Starting phenix.real_space_refine on Sat Apr 13 07:13:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7el9_31177/04_2024/7el9_31177.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7el9_31177/04_2024/7el9_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_2024/7el9_31177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7el9_31177/04_2024/7el9_31177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7el9_31177/04_2024/7el9_31177.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7el9_31177/04_2024/7el9_31177.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 14.65, per 1000 atoms: 0.52 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: 11.18 Conformation dependent library (CDL) restraints added in 4.9 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: 3.85 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: 12.91 Time building geometry restraints manager: 12.16 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: 15615 17.97 - 35.94: 1304 35.94 - 53.92: 312 53.92 - 71.89: 81 71.89 - 89.86: 32 Dihedral angle restraints: 17344 sinusoidal: 6982 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 17341 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: 1.160 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: 5.170 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 81.740 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.180 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.310 ------------------------------------------------------------------------------- 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 : 14.911 89.859 10588 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 % Allowed : 10.32 % Favored : 86.69 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 116 HIS 0.003 0.000 HIS A 472 PHE 0.017 0.001 PHE D 533 TYR 0.007 0.001 TYR D2095 ARG 0.002 0.000 ARG D 209 *********************** 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 : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ASN cc_start: 0.8203 (t0) cc_final: 0.7993 (t0) REVERT: A 341 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7882 (mmmt) REVERT: A 376 ARG cc_start: 0.6935 (mmt180) cc_final: 0.6497 (mmt180) REVERT: A 419 LYS cc_start: 0.8758 (tmtt) cc_final: 0.7675 (tptt) REVERT: A 438 GLN cc_start: 0.6053 (pp30) cc_final: 0.5688 (pp30) REVERT: A 481 PHE cc_start: 0.7392 (t80) cc_final: 0.6926 (t80) REVERT: A 526 ARG cc_start: 0.6994 (mtt180) cc_final: 0.6764 (mtt90) REVERT: A 722 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7293 (mm-30) REVERT: A 1150 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6956 (tm-30) REVERT: A 1538 GLU cc_start: 0.6741 (pm20) cc_final: 0.6505 (pm20) REVERT: A 1623 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8127 (tttt) REVERT: A 1670 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7657 (mtmt) REVERT: A 1717 TRP cc_start: 0.8182 (p-90) cc_final: 0.7695 (p-90) REVERT: A 1907 PHE cc_start: 0.4681 (m-10) cc_final: 0.4437 (m-10) REVERT: A 2108 LEU cc_start: 0.8220 (mt) cc_final: 0.7949 (mt) REVERT: A 2153 LEU cc_start: 0.7657 (mt) cc_final: 0.7425 (mp) REVERT: D 376 ARG cc_start: 0.6973 (mmt180) cc_final: 0.6595 (mmt180) REVERT: D 419 LYS cc_start: 0.8750 (tmtt) cc_final: 0.7576 (tptt) REVERT: D 481 PHE cc_start: 0.7389 (t80) cc_final: 0.6929 (t80) REVERT: D 1111 ASN cc_start: 0.8678 (m-40) cc_final: 0.8421 (p0) REVERT: D 1150 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6913 (tm-30) REVERT: D 1623 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8196 (tttm) REVERT: D 1654 ILE cc_start: 0.7460 (mp) cc_final: 0.7173 (mp) REVERT: D 1717 TRP cc_start: 0.8207 (p-90) cc_final: 0.7762 (p-90) REVERT: D 1907 PHE cc_start: 0.4678 (m-10) cc_final: 0.4430 (m-10) REVERT: D 1978 ASP cc_start: 0.7611 (p0) cc_final: 0.7263 (p0) REVERT: D 2108 LEU cc_start: 0.8172 (mt) cc_final: 0.7925 (mt) REVERT: D 2153 LEU cc_start: 0.7647 (mt) cc_final: 0.7398 (mp) outliers start: 93 outliers final: 54 residues processed: 922 average time/residue: 0.4471 time to fit residues: 630.8141 Evaluate side-chains 652 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 597 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1463 GLN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 791 LYS Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1463 GLN Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1770 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2053 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2151 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 9.9990 chunk 268 optimal weight: 7.9990 chunk 148 optimal weight: 0.1980 chunk 91 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 277 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 321 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 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 607 ASN A 628 ASN A 647 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1231 HIS A1296 HIS A1297 ASN A1331 GLN ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1463 GLN 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** A2123 GLN B 48 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN D 61 GLN D 189 HIS 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 D 647 HIS D 771 GLN ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1111 ASN D1128 ASN D1206 GLN D1231 HIS D1296 HIS D1297 ASN D1331 GLN ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1463 GLN D1503 ASN D1783 ASN D1829 GLN D1833 ASN D1837 GLN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2043 ASN D2123 GLN ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28630 Z= 0.314 Angle : 0.677 10.193 38732 Z= 0.341 Chirality : 0.042 0.158 4506 