Starting phenix.real_space_refine on Sun Mar 24 11:20:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7s_12755/03_2024/7o7s_12755.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7s_12755/03_2024/7o7s_12755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7s_12755/03_2024/7o7s_12755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7s_12755/03_2024/7o7s_12755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7s_12755/03_2024/7o7s_12755.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7s_12755/03_2024/7o7s_12755.pdb" } resolution = 4.3 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 ------------------------------------------------------------------------------- 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= 0.003 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: 4 Type Number sf(0) Gaussians S 177 5.16 5 C 26326 2.51 5 N 6891 2.21 5 O 8072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 153": "OE1" <-> "OE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A GLU 1096": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 640": "OE1" <-> "OE2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 753": "OE1" <-> "OE2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B GLU 878": "OE1" <-> "OE2" Residue "B GLU 886": "OE1" <-> "OE2" Residue "B GLU 892": "OE1" <-> "OE2" Residue "B GLU 1030": "OE1" <-> "OE2" Residue "B GLU 1184": "OE1" <-> "OE2" Residue "B GLU 1205": "OE1" <-> "OE2" Residue "B GLU 1335": "OE1" <-> "OE2" Residue "B GLU 1337": "OE1" <-> "OE2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C GLU 671": "OE1" <-> "OE2" Residue "C GLU 753": "OE1" <-> "OE2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C GLU 806": "OE1" <-> "OE2" Residue "C GLU 829": "OE1" <-> "OE2" Residue "C GLU 878": "OE1" <-> "OE2" Residue "C GLU 881": "OE1" <-> "OE2" Residue "C GLU 908": "OE1" <-> "OE2" Residue "C GLU 913": "OE1" <-> "OE2" Residue "C TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1137": "OE1" <-> "OE2" Residue "C GLU 1184": "OE1" <-> "OE2" Residue "C GLU 1198": "OE1" <-> "OE2" Residue "C GLU 1205": "OE1" <-> "OE2" Residue "C GLU 1307": "OE1" <-> "OE2" Residue "C GLU 1311": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D GLU 281": "OE1" <-> "OE2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 401": "OE1" <-> "OE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D GLU 640": "OE1" <-> "OE2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D GLU 729": "OE1" <-> "OE2" Residue "D GLU 795": "OE1" <-> "OE2" Residue "D GLU 806": "OE1" <-> "OE2" Residue "D GLU 829": "OE1" <-> "OE2" Residue "D GLU 906": "OE1" <-> "OE2" Residue "D GLU 930": "OE1" <-> "OE2" Residue "D GLU 942": "OE1" <-> "OE2" Residue "D GLU 1060": "OE1" <-> "OE2" Residue "D GLU 1337": "OE1" <-> "OE2" Residue "D GLU 1338": "OE1" <-> "OE2" Residue "D GLU 1454": "OE1" <-> "OE2" Residue "D GLU 1457": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41466 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 9958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1276, 9958 Classifications: {'peptide': 1276} Link IDs: {'PTRANS': 66, 'TRANS': 1209} Chain breaks: 1 Chain: "B" Number of atoms: 9958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1276, 9958 Classifications: {'peptide': 1276} Link IDs: {'PTRANS': 66, 'TRANS': 1209} Chain breaks: 1 Chain: "C" Number of atoms: 9967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1277, 9967 Classifications: {'peptide': 1277} Link IDs: {'PTRANS': 66, 'TRANS': 1210} Chain breaks: 1 Chain: "D" Number of atoms: 10985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 10985 Classifications: {'peptide': 1407} Link IDs: {'PTRANS': 73, 'TRANS': 1333} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 22.12, per 1000 atoms: 0.53 Number of scatterers: 41466 At special positions: 0 Unit cell: (214.608, 150.436, 189.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 177 16.00 O 8072 8.00 N 6891 7.00 C 26326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 86 " distance=2.04 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS B 431 " distance=2.02 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.04 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.02 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 689 " distance=2.05 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A1321 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 86 " distance=2.02 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 771 " distance=2.03 Simple disulfide: pdb=" SG CYS B 642 " - pdb=" SG CYS B 689 " distance=2.03 Simple disulfide: pdb=" SG CYS B 821 " - pdb=" SG CYS B 849 " distance=2.04 Simple disulfide: pdb=" SG CYS B 847 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS B 921 " - pdb=" SG CYS B1321 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1127 " distance=2.02 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 86 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 287 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS D 431 " distance=2.04 Simple disulfide: pdb=" SG CYS C 431 " - pdb=" SG CYS D 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 563 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 771 " distance=2.03 Simple disulfide: pdb=" SG CYS C 642 " - pdb=" SG CYS C 689 " distance=2.04 Simple disulfide: pdb=" SG CYS C 821 " - pdb=" SG CYS C 849 " distance=2.03 Simple disulfide: pdb=" SG CYS C 847 " - pdb=" SG CYS C 883 " distance=2.03 Simple disulfide: pdb=" SG CYS C 921 " - pdb=" SG CYS C1321 " distance=2.02 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 86 " distance=2.04 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 563 " distance=2.03 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 771 " distance=2.03 