84 (0.11), residues: 1692 sheet: -2.04 (0.27), residues: 280 loop : -3.70 (0.14), residues: 1516 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 854 time to evaluate : 3.658 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 outliers start: 93 outliers final: 54 residues processed: 922 average time/residue: 0.4220 time to fit residues: 605.9232 Evaluate side-chains 647 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 593 time to evaluate : 3.291 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.2801 time to fit residues: 32.3806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 chunk 148 optimal weight: 0.0770 chunk 91 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 277 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 321 optimal weight: 4.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 189 HIS A 288 ASN A 348 ASN A 359 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN A 449 GLN A 522 ASN A 546 GLN A 568 GLN A 607 ASN ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1231 HIS A1296 HIS A1297 ASN ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 ASN A1783 ASN A1829 GLN A1837 GLN ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2043 ASN ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN D 61 GLN D 288 ASN D 348 ASN D 359 ASN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN D 522 ASN D 546 GLN D 607 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 HIS ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 GLN D1231 HIS D1296 HIS D1297 ASN ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1503 ASN D1783 ASN D1829 GLN D1837 GLN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2043 ASN E 48 ASN ** E 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 28630 Z= 0.191 Angle : 0.645 12.355 38732 Z= 0.319 Chirality : 0.041 0.157 4506 Planarity : 0.004 0.069 4850 Dihedral : 6.206 74.225 3922 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.32 % Favored : 88.65 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.24 (0.14), residues: 3488 helix: 0.09 (0.12), residues: 1712 sheet: -1.92 (0.29), residues: 294 loop : -3.41 (0.15), residues: 1482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 660 time to evaluate : 3.337 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 outliers start: 107 outliers final: 49 residues processed: 727 average time/residue: 0.3928 time to fit residues: 460.1194 Evaluate side-chains 611 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 562 time to evaluate : 3.203 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.2619 time to fit residues: 28.4104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 322 optimal weight: 0.7980 chunk 347 optimal weight: 0.9990 chunk 286 optimal weight: 0.7980 chunk 319 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 258 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 HIS ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS D 189 HIS ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1231 HIS ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1791 HIS ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 28630 Z= 0.181 Angle : 0.629 13.780 38732 Z= 0.309 Chirality : 0.041 0.207 4506 Planarity : 0.004 0.067 4850 Dihedral : 6.245 75.848 3922 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.85 (0.14), residues: 3488 helix: 0.50 (0.13), residues: 1690 sheet: -1.64 (0.30), residues: 284 loop : -3.30 (0.15), residues: 1514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 647 time to evaluate : 4.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 29 residues processed: 697 average time/residue: 0.3896 time to fit residues: 444.0311 Evaluate side-chains 607 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 578 time to evaluate : 3.353 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2532 time to fit residues: 18.5322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 153 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 323 optimal weight: 0.0470 chunk 342 optimal weight: 0.0770 chunk 168 optimal weight: 0.8980 chunk 306 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN ** D1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 28630 Z= 0.173 Angle : 0.631 12.862 38732 Z= 0.310 Chirality : 0.041 0.224 4506 Planarity : 0.004 0.070 4850 Dihedral : 6.239 75.311 3922 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.71 (0.14), residues: 3488 helix: 0.63 (0.13), residues: 1690 sheet: -1.55 (0.29), residues: 300 loop : -3.28 (0.15), residues: 1498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 627 time to evaluate : 3.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 37 residues processed: 664 average time/residue: 0.3996 time to fit residues: 431.6304 Evaluate side-chains 613 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 576 time to evaluate : 3.294 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2983 time to fit residues: 24.4652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 254 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 chunk 236 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 307 optimal weight: 0.0870 chunk 86 optimal weight: 6.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 HIS ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1954 HIS ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1405 HIS ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN ** D1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1954 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 28630 Z= 0.203 Angle : 0.638 13.806 38732 Z= 0.316 Chirality : 0.041 0.181 4506 Planarity : 0.004 0.076 4850 Dihedral : 6.303 75.083 3922 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.35 % Favored : 88.59 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.61 (0.14), residues: 3488 helix: 0.68 (0.13), residues: 1692 sheet: -1.37 (0.30), residues: 300 loop : -3.21 (0.15), residues: 1496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 621 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 26 residues processed: 655 average time/residue: 0.3929 time to fit residues: 418.9817 Evaluate side-chains 603 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 577 time to evaluate : 3.546 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2698 time to fit residues: 18.4119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 342 optimal weight: 7.9990 chunk 284 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN A 644 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 788 ASN ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 ASN A1272 GLN ** A1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1331 GLN ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2123 GLN B 68 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN D 644 ASN D 717 GLN ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1128 ASN ** D1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1331 GLN ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN D2123 GLN E 68 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 28630 Z= 0.371 Angle : 0.727 13.039 38732 Z= 0.366 Chirality : 0.044 0.182 4506 Planarity : 0.004 0.058 4850 Dihedral : 6.752 74.573 3922 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.53 % Favored : 87.33 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.73 (0.14), residues: 3488 helix: 0.48 (0.13), residues: 1716 sheet: -1.30 (0.32), residues: 282 loop : -3.21 (0.15), residues: 1490 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 609 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 43 residues processed: 651 average time/residue: 0.3833 time to fit residues: 402.3680 Evaluate side-chains 596 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 553 time to evaluate : 3.440 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2642 time to fit residues: 26.3386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 250 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 288 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 chunk 341 optimal weight: 0.0670 chunk 213 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 157 optimal weight: 40.0000 overall best weight: 1.