Planarity : 0.004 0.070 4850 Dihedral : 9.609 77.962 4094 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.13 % Favored : 87.76 % Rotamer: Outliers : 5.31 % Allowed : 18.39 % Favored : 76.30 % 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: -2.28 (0.14), residues: 3488 helix: 0.05 (0.12), residues: 1712 sheet: -1.98 (0.28), residues: 294 loop : -3.41 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A2125 HIS 0.004 0.001 HIS D1791 PHE 0.021 0.002 PHE D 533 TYR 0.019 0.002 TYR D2095 ARG 0.006 0.001 ARG A1507 *********************** 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 815 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 650 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 CYS cc_start: 0.2254 (OUTLIER) cc_final: 0.2053 (t) REVERT: A 268 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7348 (mm-30) REVERT: A 341 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7985 (mmmt) REVERT: A 376 ARG cc_start: 0.7130 (mmt180) cc_final: 0.6689 (mmt180) REVERT: A 401 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8303 (mmtm) REVERT: A 438 GLN cc_start: 0.6151 (pp30) cc_final: 0.5750 (pp30) REVERT: A 1150 GLU cc_start: 0.7533 (tm-30) cc_final: 0.6965 (tm-30) REVERT: A 1463 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7371 (pp30) REVERT: A 1623 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8258 (tttt) REVERT: A 1670 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7866 (mtmt) REVERT: A 1717 TRP cc_start: 0.8349 (p-90) cc_final: 0.7752 (p-90) REVERT: A 1978 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7250 (p0) REVERT: D 376 ARG cc_start: 0.7152 (mmt180) cc_final: 0.6724 (mmt180) REVERT: D 401 LYS cc_start: 0.8701 (mmtm) cc_final: 0.8325 (mmtm) REVERT: D 438 GLN cc_start: 0.6154 (pp30) cc_final: 0.5738 (pp30) REVERT: D 1150 GLU cc_start: 0.7527 (tm-30) cc_final: 0.6926 (tm-30) REVERT: D 1463 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7435 (pp30) REVERT: D 1623 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8219 (tttm) REVERT: D 1654 ILE cc_start: 0.7738 (mp) cc_final: 0.7271 (mp) REVERT: D 1693 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9004 (pp) REVERT: D 1717 TRP cc_start: 0.8367 (p-90) cc_final: 0.7816 (p-90) REVERT: D 1978 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7270 (p0) REVERT: E 65 MET cc_start: 0.8002 (mtm) cc_final: 0.7786 (mtm) outliers start: 165 outliers final: 107 residues processed: 755 average time/residue: 0.4120 time to fit residues: 490.5421 Evaluate side-chains 680 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 566 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1379 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1463 GLN Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1830 ILE Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1978 ASP Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 741 ASN Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1379 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1463 GLN Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1693 LEU Chi-restraints excluded: chain D residue 1722 LYS Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1830 ILE Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1978 ASP Chi-restraints excluded: chain D residue 2028 LEU Chi-restraints excluded: chain D residue 2053 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2104 VAL Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 88 optimal weight: 0.0980 chunk 322 optimal weight: 2.9990 chunk 347 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 319 optimal weight: 0.0060 chunk 109 optimal weight: 0.7980 chunk 258 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS ** A1331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 HIS ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1738 GLN ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS D 288 ASN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1231 HIS D1405 HIS ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1738 GLN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN E 55 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1960 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= 0.168 Angle : 0.614 10.132 38732 Z= 0.305 Chirality : 0.041 0.235 4506 Planarity : 0.004 0.040 4850 Dihedral : 9.355 75.737 4071 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.69 % Favored : 89.28 % Rotamer: Outliers : 4.47 % Allowed : 20.13 % Favored : 75.40 % 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: -1.82 (0.14), residues: 3488 helix: 0.52 (0.13), residues: 1698 sheet: -1.63 (0.28), residues: 294 loop : -3.31 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1549 HIS 0.010 0.001 HIS A1751 PHE 0.024 0.001 PHE A 475 TYR 0.018 0.001 TYR A 214 ARG 0.008 0.000 ARG D 231 *********************** 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 777 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 638 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6983 (pttm) REVERT: A 268 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7286 (mm-30) REVERT: A 350 LEU cc_start: 0.9421 (mm) cc_final: 0.9201 (mm) REVERT: A 376 ARG cc_start: 0.6943 (mmt180) cc_final: 0.6629 (mmt180) REVERT: A 401 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8340 (mmtm) REVERT: A 413 TRP cc_start: 0.8238 (t60) cc_final: 0.7836 (t60) REVERT: A 438 GLN cc_start: 0.6083 (pp30) cc_final: 0.5630 (pp30) REVERT: A 1141 MET cc_start: 0.8273 (mmp) cc_final: 0.7633 (mmt) REVERT: A 1148 PHE cc_start: 0.9096 (t80) cc_final: 0.8849 (t80) REVERT: A 1150 GLU cc_start: 0.7504 (tm-30) cc_final: 0.6966 (tm-30) REVERT: A 1623 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8153 (tttt) REVERT: A 1717 TRP cc_start: 0.8259 (p-90) cc_final: 0.7685 (p-90) REVERT: A 1978 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7093 (p0) REVERT: D 227 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6863 (pttm) REVERT: D 350 LEU cc_start: 0.9406 (mm) cc_final: 0.9194 (mm) REVERT: D 376 ARG cc_start: 0.6929 (mmt180) cc_final: 0.6601 (mmt180) REVERT: D 401 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8336 (mmtm) REVERT: D 438 GLN cc_start: 0.6082 (pp30) cc_final: 0.5630 (pp30) REVERT: D 697 LEU cc_start: 0.8397 (tp) cc_final: 0.8164 (tp) REVERT: D 713 ARG cc_start: 0.8172 (ttt-90) cc_final: 0.7935 (ttt-90) REVERT: D 1111 ASN cc_start: 0.8468 (m110) cc_final: 0.8260 (p0) REVERT: D 1116 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8630 (tttp) REVERT: D 1141 MET cc_start: 0.8260 (mmp) cc_final: 0.7642 (mmt) REVERT: D 1150 GLU cc_start: 0.7507 (tm-30) cc_final: 0.6951 (tm-30) REVERT: D 1536 CYS cc_start: 0.6774 (m) cc_final: 0.6218 (t) REVERT: D 1623 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8147 (tttm) REVERT: D 1693 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8893 (pp) REVERT: D 1717 TRP cc_start: 0.8258 (p-90) cc_final: 0.7727 (p-90) REVERT: D 1978 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7207 (p0) outliers start: 139 outliers final: 82 residues processed: 731 average time/residue: 0.3976 time to fit residues: 466.1370 Evaluate side-chains 657 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 570 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1830 ILE Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1978 ASP Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1524 ASP Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1693 LEU Chi-restraints excluded: chain D residue 1722 LYS Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1830 ILE Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1978 ASP Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 51 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 323 optimal weight: 0.0670 chunk 342 optimal weight: 1.9990 chunk 168 optimal weight: 0.3980 chunk 306 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN A 644 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** 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** A1738 GLN A1954 HIS ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN D 644 ASN ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1738 GLN D1954 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28630 Z= 0.184 Angle : 0.620 10.070 38732 Z= 0.308 Chirality : 0.041 0.222 4506 Planarity : 0.004 0.043 4850 Dihedral : 9.116 75.255 4047 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.32 % Favored : 88.62 % Rotamer: Outliers : 4.79 % Allowed : 20.77 % Favored : 74.44 % 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: -1.67 (0.14), residues: 3488 helix: 0.65 (0.13), residues: 1694 sheet: -1.45 (0.29), residues: 294 loop : -3.27 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A2125 HIS 0.009 0.001 HIS D1954 PHE 0.026 0.001 PHE A 104 TYR 0.018 0.001 TYR A 558 ARG 0.006 0.000 ARG D 231 *********************** 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 750 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 601 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7161 (pttm) REVERT: A 350 LEU cc_start: 0.9428 (mm) cc_final: 0.9193 (mm) REVERT: A 376 ARG cc_start: 0.6969 (mmt180) cc_final: 0.6679 (mmt180) REVERT: A 401 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8382 (mmtm) REVERT: A 438 GLN cc_start: 0.6196 (pp30) cc_final: 0.5728 (pp30) REVERT: A 595 MET cc_start: 0.8308 (mmm) cc_final: 0.8074 (mtt) REVERT: A 764 LEU cc_start: 0.9024 (tp) cc_final: 0.8785 (mp) REVERT: A 1121 TYR cc_start: 0.8327 (p90) cc_final: 0.8102 (p90) REVERT: A 1141 MET cc_start: 0.8306 (mmp) cc_final: 0.7694 (mmt) REVERT: A 1150 GLU cc_start: 0.7533 (tm-30) cc_final: 0.6982 (tm-30) REVERT: A 1623 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8201 (tttm) REVERT: A 1717 TRP cc_start: 0.8279 (p-90) cc_final: 0.7726 (p-90) REVERT: A 1751 HIS cc_start: 0.7037 (m170) cc_final: 0.6817 (m90) REVERT: A 1794 LYS cc_start: 0.8755 (mtpp) cc_final: 0.8440 (mtmt) REVERT: A 1978 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7213 (p0) REVERT: D 227 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7018 (pttm) REVERT: D 268 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7361 (mm-30) REVERT: D 350 LEU cc_start: 0.9393 (mm) cc_final: 0.9160 (mm) REVERT: D 401 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8373 (mmtm) REVERT: D 438 GLN cc_start: 0.6151 (pp30) cc_final: 0.5683 (pp30) REVERT: D 595 MET cc_start: 0.8300 (mmm) cc_final: 0.8061 (mtt) REVERT: D 697 LEU cc_start: 0.8407 (tp) cc_final: 0.8139 (tp) REVERT: D 713 ARG cc_start: 0.8172 (ttt-90) cc_final: 0.7949 (ttt-90) REVERT: D 1111 ASN cc_start: 0.8629 (m110) cc_final: 0.8266 (p0) REVERT: D 1141 MET cc_start: 0.8290 (mmp) cc_final: 0.7675 (mmt) REVERT: D 1150 GLU cc_start: 0.7524 (tm-30) cc_final: 0.6948 (tm-30) REVERT: D 1623 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8174 (tttm) REVERT: D 1693 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8886 (pp) REVERT: D 1717 TRP cc_start: 0.8276 (p-90) cc_final: 0.7789 (p-90) REVERT: D 1794 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8500 (mtmt) REVERT: D 1978 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7221 (p0) outliers start: 149 outliers final: 107 residues processed: 701 average time/residue: 0.3956 time to fit residues: 443.8849 Evaluate side-chains 681 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 569 