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 689 " distance=2.03 Simple disulfide: pdb=" SG CYS D 821 " - pdb=" SG CYS D 849 " distance=2.04 Simple disulfide: pdb=" SG CYS D 847 " - pdb=" SG CYS D 883 " distance=2.04 Simple disulfide: pdb=" SG CYS D 921 " - pdb=" SG CYS D1321 " distance=2.04 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1127 " distance=2.04 Simple disulfide: pdb=" SG CYS D1352 " - pdb=" SG CYS D1467 " distance=2.02 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 Links applied ALPHA1-6 " BMA L 3 " - " MAN L 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG A2001 " - " ASN A 55 " " NAG A2002 " - " ASN A 70 " " NAG A2003 " - " ASN A 247 " " NAG A2004 " - " ASN A 396 " " NAG A2005 " - " ASN A 410 " " NAG B2001 " - " ASN B 55 " " NAG B2002 " - " ASN B 70 " " NAG B2003 " - " ASN B 247 " " NAG B2004 " - " ASN B 396 " " NAG B2005 " - " ASN B 410 " " NAG C2001 " - " ASN C 55 " " NAG C2002 " - " ASN C 70 " " NAG C2003 " - " ASN C 247 " " NAG C2004 " - " ASN C 396 " " NAG C2005 " - " ASN C 410 " " NAG D2001 " - " ASN D 55 " " NAG D2002 " - " ASN D 70 " " NAG D2003 " - " ASN D 869 " " NAG D2004 " - " ASN D 991 " " NAG D2005 " - " ASN D1424 " " NAG E 1 " - " ASN A 869 " " NAG F 1 " - " ASN A 991 " " NAG G 1 " - " ASN B 869 " " NAG H 1 " - " ASN B 991 " " NAG I 1 " - " ASN C 869 " " NAG J 1 " - " ASN C 991 " " NAG K 1 " - " ASN D 247 " " NAG L 1 " - " ASN D 396 " " NAG M 1 " - " ASN D 410 " Time building additional restraints: 17.78 Conformation dependent library (CDL) restraints added in 7.7 seconds 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9826 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 16.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 602 through 607 Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 953 through 965 removed outlier: 6.708A pdb=" N SER A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N MET A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 993 Proline residue: A 982 - end of helix removed outlier: 3.816A pdb=" N TYR A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1017 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1060 through 1073 Processing helix chain 'A' and resid 1098 through 1111 Processing helix chain 'A' and resid 1119 through 1137 Processing helix chain 'A' and resid 1144 through 1157 Processing helix chain 'A' and resid 1160 through 1172 Processing helix chain 'A' and resid 1225 through 1241 Processing helix chain 'A' and resid 1251 through 1268 Processing helix chain 'A' and resid 1294 through 1297 No H-bonds generated for 'chain 'A' and resid 1294 through 1297' Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 666 through 673 Processing helix chain 'B' and resid 953 through 965 removed outlier: 7.448A pdb=" N SER B 957 " --> pdb=" O ASP B 953 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 958 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N MET B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLN B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 993 Proline residue: B 982 - end of helix removed outlier: 3.797A pdb=" N TYR B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1017 Processing helix chain 'B' and resid 1039 through 1055 Processing helix chain 'B' and resid 1060 through 1073 Processing helix chain 'B' and resid 1098 through 1111 Processing helix chain 'B' and resid 1119 through 1137 removed outlier: 4.440A pdb=" N ASN B1123 " --> pdb=" O PRO B1119 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B1124 " --> pdb=" O VAL B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1157 Processing helix chain 'B' and resid 1160 through 1172 Processing helix chain 'B' and resid 1225 through 1241 Processing helix chain 'B' and resid 1251 through 1268 Processing helix chain 'B' and resid 1294 through 1297 No H-bonds generated for 'chain 'B' and resid 1294 through 1297' Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 602 through 607 Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 666 through 673 Processing helix chain 'C' and resid 953 through 965 removed outlier: 6.224A pdb=" N SER C 957 " --> pdb=" O ASP C 953 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA C 958 " --> pdb=" O ILE C 954 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N MET C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N GLN C 960 " --> pdb=" O GLY C 956 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 993 Proline residue: C 982 - end of helix removed outlier: 4.012A pdb=" N TYR C 985 " --> pdb=" O ALA C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1017 Processing helix chain 'C' and resid 1039 through 1055 Processing helix chain 'C' and resid 1060 through 1073 Processing helix chain 'C' and resid 1098 through 1111 Processing helix chain 'C' and resid 1119 through 1137 Processing helix chain 'C' and resid 1144 through 1157 Processing helix chain 'C' and resid 1160 through 1172 Processing helix chain 'C' and resid 1225 through 1241 Processing helix chain 'C' and resid 1251 through 1268 Processing helix chain 'C' and resid 1294 through 1297 No H-bonds generated for 'chain 'C' and resid 1294 through 1297' Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 602 through 607 Processing helix chain 'D' and resid 615 through 621 Processing helix chain 'D' and resid 666 through 673 removed outlier: 4.875A pdb=" N MET D 673 " --> pdb=" O PHE D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 962 removed outlier: 7.617A pdb=" N THR D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 958 through 962' Processing helix chain 'D' and resid 973 through 993 removed outlier: 4.929A pdb=" N MET D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL D 978 " --> pdb=" O GLU D 974 " (cutoff:3.500A) Proline