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN A 476 GLN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 GLN ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN ** A1751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN D1738 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 28630 Z= 0.260 Angle : 0.693 12.958 38732 Z= 0.347 Chirality : 0.043 0.240 4506 Planarity : 0.004 0.062 4850 Dihedral : 6.761 74.011 3922 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.70 % Favored : 88.13 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.66 (0.14), residues: 3488 helix: 0.53 (0.13), residues: 1720 sheet: -1.30 (0.32), residues: 282 loop : -3.17 (0.15), residues: 1486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 604 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 27 residues processed: 639 average time/residue: 0.4173 time to fit residues: 431.4951 Evaluate side-chains 582 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 555 time to evaluate : 3.505 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2657 time to fit residues: 18.6245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 67 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 232 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 476 GLN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN A1738 GLN ** A1751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1308 GLN ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN D1738 GLN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 28630 Z= 0.186 Angle : 0.677 13.154 38732 Z= 0.337 Chirality : 0.042 0.206 4506 Planarity : 0.004 0.066 4850 Dihedral : 6.682 73.336 3922 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.01 % Favored : 88.85 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.50 (0.15), residues: 3488 helix: 0.65 (0.13), residues: 1706 sheet: -0.98 (0.33), residues: 260 loop : -3.06 (0.15), residues: 1522 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 603 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 10 residues processed: 616 average time/residue: 0.4104 time to fit residues: 408.1326 Evaluate side-chains 569 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 559 time to evaluate : 3.329 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2670 time to fit residues: 8.9439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 9.9990 chunk 326 optimal weight: 20.0000 chunk 298 optimal weight: 7.9990 chunk 317 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 287 optimal weight: 4.9990 chunk 300 optimal weight: 0.0770 chunk 316 optimal weight: 2.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 ASN A1712 ASN A1713 GLN A1815 GLN ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN D 476 GLN D 607 ASN ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1292 GLN ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN D1713 GLN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 28630 Z= 0.256 Angle : 0.707 12.687 38732 Z= 0.353 Chirality : 0.043 0.212 4506 Planarity : 0.004 0.063 4850 Dihedral : 6.618 72.550 3922 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.50 % Favored : 88.39 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.55 (0.15), residues: 3488 helix: 0.58 (0.13), residues: 1714 sheet: -1.25 (0.32), residues: 282 loop : -3.04 (0.15), residues: 1492 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 575 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 587 average time/residue: 0.4122 time to fit residues: 392.4040 Evaluate side-chains 560 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 546 time to evaluate : 3.319 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2753 time to fit residues: 12.0982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 6.9990 chunk 336 optimal weight: 0.0050 chunk 205 optimal weight: 0.5980 chunk 159 optimal weight: 0.6980 chunk 233 optimal weight: 3.9990 chunk 352 optimal weight: 1.9990 chunk 324 optimal weight: 0.9990 chunk 280 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 216 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN A1713 GLN ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN D 704 HIS ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN D1713 GLN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 28630 Z= 0.191 Angle : 0.695 12.353 38732 Z= 0.345 Chirality : 0.043 0.301 4506 Planarity : 0.004 0.064 4850 Dihedral : 6.492 76.395 3922 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.78 % Favored : 89.11 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.15), residues: 3488 helix: 0.70 (0.13), residues: 1692 sheet: -1.02 (0.34), residues: 244 loop : -2.97 (0.15), residues: 1552 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 585 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 588 average time/residue: 0.4355 time to fit residues: 413.6330 Evaluate side-chains 564 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 556 time to evaluate : 3.497 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2562 time to fit residues: 8.2660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 0.8980 chunk 299 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 258 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 281 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 288 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1713 GLN ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 GLN D 607 ASN ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1711 ASN D1712 ASN D1713 GLN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.175797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145022 restraints weight = 46458.926| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.57 r_work: 0.3707 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 28630 Z= 0.208 Angle : 0.692 12.163 38732 Z= 0.344 Chirality : 0.042 0.271 4506 Planarity : 0.004 0.063 4850 Dihedral : 6.472 76.250 3922 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.89 % Favored : 88.96 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.45 (0.15), residues: 3488 helix: 0.70 (0.13), residues: 1700 sheet: -1.34 (0.32), residues: 272 loop : -2.96 (0.15), residues: 1516 =============================================================================== Job complete usr+sys time: 7776.49 seconds wall clock time: 141 minutes 2.78 seconds (8462.78 seconds total)