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1524 ASP Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1830 ILE Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1978 ASP Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 767 THR Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1208 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1693 LEU Chi-restraints excluded: chain D residue 1722 LYS Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1830 ILE Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1978 ASP Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 254 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 236 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 307 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 ASN ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2123 GLN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1871 GLN ** D2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28630 Z= 0.256 Angle : 0.647 14.617 38732 Z= 0.325 Chirality : 0.042 0.187 4506 Planarity : 0.004 0.048 4850 Dihedral : 9.261 75.753 4046 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.93 % Favored : 87.90 % Rotamer: Outliers : 5.21 % Allowed : 21.96 % Favored : 72.83 % 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: -1.60 (0.15), residues: 3488 helix: 0.66 (0.13), residues: 1706 sheet: -1.13 (0.31), residues: 280 loop : -3.24 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 43 HIS 0.005 0.001 HIS D1751 PHE 0.025 0.002 PHE A 475 TYR 0.018 0.001 TYR D2095 ARG 0.004 0.000 ARG D 231 *********************** 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 757 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 595 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7241 (pttm) REVERT: A 350 LEU cc_start: 0.9440 (mm) cc_final: 0.9193 (mm) REVERT: A 376 ARG cc_start: 0.7059 (mmt180) cc_final: 0.6842 (mmt180) REVERT: A 401 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8385 (mmtm) REVERT: A 438 GLN cc_start: 0.6172 (pp30) cc_final: 0.5696 (pp30) REVERT: A 712 ASP cc_start: 0.7599 (t0) cc_final: 0.7375 (t0) REVERT: A 1141 MET cc_start: 0.8297 (mmp) cc_final: 0.7754 (mmt) REVERT: A 1150 GLU cc_start: 0.7561 (tm-30) cc_final: 0.6987 (tm-30) REVERT: A 1389 MET cc_start: 0.8089 (ptm) cc_final: 0.7346 (ptm) REVERT: A 1623 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8224 (tttm) REVERT: A 1670 LYS cc_start: 0.8174 (mttt) cc_final: 0.7958 (mttp) REVERT: A 1717 TRP cc_start: 0.8325 (p-90) cc_final: 0.7769 (p-90) REVERT: A 1734 ASN cc_start: 0.8648 (p0) cc_final: 0.8431 (p0) REVERT: A 1751 HIS cc_start: 0.7085 (m170) cc_final: 0.6869 (m90) REVERT: A 1794 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8554 (mtmt) REVERT: A 1978 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7201 (p0) REVERT: B 36 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6473 (ptt90) REVERT: D 350 LEU cc_start: 0.9429 (mm) cc_final: 0.9162 (mm) REVERT: D 401 LYS cc_start: 0.8811 (mmtm) cc_final: 0.8412 (mmtm) REVERT: D 438 GLN cc_start: 0.6065 (pp30) cc_final: 0.5600 (pp30) REVERT: D 713 ARG cc_start: 0.8196 (ttt-90) cc_final: 0.7987 (ttt-90) REVERT: D 1111 ASN cc_start: 0.8492 (m110) cc_final: 0.8242 (p0) REVERT: D 1141 MET cc_start: 0.8268 (mmp) cc_final: 0.7722 (mmt) REVERT: D 1150 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6943 (tm-30) REVERT: D 1623 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8231 (tttm) REVERT: D 1693 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8994 (pp) REVERT: D 1717 TRP cc_start: 0.8313 (p-90) cc_final: 0.7801 (p-90) REVERT: D 1978 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7093 (p0) outliers start: 162 outliers final: 124 residues processed: 694 average time/residue: 0.4039 time to fit residues: 449.0569 Evaluate side-chains 695 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 566 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 741 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1524 ASP Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1830 ILE Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1978 ASP Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 741 ASN Chi-restraints excluded: chain D residue 767 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1208 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1524 ASP Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1693 LEU Chi-restraints excluded: chain D residue 1722 LYS Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1830 ILE Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1978 ASP Chi-restraints excluded: chain D residue 1994 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2079 VAL Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 342 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 348 ASN A 384 GLN A 476 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN ** A1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN D 476 GLN ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28630 Z= 0.247 Angle : 0.653 12.776 38732 Z= 0.326 Chirality : 0.041 0.218 4506 Planarity : 0.004 0.057 4850 Dihedral : 9.259 75.134 4046 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.10 % Favored : 87.76 % Rotamer: Outliers : 5.27 % Allowed : 22.60 % Favored : 72.12 % 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: -1.58 (0.15), residues: 3488 helix: 0.68 (0.13), residues: 1712 sheet: -1.35 (0.30), residues: 302 loop : -3.21 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 43 HIS 0.008 0.001 HIS D1751 PHE 0.031 0.002 PHE A 104 TYR 0.022 0.001 TYR D 214 ARG 0.003 0.000 ARG A 459 *********************** 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 775 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 