residue: D 982 - end of helix removed outlier: 4.366A pdb=" N TYR D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASP D 988 " --> pdb=" O ILE D 984 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR D 989 " --> pdb=" O TYR D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1017 removed outlier: 3.769A pdb=" N THR D1010 " --> pdb=" O GLY D1006 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1052 removed outlier: 4.757A pdb=" N LYS D1047 " --> pdb=" O ALA D1043 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR D1048 " --> pdb=" O PHE D1044 " (cutoff:3.500A) Processing helix chain 'D' and resid 1060 through 1073 removed outlier: 4.086A pdb=" N ALA D1066 " --> pdb=" O HIS D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1098 through 1111 removed outlier: 3.577A pdb=" N THR D1106 " --> pdb=" O SER D1102 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU D1111 " --> pdb=" O ILE D1107 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1137 Processing helix chain 'D' and resid 1144 through 1157 removed outlier: 5.409A pdb=" N ALA D1151 " --> pdb=" O LYS D1147 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR D1152 " --> pdb=" O ALA D1148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D1154 " --> pdb=" O LEU D1150 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU D1156 " --> pdb=" O TYR D1152 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA D1157 " --> pdb=" O ALA D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1172 removed outlier: 4.115A pdb=" N LYS D1168 " --> pdb=" O LYS D1164 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER D1169 " --> pdb=" O GLU D1165 " (cutoff:3.500A) Processing helix chain 'D' and resid 1205 through 1217 removed outlier: 3.546A pdb=" N LEU D1217 " --> pdb=" O LEU D1213 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1241 removed outlier: 4.031A pdb=" N THR D1229 " --> pdb=" O SER D1225 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN D1233 " --> pdb=" O THR D1229 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TRP D1237 " --> pdb=" O ASN D1233 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D1238 " --> pdb=" O ILE D1234 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1268 removed outlier: 5.887A pdb=" N VAL D1255 " --> pdb=" O THR D1251 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL D1256 " --> pdb=" O GLN D1252 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D1258 " --> pdb=" O THR D1254 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS D1259 " --> pdb=" O VAL D1255 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA D1260 " --> pdb=" O VAL D1256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU D1261 " --> pdb=" O ALA D1257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA D1266 " --> pdb=" O SER D1262 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA D1267 " --> pdb=" O LYS D1263 " (cutoff:3.500A) Processing helix chain 'D' and resid 1294 through 1297 No H-bonds generated for 'chain 'D' and resid 1294 through 1297' Processing helix chain 'D' and resid 1393 through 1400 517 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.55 Time building geometry restraints manager: 18.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12883 1.34 - 1.47: 10310 1.47 - 1.60: 18921 1.60 - 1.73: 0 1.73 - 1.86: 260 Bond restraints: 42374 Sorted by residual: bond pdb=" C LEU D 468 " pdb=" N PRO D 469 " ideal model delta sigma weight residual 1.335 1.375 -0.040 8.70e-03 1.32e+04 2.07e+01 bond pdb=" C PRO B 936 " pdb=" N PRO B 937 " ideal model delta sigma weight residual 1.332 1.383 -0.051 1.12e-02 7.97e+03 2.05e+01 bond pdb=" C LEU D 987 " pdb=" O LEU D 987 " ideal model delta sigma weight residual 1.236 1.287 -0.051 1.22e-02 6.72e+03 1.75e+01 bond pdb=" N PRO B 969 " pdb=" CA PRO B 969 " ideal model delta sigma weight residual 1.470 1.518 -0.048 1.23e-02 6.61e+03 1.54e+01 bond pdb=" C ALA C 599 " pdb=" N VAL C 600 " ideal model delta sigma weight residual 1.332 1.280 0.052 1.39e-02 5.18e+03 1.38e+01 ... (remaining 42369 not shown) Histogram of bond angle deviations from ideal: 96.46 - 104.03: 732 104.03 - 111.60: 17902 111.60 - 119.18: 17138 119.18 - 126.75: 21236 126.75 - 134.33: 564 Bond angle restraints: 57572 Sorted by residual: angle pdb=" N PRO D 454 " pdb=" CA PRO D 454 " pdb=" C PRO D 454 " ideal model delta sigma weight residual 114.27 100.39 13.88 1.35e+00 5.49e-01 1.06e+02 angle pdb=" C TYR D 989 " pdb=" CA TYR D 989 " pdb=" CB TYR D 989 " ideal model delta sigma weight residual 110.88 96.52 14.36 1.57e+00 4.06e-01 8.36e+01 angle pdb=" N ALA B 391 " pdb=" CA ALA B 391 " pdb=" C ALA B 391 " ideal model delta sigma weight residual 113.28 102.31 10.97 1.22e+00 6.72e-01 8.08e+01 angle pdb=" N PRO C 609 " pdb=" CA PRO C 609 " pdb=" C PRO C 609 " ideal model delta sigma weight residual 110.80 99.52 11.28 1.51e+00 4.39e-01 5.58e+01 angle pdb=" N VAL D1116 " pdb=" CA VAL D1116 " pdb=" C VAL D1116 " ideal model delta sigma weight residual 111.81 105.73 6.08 8.60e-01 1.35e+00 5.00e+01 ... (remaining 57567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 23472 21.48 - 42.96: 2275 42.96 - 64.44: 333 64.44 - 85.93: 101 85.93 - 107.41: 28 Dihedral angle restraints: 26209 sinusoidal: 10953 harmonic: 15256 Sorted by residual: dihedral pdb=" C ASN A 55 " pdb=" N ASN A 55 " pdb=" CA ASN A 55 " pdb=" CB ASN A 55 " ideal model delta harmonic sigma weight residual -122.60 -142.52 19.92 0 2.50e+00 1.60e-01 6.35e+01 dihedral pdb=" CB CYS A 431 " pdb=" SG CYS A 431 " pdb=" SG CYS B 278 " pdb=" CB CYS B 278 " ideal model delta sinusoidal sigma weight residual 93.00 158.59 -65.59 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" C TYR D 989 " pdb=" N TYR D 989 " pdb=" CA TYR D 989 " pdb=" CB TYR D 989 " ideal model delta