611 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7706 (ptpt) cc_final: 0.7175 (pttm) REVERT: A 268 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7330 (mm-30) REVERT: A 350 LEU cc_start: 0.9437 (mm) cc_final: 0.9179 (mm) REVERT: A 401 LYS cc_start: 0.8831 (mmtm) cc_final: 0.8455 (mmtm) REVERT: A 438 GLN cc_start: 0.6224 (pp30) cc_final: 0.5729 (pp30) REVERT: A 1141 MET cc_start: 0.8290 (mmt) cc_final: 0.7770 (mmt) REVERT: A 1150 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7030 (tm-30) REVERT: A 1623 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8203 (tttm) REVERT: A 1670 LYS cc_start: 0.8168 (mttt) cc_final: 0.7960 (mttp) REVERT: A 1717 TRP cc_start: 0.8321 (p-90) cc_final: 0.7767 (p-90) REVERT: A 1734 ASN cc_start: 0.8641 (p0) cc_final: 0.8425 (p0) REVERT: A 1751 HIS cc_start: 0.7131 (m170) cc_final: 0.6879 (m90) REVERT: A 1978 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7223 (p0) REVERT: D 350 LEU cc_start: 0.9426 (mm) cc_final: 0.9160 (mm) REVERT: D 401 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8452 (mmtm) REVERT: D 438 GLN cc_start: 0.6172 (pp30) cc_final: 0.5674 (pp30) REVERT: D 713 ARG cc_start: 0.8217 (ttt-90) cc_final: 0.7993 (ttt-90) REVERT: D 764 LEU cc_start: 0.8941 (tp) cc_final: 0.8731 (mp) REVERT: D 1111 ASN cc_start: 0.8508 (m110) cc_final: 0.8247 (p0) REVERT: D 1141 MET cc_start: 0.8249 (mmp) cc_final: 0.7730 (mmt) REVERT: D 1143 ARG cc_start: 0.7293 (ttp-110) cc_final: 0.7056 (ttp-110) REVERT: D 1150 GLU cc_start: 0.7545 (tm-30) cc_final: 0.6977 (tm-30) REVERT: D 1623 LYS cc_start: 0.8792 (ttmt) cc_final: 0.8187 (tttm) REVERT: D 1693 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8969 (pp) REVERT: D 1717 TRP cc_start: 0.8295 (p-90) cc_final: 0.7798 (p-90) REVERT: D 1794 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8506 (mtmt) REVERT: D 1978 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7077 (p0) outliers start: 164 outliers final: 129 residues processed: 714 average time/residue: 0.4130 time to fit residues: 469.7385 Evaluate side-chains 706 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 574 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 741 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1524 ASP Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1830 ILE Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1978 ASP Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 473 LYS Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 741 ASN Chi-restraints excluded: chain D residue 767 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1524 ASP Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1578 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1693 LEU Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1830 ILE Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1978 ASP Chi-restraints excluded: chain D residue 1994 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2079 VAL Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2104 VAL Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 288 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 341 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 157 optimal weight: 40.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 GLN ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 HIS ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28630 Z= 0.288 Angle : 0.679 11.445 38732 Z= 0.341 Chirality : 0.043 0.203 4506 Planarity : 0.004 0.061 4850 Dihedral : 9.302 75.756 4044 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.41 % Favored : 87.44 % Rotamer: Outliers : 5.53 % Allowed : 22.80 % Favored : 71.67 % 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: -1.60 (0.15), residues: 3488 helix: 0.61 (0.13), residues: 1716 sheet: -1.34 (0.30), residues: 302 loop : -3.17 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 43 HIS 0.008 0.001 HIS D1751 PHE 0.024 0.002 PHE A1834 TYR 0.021 0.002 TYR D2095 ARG 0.004 0.000 ARG D 459 *********************** 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 753 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 581 time to evaluate : 3.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 LEU cc_start: 0.9447 (mm) cc_final: 0.9199 (mm) REVERT: A 401 LYS cc_start: 0.8851 (mmtm) cc_final: 0.8462 (mmtm) REVERT: A 438 GLN cc_start: 0.6285 (pp30) cc_final: 0.5683 (pp30) REVERT: A 440 ASP cc_start: 0.7119 (t0) cc_final: 0.6909 (t70) REVERT: A 1121 TYR cc_start: 0.8619 (p90) cc_final: 0.8388 (p90) REVERT: A 1141 MET cc_start: 0.8338 (mmt) cc_final: 0.7862 (mmp) REVERT: A 1150 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7020 (tm-30) REVERT: A 1623 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8103 (tttt) REVERT: A 1717 TRP cc_start: 0.8316 (p-90) cc_final: 0.7783 (p-90) REVERT: A 1734 ASN cc_start: 0.8661 (p0) cc_final: 0.8405 (p0) REVERT: A 1751 HIS cc_start: 0.7094 (m170) cc_final: 0.6860 (m90) REVERT: A 1794 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8535 (mtmt) REVERT: A 1978 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7064 (p0) REVERT: A 2028 LEU cc_start: 0.2168 (OUTLIER) cc_final: 0.1813 (tm) REVERT: D 350 LEU cc_start: 0.9437 (mm) cc_final: 0.9197 (mm) REVERT: D 401 LYS cc_start: 0.8819 (mmtm) cc_final: 0.8464 (mmtm) REVERT: D 438 GLN cc_start: 0.6318 (pp30) cc_final: 0.5773 (pp30) REVERT: D 764 LEU cc_start: 0.8994 (tp) cc_final: 0.8762 (mp) REVERT: D 1111 ASN cc_start: 0.8540 (m110) cc_final: 0.8259 (p0) REVERT: D 1141 MET cc_start: 0.8343 (mmp) cc_final: 0.7905 (mmp) REVERT: D 1150 GLU cc_start: 0.7533 (tm-30) cc_final: 0.6959 (tm-30) REVERT: D 1623 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8125 (tttt) REVERT: D 1693 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8956 (pp) REVERT: D 1717 TRP cc_start: 0.8301 (p-90) cc_final: 0.7819 (p-90) REVERT: D 1751 HIS cc_start: 0.7163 (m170) cc_final: 0.6952 (m170) REVERT: D 1794 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8502 (mtmt) REVERT: D 1978 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.6906 (p0) REVERT: D 2028 LEU cc_start: 0.1906 (OUTLIER) cc_final: 0.1597 (tm) outliers start: 172 outliers final: 138 residues processed: 688 average time/residue: 0.4024 time to fit residues: 440.3246 Evaluate side-chains 697 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 554 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1182 ASP Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1524 ASP Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1830 ILE Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1978 ASP Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2079 VAL Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 741 ASN Chi-restraints excluded: chain D residue 767 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1524 ASP Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1578 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1693 LEU Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1773 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1830 ILE Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1978 ASP Chi-restraints excluded: chain D residue 1994 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2028 LEU Chi-restraints excluded: chain D residue 2051 LEU Chi-restraints excluded: chain D residue 2079 VAL Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2104 VAL Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 268 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN A1738 GLN ** A1886 ASN ** 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** D1292 GLN ** D1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN ** D1751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3049 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= 0.210 Angle : 0.662 10.893 38732 Z= 0.331 Chirality : 0.042 0.223 4506 Planarity : 0.004 0.063 4850 Dihedral : 9.088 76.049 4036 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.55 % Favored : 88.27 % Rotamer: Outliers : 4.76 % Allowed : 23.79 % Favored : 71.45 % 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: -1.52 (0.15), residues: 3488 helix: 0.66 (0.13), residues: 1720 sheet: -1.30 (0.30), residues: 302 loop : -3.12 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 413 HIS 0.007 0.001 HIS D1751 PHE 0.024 0.002 PHE D1511 TYR 0.021 0.001 TYR D 214 ARG 0.004 0.000 ARG D 459 *********************** 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 743 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 595 time to evaluate : 3.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 LEU cc_start: 0.9436 (mm) cc_final: 0.9185 (mm) REVERT: A 401 LYS cc_start: 0.8819 (mmtm) cc_final: 0.8432 (mmtm) REVERT: A 438 GLN cc_start: 0.6299 (pp30) cc_final: 0.5748 (pp30) REVERT: A 1121 TYR cc_start: 0.8540 (p90) cc_final: 0.8302 (p90) REVERT: A 1141 MET cc_start: 0.8317 (mmt) cc_final: 0.7916 (mmp) REVERT: A 1150 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6955 (tm-30) REVERT: A 1623 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8109 (tttt) REVERT: A 1717 TRP cc_start: 0.8277 (p-90) cc_final: 0.7785 (p-90) REVERT: A 1734 ASN cc_start: 0.8628 (p0) cc_final: 0.8375 (p0) REVERT: A 1751 HIS cc_start: 0.7138 (m170) cc_final: 0.6893 (m90) REVERT: A 1794 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8544 (mtmt) REVERT: A 1978 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.6776 (p0) REVERT: A 2028 LEU cc_start: 0.2065 (OUTLIER) cc_final: 0.1721 (tm) REVERT: D 116 TRP cc_start: 0.5673 (OUTLIER) cc_final: 0.3981 (t60) REVERT: D 120 MET cc_start: 0.3546 (mmm) cc_final: 0.2896 (mtt) REVERT: D 350 LEU cc_start: 0.9452 (mm) cc_final: 0.9175 (mm) REVERT: D 401 LYS cc_start: 0.8820 (mmtm) cc_final: 0.8497 (mmtm) REVERT: D 438 GLN cc_start: 0.6299 (pp30) cc_final: 0.5818 (pp30) REVERT: D 697 LEU cc_start: 0.8394 (tp) cc_final: 0.8172 (tp) REVERT: D 1111 ASN cc_start: 0.8508 (m110) cc_final: 0.8242 (p0) REVERT: D 1141 MET cc_start: 0.8295 (mmt) cc_final: 0.7888 (mmp) REVERT: D 1150 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6969 (tm-30) REVERT: D 1268 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: D 1588 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7405 (tttp) REVERT: D 1623 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8103 (tttm) REVERT: D 1693 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8948 (pp) REVERT: D 1717 TRP cc_start: 0.8273 (p-90) cc_final: 0.7804 (p-90) REVERT: D 1734 ASN cc_start: 0.8624 (p0) cc_final: 0.8381 (p0) REVERT: D 1751 HIS cc_start: 0.6995 (m170) cc_final: 0.6751 (m170) REVERT: D 1794 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8507 (mtmt) REVERT: D 1978 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.6766 (p0) REVERT: D 2028 LEU cc_start: 0.2053 (OUTLIER) cc_final: 0.1721 (tm) outliers start: 148 outliers final: 124 residues processed: 692 average time/residue: 0.4011 time to fit residues: 443.1648 Evaluate side-chains 700 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 569 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1182 ASP Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1425 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1978 ASP Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 767 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1135 ASP Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1268 GLU Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1425 GLN Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1693 LEU Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1773 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1978 ASP Chi-restraints excluded: chain D residue 1994 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2028 LEU Chi-restraints excluded: chain D residue 2051 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2104 VAL Chi-restraints excluded: chain D residue 2128 LEU Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 5.9990 chunk 326 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 chunk 317 optimal weight: 0.0470 chunk 191 optimal weight: 10.0000 chunk 138 optimal weight: 0.5980 chunk 249 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 287 optimal weight: 0.5980 chunk 300 optimal weight: 0.9980 chunk 316 optimal weight: 6.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 GLN ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN 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** D1308 GLN ** D1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN ** D1751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1791 HIS ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28630 Z= 0.182 Angle : 0.663 11.013 38732 Z= 0.329 Chirality : 0.041 0.182 4506 Planarity : 0.004 0.065 4850 Dihedral : 8.934 75.764 4036 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.44 % Favored : 88.45 % Rotamer: Outliers : 4.21 % Allowed : 24.69 % Favored : 71.09 % 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: -1.47 (0.15), residues: 3488 helix: 0.67 (0.13), residues: 1720 sheet: -1.35 (0.31), residues: 288 loop : -3.03 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1351 HIS 0.008 0.001 HIS D1751 PHE 0.031 0.002 PHE A1511 TYR 0.020 0.001 TYR D 214 ARG 0.007 0.000 ARG A 713 *********************** 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 730 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 599 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7956 (pm20) cc_final: 0.7745 (pp20) REVERT: A 268 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7325 (mm-30) REVERT: A 350 LEU cc_start: 0.9424 (mm) cc_final: 0.9165 (mm) REVERT: A 401 LYS cc_start: 0.8716 (mmtm) cc_final: 0.8348 (mmtm) REVERT: A 438 GLN cc_start: 0.6300 (pp30) cc_final: 0.6023 (pp30) REVERT: A 697 LEU cc_start: 0.8407 (tp) cc_final: 0.8177 (tp) REVERT: A 1121 TYR cc_start: 0.8364 (p90) cc_final: 0.8137 (p90) REVERT: A 1141 MET cc_start: 0.8268 (mmt) cc_final: 0.7978 (mmp) REVERT: A 1150 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7000 (tm-30) REVERT: A 1623 LYS cc_start: 0.8714 (ttmt) cc_final: 0.7989 (tttt) REVERT: A 1654 ILE cc_start: 0.7876 (mp) cc_final: 0.7517 (mp) REVERT: A 1717 TRP cc_start: 0.8275 (p-90) cc_final: 0.7762 (p-90) REVERT: A 1734 ASN cc_start: 0.8601 (p0) cc_final: 0.8313 (p0) REVERT: A 1751 HIS cc_start: 0.7146 (m170) cc_final: 0.6913 (m90) REVERT: A 1794 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8489 (mtmt) REVERT: A 1978 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.6837 (p0) REVERT: A 2028 LEU cc_start: 0.1978 (OUTLIER) cc_final: 0.1650 (tm) REVERT: D 216 GLU cc_start: 0.7982 (pm20) cc_final: 0.7762 (pp20) REVERT: D 268 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7325 (mm-30) REVERT: D 350 LEU cc_start: 0.9454 (mm) cc_final: 0.9174 (mm) REVERT: D 401 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8472 (mmtm) REVERT: D 438 GLN cc_start: 0.6106 (pp30) cc_final: 0.5778 (pp30) REVERT: D 764 LEU cc_start: 0.8932 (tp) cc_final: 0.8725 (mp) REVERT: D 1111 ASN cc_start: 0.8485 (m110) cc_final: 0.8220 (p0) REVERT: D 1150 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6983 (tm-30) REVERT: D 1268 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: D 1623 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8026 (tttm) REVERT: D 1654 ILE cc_start: 0.7885 (mp) cc_final: 0.7598 (mp) REVERT: D 1693 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8897 (pp) REVERT: D 1717 TRP cc_start: 0.8253 (p-90) cc_final: 0.7795 (p-90) REVERT: D 1751 HIS cc_start: 0.6813 (m170) cc_final: 0.6552 (m170) REVERT: D 1794 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8427 (mtmt) REVERT: D 1978 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7192 (p0) REVERT: D 2028 LEU cc_start: 0.1915 (OUTLIER) cc_final: 0.1606 (tm) outliers start: 131 outliers final: 120 residues processed: 684 average time/residue: 0.4057 time to fit residues: 443.3182 Evaluate side-chains 680 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 554 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 741 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1182 ASP Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1557 ASP Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1978 ASP Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 473 LYS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 767 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1135 ASP Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1268 GLU Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1557 ASP Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1693 LEU Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1773 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1978 ASP Chi-restraints excluded: chain D residue 1994 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2028 LEU Chi-restraints excluded: chain D residue 2051 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2128 LEU Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 0.0670 chunk 336 optimal weight: 0.3980 chunk 205 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 352 optimal weight: 4.9990 chunk 324 optimal weight: 9.9990 chunk 280 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 216 optimal weight: 0.1980 chunk 172 optimal weight: 0.0870 overall best weight: 0.2696 ------------------------------------------------------------------------------- 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 ASN ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN ** D 483 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** D1272 GLN D1429 ASN D1712 ASN ** D2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28630 Z= 0.173 Angle : 0.672 10.748 38732 Z= 0.332 Chirality : 0.042 0.261 4506 Planarity : 0.004 0.063 4850 Dihedral : 8.788 75.337 4034 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.01 % Favored : 88.93 % Rotamer: Outliers : 3.73 % Allowed : 25.66 % Favored : 70.61 % 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: -1.41 (0.15), residues: 3488 helix: 0.75 (0.13), residues: 1704 sheet: -1.30 (0.31), residues: 288 loop : -3.01 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1351 HIS 0.009 0.001 HIS D1751 PHE 0.028 0.002 PHE D 475 TYR 0.021 0.001 TYR D 214 ARG 0.004 0.000 ARG D 459 ********************** 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 696 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 580 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 350 LEU cc_start: 0.9424 (mm) cc_final: 0.9160 (mm) REVERT: A 401 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8357 (mmtm) REVERT: A 595 MET cc_start: 0.8179 (mmm) cc_final: 0.7912 (mtt) REVERT: A 697 LEU cc_start: 0.8400 (tp) cc_final: 0.8175 (tp) REVERT: A 1150 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6953 (tm-30) REVERT: A 1513 GLU cc_start: 0.7536 (mp0) cc_final: 0.7099 (mp0) REVERT: A 1623 LYS cc_start: 0.8693 (ttmt) cc_final: 0.7981 (tttt) REVERT: A 1654 ILE cc_start: 0.7838 (mp) cc_final: 0.7485 (mp) REVERT: A 1717 TRP cc_start: 0.8266 (p-90) cc_final: 0.7774 (p-90) REVERT: A 1751 HIS cc_start: 0.7077 (m170) cc_final: 0.6839 (m90) REVERT: A 1782 MET cc_start: 0.8151 (mmm) cc_final: 0.7902 (ppp) REVERT: A 1978 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7095 (p0) REVERT: A 2028 LEU cc_start: 0.1787 (OUTLIER) cc_final: 0.1480 (tm) REVERT: B 65 MET cc_start: 0.7817 (mtm) cc_final: 0.7571 (mtm) REVERT: D 216 GLU cc_start: 0.7966 (pm20) cc_final: 0.7706 (pp20) REVERT: D 268 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7322 (mm-30) REVERT: D 350 LEU cc_start: 0.9440 (mm) cc_final: 0.9152 (mm) REVERT: D 401 LYS cc_start: 0.8782 (mmtm) cc_final: 0.8464 (mmtm) REVERT: D 438 GLN cc_start: 0.6117 (pp30) cc_final: 0.5819 (pp30) REVERT: D 1111 ASN cc_start: 0.8467 (m110) cc_final: 0.8194 (p0) REVERT: D 1150 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6967 (tm-30) REVERT: D 1623 LYS cc_start: 0.8689 (ttmt) cc_final: 0.7984 (tttt) REVERT: D 1654 ILE cc_start: 0.7829 (mp) cc_final: 0.7485 (mp) REVERT: D 1717 TRP cc_start: 0.8235 (p-90) cc_final: 0.7760 (p-90) REVERT: D 1751 HIS cc_start: 0.6771 (m170) cc_final: 0.6497 (m170) REVERT: D 1794 LYS cc_start: 0.8664 (mtpp) cc_final: 0.8456 (mtmt) REVERT: D 1978 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7210 (p0) REVERT: D 2028 LEU cc_start: 0.1590 (OUTLIER) cc_final: 0.1292 (tm) outliers start: 116 outliers final: 102 residues processed: 652 average time/residue: 0.4116 time to fit residues: 427.6403 Evaluate side-chains 664 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 558 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1182 ASP Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1425 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1978 ASP Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 473 LYS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 767 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1135 ASP Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1429 ASN Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1773 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1978 ASP Chi-restraints excluded: chain D residue 1994 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2017 LEU Chi-restraints excluded: chain D residue 2028 LEU Chi-restraints excluded: chain D residue 2051 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2128 LEU Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 6.9990 chunk 299 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 281 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 288 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN ** D 483 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** D1712 ASN D1738 GLN ** D1751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.177019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.144393 restraints weight = 46288.392| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.81 r_work: 0.3715 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.218 28630 Z= 0.226 Angle : 0.780 59.127 38732 Z= 0.414 Chirality : 0.043 0.495 4506 Planarity : 0.004 0.079 4850 Dihedral : 8.786 75.331 4034 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.95 % Favored : 88.99 % Rotamer: Outliers : 3.70 % Allowed : 25.92 % Favored : 70.39 % 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: -1.41 (0.15), residues: 3488 helix: 0.75 (0.13), residues: 1704 sheet: -1.30 (0.31), residues: 288 loop : -3.00 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1351 HIS 0.007 0.001 HIS D1751 PHE 0.027 0.002 PHE D 475 TYR 0.019 0.001 TYR D 214 ARG 0.007 0.000 ARG A 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8275.23 seconds wall clock time: 150 minutes 57.19 seconds (9057.19 seconds total)