harmonic sigma weight residual -122.60 -103.94 -18.66 0 2.50e+00 1.60e-01 5.57e+01 ... (remaining 26206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.392: 6674 0.392 - 0.783: 10 0.783 - 1.175: 1 1.175 - 1.566: 0 1.566 - 1.958: 1 Chirality restraints: 6686 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.24e+02 chirality pdb=" CB VAL B1120 " pdb=" CA VAL B1120 " pdb=" CG1 VAL B1120 " pdb=" CG2 VAL B1120 " both_signs ideal model delta sigma weight residual False -2.63 -0.67 -1.96 2.00e-01 2.50e+01 9.58e+01 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.96e+01 ... (remaining 6683 not shown) Planarity restraints: 7387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D2003 " -0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG D2003 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG D2003 " -0.116 2.00e-02 2.50e+03 pdb=" N2 NAG D2003 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG D2003 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2004 " 0.353 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG A2004 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A2004 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG A2004 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG A2004 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C2004 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C2004 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C2004 " 0.127 2.00e-02 2.50e+03 pdb=" N2 NAG C2004 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NAG C2004 " 0.146 2.00e-02 2.50e+03 ... (remaining 7384 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 579 2.47 - 3.07: 32362 3.07 - 3.68: 69201 3.68 - 4.29: 94035 4.29 - 4.90: 144446 Nonbonded interactions: 340623 Sorted by model distance: nonbonded pdb=" SG CYS D 972 " pdb=" CD GLN D 975 " model vdw 1.857 3.630 nonbonded pdb=" O TYR C 394 " pdb=" O6 NAG C2004 " model vdw 1.968 2.440 nonbonded pdb=" OG SER D 457 " pdb=" OD1 ASN D 483 " model vdw 2.010 2.440 nonbonded pdb=" O ALA C 590 " pdb=" OG SER C 593 " model vdw 2.012 2.440 nonbonded pdb=" OE2 GLU A 926 " pdb=" OG SER A 928 " model vdw 2.027 2.440 ... (remaining 340618 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' and (resid 29 through 974 or (resid 975 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1)) or resid 976 throug \ h 1337 or resid 2001 through 2005)) selection = (chain 'B' and (resid 29 through 974 or (resid 975 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1)) or resid 976 throug \ h 1337 or resid 2001 through 2005)) selection = (chain 'C' and (resid 29 through 974 or (resid 975 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1)) or resid 976 throug \ h 1337 or resid 2001 through 2005)) selection = (chain 'D' and (resid 29 through 695 or resid 730 through 1337 or resid 2001 thr \ ough 2005)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.550 Check model and map are aligned: 0.700 Set scattering table: 0.400 Process input model: 102.690 Find NCS groups from input model: 4.000 Set up NCS constraints: 0.380 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: 0.000 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 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 : 0.009 0.095 42374 Z= 0.601 Angle : 1.282 14.498 57572 Z= 0.718 Chirality : 0.074 1.958 6686 Planarity : 0.021 0.306 7358 Dihedral : 17.306 107.408 16248 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.69 % Allowed : 20.13 % Favored : 79.18 % Rotamer: Outliers : 1.09 % Allowed : 10.64 % Favored : 88.27 % Cbeta Deviations : 0.14 % 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: -5.96 (0.09), residues: 5220 helix: -3.07 (0.14), residues: 771 sheet: -3.71 (0.13), residues: 1127 loop : -4.56 (0.08), residues: 3322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 739 HIS 0.014 0.002 HIS C1118 PHE 0.051 0.004 PHE D1049 TYR 0.043 0.003 TYR C1152 ARG 0.018 0.001 ARG C 598 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 632 time to evaluate : 5.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6974 (mm-30) REVERT: A 121 MET cc_start: 0.8955 (ttt) cc_final: 0.8734 (ttt) REVERT: A 229 PHE cc_start: 0.7332 (p90) cc_final: 0.6716 (p90) REVERT: A 310 GLN cc_start: 0.7999 (mp-120) cc_final: 0.7464 (mp10) REVERT: A 411 THR cc_start: 0.6848 (OUTLIER) cc_final: 0.6529 (p) REVERT: A 440 GLU cc_start: 0.6368 (tt0) cc_final: 0.5269 (mm-30) REVERT: A 464 MET cc_start: 0.8752 (ttt) cc_final: 0.8519 (ttt) REVERT: A 561 GLU cc_start: 0.7733 (tp30) cc_final: 0.7408 (tp30) REVERT: A 586 ARG cc_start: 0.7653 (ttt90) cc_final: 0.7224 (mmm-85) REVERT: A 959 MET cc_start: 0.5759 (mtt) cc_final: 0.5278 (ptt) REVERT: A 1122 ARG cc_start: 0.8892 (mtp180) cc_final: 0.8272 (mmm160) REVERT: A 1133 LYS cc_start: 0.9046 (tttt) cc_final: 0.8662 (tptt) REVERT: A 1216 TYR cc_start: 0.8193 (m-80) cc_final: 0.7974 (m-80) REVERT: B 142 GLN cc_start: 0.8273 (mt0) cc_final: 0.7847 (mt0) REVERT: B 226 LEU cc_start: 0.8252 (mp) cc_final: 0.7620 (pt) REVERT: B 256 TYR cc_start: 0.8474 (t80) cc_final: 0.8270 (t80) REVERT: B 325 GLN cc_start: 0.9151 (tt0) cc_final: 0.8918 (tm-30) REVERT: B 354 LYS cc_start: 0.8977 (tttp) cc_final: 0.8763 (tttt) REVERT: B 409 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8001 (tp) REVERT: B 462 GLU cc_start: 0.8609 (pt0) cc_final: 0.8329 (pm20) REVERT: B 531 LYS cc_start: 0.7870 (pttm) cc_final: 0.7533 (tttt) REVERT: B 619 TYR cc_start: 0.7512 (m-10) cc_final: 0.7288 (m-80) REVERT: B 636 ASP cc_start: 0.6712 (p0) cc_final: 0.6466 (p0) REVERT: B 789 PHE cc_start: 0.6326 (t80) cc_final: 0.6076 (t80) REVERT: B 1040 TRP cc_start: 0.6068 (t60) cc_final: 0.5813 (t60) REVERT: B 1207 GLU cc_start: 0.6644 (pp20) cc_final: 0.6222 (pt0) REVERT: B 1274 LYS cc_start: 0.8938 (pttt) cc_final: 0.8718 (ptmt) REVERT: B 1296 ASN cc_start: 0.8750 (t0) cc_final: 0.8514 (t0) REVERT: C 209 LYS cc_start: 0.7635 (mtmt) cc_final: 0.7409 (tmtt) REVERT: C 335 LEU cc_start: 0.8855 (tt) cc_final: 0.8294 (pt) REVERT: C 356 ASP cc_start: 0.9109 (t0) cc_final: 0.8890 (t0) REVERT: C 363 ILE cc_start: 0.8465 (tp) cc_final: 0.8237 (tp) REVERT: C 373 ASP cc_start: 0.7854 (t70) cc_final: 0.7363 (m-30) REVERT: C 449 TYR cc_start: 0.7217 (m-80) cc_final: 0.6915 (m-80) REVERT: C 464 MET cc_start: 0.7714 (ttm) cc_final: 0.7474 (mtm) REVERT: C 528 ILE cc_start: 0.7097 (pt) cc_final: 0.6851 (pt) REVERT: C 569 ASP cc_start: 0.8390 (t0) cc_final: 0.8188 (t0) REVERT: C 945 ARG cc_start: 0.7458 (tmt170) cc_final: 0.7046 (ttt180) REVERT: C 1005 ILE cc_start: 0.5185 (mt) cc_final: 0.4801 (mt) REVERT: C 1104 TYR cc_start: 0.5544 (t80) cc_final: 0.3845 (t80) REVERT: C 1126 PHE cc_start: 0.8990 (m-80) cc_final: 0.8620 (m-80) REVERT: C 1136 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8557 (tm-30) REVERT: C 1325 GLN cc_start: 0.9257 (tt0) cc_final: 0.8339 (tt0) REVERT: D 48 CYS cc_start: 0.3556 (OUTLIER) cc_final: 0.3015 (p) REVERT: D 130 PHE cc_start: 0.9092 (p90) cc_final: 0.8776 (p90) REVERT: D 149 VAL cc_start: 0.6346 (t) cc_final: 0.5573 (t) REVERT: D 286 PHE cc_start: 0.8066 (m-80) cc_final: 0.7810 (m-80) REVERT: D 387 ARG cc_start: 0.9138 (mmp-170) cc_final: 0.8762 (mmp80) REVERT: D 406 GLN cc_start: 0.9271 (tm-30) cc_final: 0.9001 (tm-30) REVERT: D 446 HIS cc_start: 0.5968 (t70) cc_final: 0.5603 (t70) REVERT: D 550 ASP cc_start: 0.7866 (t0) cc_final: 0.7531 (t0) REVERT: D 567 LYS cc_start: 0.9149 (tmtt) cc_final: 0.8819 (tptp) REVERT: D 569 ASP cc_start: 0.9613 (t0) cc_final: 0.9397 (t70) REVERT: D 968 MET cc_start: -0.1215 (tpt) cc_final: -0.1741 (ttt) REVERT: D 988 ASP cc_start: 0.0042 (OUTLIER) cc_final: -0.0333 (p0) REVERT: D 1012 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7968 (p90) REVERT: D 1173 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7796 (mm-30) REVERT: D 1378 MET cc_start: 0.7736 (mmt) cc_final: 0.5964 (tpt) outliers start: 50 outliers final: 12 residues processed: 677 average time/residue: 0.5296 time to fit residues: 584.9373 Evaluate side-chains 456 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 439 time to evaluate : 4.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 439 optimal weight: 8.9990 chunk 394 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 266 optimal weight: 0.5980 chunk 210 optimal weight: 8.9990 chunk 408 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 303 optimal weight: 10.0000 chunk 473 optimal weight: 1.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS A 479 HIS A 511 HIS A 584 HIS A 967 GLN A1035 ASN A1171 ASN B 81 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS B 511 HIS B 584 HIS B 694 GLN B 880 GLN B 983 ASN B1013 GLN ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1243 ASN C 97 ASN C 173 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 HIS ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1035 ASN ** C1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 177 GLN D 182 GLN D 217 HIS ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN D 477 GLN ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 HIS D 647 ASN D 843 GLN D 938 ASN D1051 GLN D1062 HIS D1159 ASN D1259 HIS D1331 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5664 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 42374 Z= 0.304 Angle : 0.960 11.645 57572 Z= 0.484 Chirality : 0.055 0.548 6686 Planarity : 0.007 0.088 7358 Dihedral : 11.049 66.560 6502 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.29 % Allowed : 15.71 % Favored : 84.00 % Rotamer: Outliers : 0.42 % Allowed : 9.02 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.10 % 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: -5.25 (0.09), residues: 5220 helix: -2.27 (0.15), residues: 791 sheet: -3.22 (0.13), residues: 1235 loop : -4.15 (0.09), residues: 3194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A1132 HIS 0.012 0.001 HIS A1195 PHE 0.041 0.003 PHE A 980 TYR 0.028 0.003 TYR D1007 ARG 0.012 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 574 time to evaluate : 5.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 80 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.5987 (pm20) REVERT: A 82 ASP cc_start: 0.9516 (m-30) cc_final: 0.9146 (m-30) REVERT: A 121 MET cc_start: 0.8926 (ttt) cc_final: 0.8723 (ttt) REVERT: A 179 GLN cc_start: 0.6167 (tt0) cc_final: 0.5930 (tm-30) REVERT: A 229 PHE cc_start: 0.7341 (p90) cc_final: 0.6688 (p90) REVERT: A 436 TRP cc_start: 0.6751 (m100) cc_final: 0.6098 (t-100) REVERT: A 440 GLU cc_start: 0.5926 (tt0) cc_final: 0.5014 (mm-30) REVERT: A 464 MET cc_start: 0.8844 (ttt) cc_final: 0.8460 (ttt) REVERT: A 481 ILE cc_start: 0.8850 (mp) cc_final: 0.8524 (mp) REVERT: A 530 VAL cc_start: 0.8162 (t) cc_final: 0.7843 (t) REVERT: A 561 GLU cc_start: 0.7269 (tp30) cc_final: 0.6979 (tp30) REVERT: A 567 LYS cc_start: 0.8799 (tttt) cc_final: 0.8314 (mptt) REVERT: A 586 ARG cc_start: 0.7770 (ttt90) cc_final: 0.7075 (mmm-85) REVERT: A 597 LEU cc_start: 0.6329 (mp) cc_final: 0.6029 (mp) REVERT: A 673 MET cc_start: 0.8556 (tpt) cc_final: 0.8147 (tpp) REVERT: A 959 MET cc_start: 0.5880 (mtt) cc_final: 0.5042 (ptp) REVERT: A 995 GLN cc_start: 0.3322 (tt0) cc_final: 0.3064 (mt0) REVERT: A 1064 THR cc_start: 0.7719 (m) cc_final: 0.7487 (p) REVERT: A 1122 ARG cc_start: 0.8842 (mtp180) cc_final: 0.8318 (mmm160) REVERT: A 1136 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8483 (tm-30) REVERT: A 1154 PHE cc_start: 0.5468 (m-80) cc_final: 0.5140 (m-80) REVERT: B 325 GLN cc_start: 0.9120 (tt0) cc_final: 0.8762 (tm-30) REVERT: B 348 THR cc_start: 0.8118 (m) cc_final: 0.7197 (p) REVERT: B 461 LEU cc_start: 0.7907 (mp) cc_final: 0.6877 (tp) REVERT: B 479 HIS cc_start: 0.8342 (m170) cc_final: 0.7966 (m-70) REVERT: B 531 LYS cc_start: 0.8132 (pttm) cc_final: 0.7806 (tttt) REVERT: B 550 ASP cc_start: 0.8840 (t70) cc_final: 0.8506 (m-30) REVERT: B 557 LYS cc_start: 0.8012 (ptmt) cc_final: 0.7704 (mptt) REVERT: B 619 TYR cc_start: 0.7244 (m-10) cc_final: 0.6780 (m-10) REVERT: B 789 PHE cc_start: 0.6264 (t80) cc_final: 0.5906 (t80) REVERT: B 1258 LEU cc_start: 0.8546 (mt) cc_final: 0.8291 (tp) REVERT: B 1296 ASN cc_start: 0.8854 (t0) cc_final: 0.8627 (t0) REVERT: C 121 MET cc_start: -0.2737 (ptm) cc_final: -0.3009 (ptm) REVERT: C 151 MET cc_start: 0.2904 (mmm) cc_final: 0.0781 (mmm) REVERT: C 363 ILE cc_start: 0.8659 (tp) cc_final: 0.8409 (tp) REVERT: C 370 ARG cc_start: 0.8322 (ttm170) cc_final: 0.8118 (ttm-80) REVERT: C 373 ASP cc_start: 0.7875 (t70) cc_final: 0.7405 (m-30) REVERT: C 418 SER cc_start: 0.9285 (m) cc_final: 0.8962 (p) REVERT: C 464 MET cc_start: 0.7792 (ttm) cc_final: 0.7366 (mtt) REVERT: C 558 TYR cc_start: 0.7512 (m-80) cc_final: 0.6944 (m-80) REVERT: C 569 ASP cc_start: 0.8499 (t0) cc_final: 0.8225 (t70) REVERT: C 1104 TYR cc_start: 0.5504 (t80) cc_final: 0.3973 (t80) REVERT: C 1126 PHE cc_start: 0.8958 (m-80) cc_final: 0.8600 (m-80) REVERT: C 1136 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8610 (tm-30) REVERT: C 1325 GLN cc_start: 0.9302 (tt0) cc_final: 0.8827 (tt0) REVERT: D 121 MET cc_start: 0.8914 (tmm) cc_final: 0.8669 (tmm) REVERT: D 130 PHE cc_start: 0.9106 (p90) cc_final: 0.8832 (p90) REVERT: D 149 VAL cc_start: 0.6178 (t) cc_final: 0.5600 (t) REVERT: D 181 PHE cc_start: 0.6480 (p90) cc_final: 0.6157 (p90) REVERT: D 286 PHE cc_start: 0.8261 (m-80) cc_final: 0.7959 (m-80) REVERT: D 387 ARG cc_start: 0.9216 (mmp-170) cc_final: 0.8813 (mmp80) REVERT: D 446 HIS cc_start: 0.5921 (t70) cc_final: 0.5614 (t70) REVERT: D 449 TYR cc_start: 0.7044 (m-80) cc_final: 0.6250 (m-80) REVERT: D 550 ASP cc_start: 0.7734 (t0) cc_final: 0.7455 (t0) REVERT: D 554 ASP cc_start: 0.8826 (p0) cc_final: 0.8308 (p0) REVERT: D 853 ARG cc_start: 0.9228 (tmm160) cc_final: 0.9005 (mmt-90) REVERT: D 968 MET cc_start: -0.1328 (tpt) cc_final: -0.1882 (ttt) REVERT: D 1007 TYR cc_start: 0.6574 (m-80) cc_final: 0.5883 (t80) REVERT: D 1173 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7769 (mm-30) outliers start: 19 outliers final: 5 residues processed: 593 average time/residue: 0.5271 time to fit residues: 515.7431 Evaluate side-chains 440 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 434 time to evaluate : 4.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 262 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 393 optimal weight: 4.9990 chunk 322 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 473 optimal weight: 4.9990 chunk 512 optimal weight: 50.0000 chunk 422 optimal weight: 10.0000 chunk 470 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 380 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN A1035 ASN A1171 ASN ** A1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 361 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1020 HIS C1123 ASN C1242 GLN C1281 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN D 602 GLN ** D 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS ** D1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 42374 Z= 0.398 Angle : 1.015 12.595 57572 Z= 0.515 Chirality : 0.057 0.545 6686 Planarity : 0.007 0.171 7358 Dihedral : 9.956 59.251 6502 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 35.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 17.59 % Favored : 82.18 % Rotamer: Outliers : 0.55 % Allowed : 9.57 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.10 % 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: -5.02 (0.10), residues: 5220 helix: -2.03 (0.16), residues: 779 sheet: -3.02 (0.13), residues: 1252 loop : -4.04 (0.09), residues: 3189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A1132 HIS 0.013 0.002 HIS D 358 PHE 0.036 0.003 PHE C 980 TYR 0.044 0.003 TYR D 619 ARG 0.017 0.001 ARG C 598 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 548 time to evaluate : 5.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.9557 (m-30) cc_final: 0.9203 (m-30) REVERT: A 121 MET cc_start: 0.9110 (ttt) cc_final: 0.8886 (ttt) REVERT: A 179 GLN cc_start: 0.6471 (tt0) cc_final: 0.6087 (tm-30) REVERT: A 229 PHE cc_start: 0.7527 (p90) cc_final: 0.6822 (p90) REVERT: A 286 PHE cc_start: 0.8779 (m-80) cc_final: 0.8519 (m-80) REVERT: A 384 ILE cc_start: 0.9462 (pt) cc_final: 0.9253 (mp) REVERT: A 415 MET cc_start: 0.4424 (ttt) cc_final: 0.3583 (ttt) REVERT: A 440 GLU cc_start: 0.6258 (tt0) cc_final: 0.5070 (mm-30) REVERT: A 464 MET cc_start: 0.8888 (ttt) cc_final: 0.8465 (ttt) REVERT: A 561 GLU cc_start: 0.7631 (tp30) cc_final: 0.7387 (tp30) REVERT: A 567 LYS cc_start: 0.9048 (tttt) cc_final: 0.8636 (mptt) REVERT: A 586 ARG cc_start: 0.8046 (ttt90) cc_final: 0.7255 (mmm-85) REVERT: A 597 LEU cc_start: 0.6935 (mp) cc_final: 0.6568 (mp) REVERT: A 959 MET cc_start: 0.6035 (mtt) cc_final: 0.5375 (ptp) REVERT: A 1064 THR cc_start: 0.7714 (m) cc_final: 0.7423 (p) REVERT: A 1112 ILE cc_start: 0.7836 (mt) cc_final: 0.7632 (mt) REVERT: A 1122 ARG cc_start: 0.8794 (mtp180) cc_final: 0.8445 (mmm160) REVERT: A 1133 LYS cc_start: 0.9049 (tptp) cc_final: 0.8751 (tptt) REVERT: A 1136 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8519 (tm-30) REVERT: A 1154 PHE cc_start: 0.5862 (m-80) cc_final: 0.5533 (m-80) REVERT: A 1211 TYR cc_start: 0.6830 (m-80) cc_final: 0.6430 (m-80) REVERT: B 256 TYR cc_start: 0.8462 (t80) cc_final: 0.8083 (t80) REVERT: B 293 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8012 (pp30) REVERT: B 325 GLN cc_start: 0.9214 (tt0) cc_final: 0.8719 (pp30) REVERT: B 354 LYS cc_start: 0.8836 (tttp) cc_final: 0.8467 (ttmt) REVERT: B 409 ILE cc_start: 0.7536 (mp) cc_final: 0.6874 (tp) REVERT: B 461 LEU cc_start: 0.8163 (mp) cc_final: 0.7598 (tp) REVERT: B 510 THR cc_start: 0.6777 (t) cc_final: 0.6348 (t) REVERT: B 531 LYS cc_start: 0.8286 (pttm) cc_final: 0.7879 (tttt) REVERT: B 550 ASP cc_start: 0.8867 (t70) cc_final: 0.8323 (m-30) REVERT: B 557 LYS cc_start: 0.8289 (pttt) cc_final: 0.8018 (pttt) REVERT: B 586 ARG cc_start: 0.7330 (mtp85) cc_final: 0.7039 (mtp180) REVERT: B 619 TYR cc_start: 0.7730 (m-10) cc_final: 0.6513 (m-10) REVERT: B 789 PHE cc_start: 0.6412 (t80) cc_final: 0.6125 (t80) REVERT: B 977 MET cc_start: 0.9087 (mmp) cc_final: 0.8723 (mmp) REVERT: B 1207 GLU cc_start: 0.7019 (pp20) cc_final: 0.6331 (pt0) REVERT: B 1314 MET cc_start: 0.9090 (tmm) cc_final: 0.8697 (ptp) REVERT: B 1328 LEU cc_start: 0.9659 (tp) cc_final: 0.9105 (tp) REVERT: C 101 MET cc_start: 0.7708 (mpp) cc_final: 0.7329 (mpp) REVERT: C 151 MET cc_start: 0.4188 (OUTLIER) cc_final: 0.3350 (tpp) REVERT: C 203 TYR cc_start: 0.7701 (m-80) cc_final: 0.7476 (m-80) REVERT: C 370 ARG cc_start: 0.8510 (ttm170) cc_final: 0.8300 (tpp80) REVERT: C 373 ASP cc_start: 0.7934 (t70) cc_final: 0.7433 (m-30) REVERT: C 666 MET cc_start: 0.8482 (tpp) cc_final: 0.7782 (tpt) REVERT: C 977 MET cc_start: 0.6405 (ptt) cc_final: 0.6015 (ptt) REVERT: C 1005 ILE cc_start: 0.5116 (mt) cc_final: 0.4753 (mt) REVERT: C 1104 TYR cc_start: 0.5868 (t80) cc_final: 0.4380 (t80) REVERT: C 1123 ASN cc_start: 0.8541 (m-40) cc_final: 0.8292 (m-40) REVERT: C 1126 PHE cc_start: 0.9069 (m-80) cc_final: 0.8634 (m-80) REVERT: C 1136 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8595 (tm-30) REVERT: C 1325 GLN cc_start: 0.9323 (tt0) cc_final: 0.8902 (tt0) REVERT: D 121 MET cc_start: 0.8947 (tmm) cc_final: 0.8644 (tmm) REVERT: D 181 PHE cc_start: 0.6438 (p90) cc_final: 0.6026 (p90) REVERT: D 214 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.7667 (ttt90) REVERT: D 286 PHE cc_start: 0.8545 (m-80) cc_final: 0.8333 (m-80) REVERT: D 358 HIS cc_start: 0.7420 (p-80) cc_final: 0.7105 (p-80) REVERT: D 385 PHE cc_start: 0.7961 (m-10) cc_final: 0.7717 (m-10) REVERT: D 449 TYR cc_start: 0.7348 (m-80) cc_final: 0.6752 (m-80) REVERT: D 546 LEU cc_start: 0.7110 (tp) cc_final: 0.6789 (tp) REVERT: D 550 ASP cc_start: 0.7950 (t0) cc_final: 0.7517 (t0) REVERT: D 554 ASP cc_start: 0.8941 (p0) cc_final: 0.8731 (p0) REVERT: D 662 ASN cc_start: 0.9373 (p0) cc_final: 0.9065 (p0) REVERT: D 968 MET cc_start: -0.1442 (tpt) cc_final: -0.1971 (ttt) REVERT: D 1007 TYR cc_start: 0.6860 (m-80) cc_final: 0.5978 (t80) outliers start: 25 outliers final: 12 residues processed: 570 average time/residue: 0.5301 time to fit residues: 494.6891 Evaluate side-chains 446 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 432 time to evaluate : 4.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 468 optimal weight: 6.9990 chunk 356 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 chunk 52 optimal weight: 0.0980 chunk 226 optimal weight: 8.9990 chunk 318 optimal weight: 0.6980 chunk 475 optimal weight: 6.9990 chunk 503 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 chunk 450 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN A1171 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN B 132 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN B 694 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 ASN ** C1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1281 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS ** D1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 42374 Z= 0.365 Angle : 0.970 13.842 57572 Z= 0.493 Chirality : 0.055 0.446 6686 Planarity : 0.007 0.108 7358 Dihedral : 9.527 59.853 6502 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 35.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.28 % Favored : 83.52 % Rotamer: Outliers : 0.09 % Allowed : 7.52 % Favored : 92.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.10), residues: 5220 helix: -1.88 (0.16), residues: 788 sheet: -2.90 (0.13), residues: 1217 loop : -3.90 (0.09), residues: 3215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A1183 HIS 0.018 0.002 HIS D 85 PHE 0.055 0.003 PHE B1126 TYR 0.041 0.003 TYR D1197 ARG 0.020 0.001 ARG B1122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 525 time to evaluate : 4.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.9542 (m-30) cc_final: 0.9231 (m-30) REVERT: A 121 MET cc_start: 0.8986 (ttt) cc_final: 0.8707 (ttt) REVERT: A 179 GLN cc_start: 0.6674 (tt0) cc_final: 0.5945 (tm-30) REVERT: A 229 PHE cc_start: 0.7760 (p90) cc_final: 0.6553 (p90) REVERT: A 237 LYS cc_start: 0.9077 (tmmt) cc_final: 0.8749 (tmtt) REVERT: A 415 MET cc_start: 0.3861 (ttt) cc_final: 0.3409 (ttt) REVERT: A 440 GLU cc_start: 0.6333 (tt0) cc_final: 0.5121 (mm-30) REVERT: A 464 MET cc_start: 0.8799 (ttt) cc_final: 0.8501 (ttt) REVERT: A 481 ILE cc_start: 0.8948 (mp) cc_final: 0.8678 (mp) REVERT: A 490 LEU cc_start: 0.9021 (mp) cc_final: 0.8715 (tt) REVERT: A 530 VAL cc_start: 0.8207 (t) cc_final: 0.7970 (t) REVERT: A 567 LYS cc_start: 0.8994 (tttt) cc_final: 0.8668 (mptt) REVERT: A 597 LEU cc_start: 0.7164 (mp) cc_final: 0.6649 (mp) REVERT: A 742 ASP cc_start: 0.5840 (OUTLIER) cc_final: 0.5053 (p0) REVERT: A 959 MET cc_start: 0.6141 (mtt) cc_final: 0.5603 (ptt) REVERT: A 1122 ARG cc_start: 0.8859 (mtp180) cc_final: 0.8508 (mmm160) REVERT: A 1133 LYS cc_start: 0.9262 (tptp) cc_final: 0.8677 (tptt) REVERT: A 1136 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8558 (tm-30) REVERT: A 1154 PHE cc_start: 0.6072 (m-80) cc_final: 0.5802 (m-80) REVERT: A 1325 GLN cc_start: 0.6581 (tt0) cc_final: 0.6312 (tt0) REVERT: B 256 TYR cc_start: 0.8491 (t80) cc_final: 0.8094 (t80) REVERT: B 309 PHE cc_start: 0.8199 (m-80) cc_final: 0.7877 (m-80) REVERT: B 354 LYS cc_start: 0.8731 (tttp) cc_final: 0.8393 (ttmt) REVERT: B 385 PHE cc_start: 0.7982 (m-80) cc_final: 0.7498 (m-80) REVERT: B 415 MET cc_start: 0.1630 (ttp) cc_final: 0.0278 (tpt) REVERT: B 461 LEU cc_start: 0.8508 (mp) cc_final: 0.8178 (tp) REVERT: B 510 THR cc_start: 0.6727 (t) cc_final: 0.6373 (t) REVERT: B 531 LYS cc_start: 0.8257 (pttm) cc_final: 0.7880 (tttt) REVERT: B 557 LYS cc_start: 0.8505 (pttt) cc_final: 0.8079 (pttt) REVERT: B 571 SER cc_start: 0.8606 (t) cc_final: 0.8022 (t) REVERT: B 586 ARG cc_start: 0.7539 (mtp85) cc_final: 0.6792 (mtp85) REVERT: B 619 TYR cc_start: 0.7883 (m-10) cc_final: 0.6652 (m-10) REVERT: B 666 MET cc_start: 0.7541 (ttp) cc_final: 0.6953 (ttp) REVERT: B 977 MET cc_start: 0.9091 (mmp) cc_final: 0.8789 (mmp) REVERT: B 1012 TYR cc_start: 0.7985 (t80) cc_final: 0.7702 (t80) REVERT: B 1207 GLU cc_start: 0.6832 (pp20) cc_final: 0.6110 (pt0) REVERT: B 1328 LEU cc_start: 0.9641 (tp) cc_final: 0.9241 (tp) REVERT: C 373 ASP cc_start: 0.7875 (t70) cc_final: 0.7369 (m-30) REVERT: C 586 ARG cc_start: 0.8662 (mtt180) cc_final: 0.8340 (tpt90) REVERT: C 945 ARG cc_start: 0.7774 (tmt170) cc_final: 0.6806 (ttt180) REVERT: C 1005 ILE cc_start: 0.4947 (mt) cc_final: 0.4703 (mt) REVERT: C 1104 TYR cc_start: 0.5915 (t80) cc_final: 0.4511 (t80) REVERT: C 1123 ASN cc_start: 0.8760 (m-40) cc_final: 0.8226 (m-40) REVERT: C 1126 PHE cc_start: 0.9140 (m-80) cc_final: 0.8756 (m-80) REVERT: C 1136 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8581 (tm-30) REVERT: D 151 MET cc_start: 0.5762 (ttm) cc_final: 0.5179 (tpp) REVERT: D 181 PHE cc_start: 0.6578 (p90) cc_final: 0.6104 (p90) REVERT: D 214 ARG cc_start: 0.8275 (mtp-110) cc_final: 0.7664 (ttt90) REVERT: D 223 GLU cc_start: 0.8941 (pm20) cc_final: 0.8730 (pm20) REVERT: D 246 MET cc_start: 0.0391 (ttm) cc_final: -0.0419 (mtt) REVERT: D 393 TYR cc_start: 0.8451 (t80) cc_final: 0.8233 (t80) REVERT: D 449 TYR cc_start: 0.7506 (m-80) cc_final: 0.6945 (m-80) REVERT: D 546 LEU cc_start: 0.7408 (tp) cc_final: 0.7015 (tp) REVERT: D 550 ASP cc_start: 0.7871 (t0) cc_final: 0.7360 (t0) REVERT: D 554 ASP cc_start: 0.9024 (p0) cc_final: 0.8786 (p0) REVERT: D 662 ASN cc_start: 0.9378 (p0) cc_final: 0.9001 (p0) REVERT: D 963 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7194 (tt0) REVERT: D 968 MET cc_start: -0.1553 (tpt) cc_final: -0.2162 (ttt) REVERT: D 1007 TYR cc_start: 0.6769 (m-80) cc_final: 0.6010 (t80) outliers start: 4 outliers final: 1 residues processed: 529 average time/residue: 0.5363 time to fit residues: 469.1238 Evaluate side-chains 412 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 410 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 419 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 374 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 429 optimal weight: 20.0000 chunk 348 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 452 optimal weight: 0.0770 chunk 127 optimal weight: 20.0000 overall best weight: 3.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 GLN A 182 GLN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN A1171 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1243 ASN C1302 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 GLN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN ** D 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS D1143 HIS ** D1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 42374 Z= 0.305 Angle : 0.896 11.851 57572 Z= 0.454 Chirality : 0.053 0.531 6686 Planarity : 0.006 0.124 7358 Dihedral : 9.139 59.883 6502 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 33.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 16.13 % Favored : 83.72 % Rotamer: Outliers : 0.11 % Allowed : 5.90 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.10), residues: 5220 helix: -1.55 (0.16), residues: 795 sheet: -2.75 (0.14), residues: 1258 loop : -3.81 (0.09), residues: 3167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 765 HIS 0.010 0.001 HIS A1195 PHE 0.053 0.003 PHE D1049 TYR 0.039 0.003 TYR D 619 ARG 0.018 0.001 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 531 time to evaluate : 4.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.9517 (m-30) cc_final: 0.9197 (m-30) REVERT: A 121 MET cc_start: 0.9052 (ttt) cc_final: 0.8717 (ttt) REVERT: A 209 LYS cc_start: 0.8213 (mttt) cc_final: 0.7873 (mttt) REVERT: A 229 PHE cc_start: 0.7950 (p90) cc_final: 0.6503 (p90) REVERT: A 332 VAL cc_start: 0.6562 (t) cc_final: 0.6362 (t) REVERT: A 384 ILE cc_start: 0.9343 (pt) cc_final: 0.9015 (mm) REVERT: A 440 GLU cc_start: 0.6238 (tt0) cc_final: 0.5308 (mp0) REVERT: A 464 MET cc_start: 0.8798 (ttt) cc_final: 0.8412 (ttt) REVERT: A 491 LYS cc_start: 0.9079 (tptt) cc_final: 0.8788 (tppt) REVERT: A 567 LYS cc_start: 0.8962 (tttt) cc_final: 0.8641 (mptt) REVERT: A 959 MET cc_start: 0.6107 (mtt) cc_final: 0.5650 (ptt) REVERT: A 1036 GLN cc_start: 0.2028 (OUTLIER) cc_final: 0.1506 (pp30) REVERT: A 1112 ILE cc_start: 0.8075 (mt) cc_final: 0.7871 (mt) REVERT: A 1122 ARG cc_start: 0.8767 (mtp180) cc_final: 0.8554 (mmm160) REVERT: A 1154 PHE cc_start: 0.6041 (m-80) cc_final: 0.5796 (m-80) REVERT: A 1259 HIS cc_start: 0.5279 (OUTLIER) cc_final: 0.4871 (m170) REVERT: A 1263 LYS cc_start: 0.8567 (mmpt) cc_final: 0.8124 (mmmt) REVERT: A 1280 ILE cc_start: 0.8338 (mp) cc_final: 0.8016 (mp) REVERT: A 1314 MET cc_start: 0.8315 (mpp) cc_final: 0.7975 (mpp) REVERT: B 32 MET cc_start: 0.3598 (tmm) cc_final: 0.3382 (tmm) REVERT: B 256 TYR cc_start: 0.8420 (t80) cc_final: 0.8028 (t80) REVERT: B 309 PHE cc_start: 0.8252 (m-80) cc_final: 0.8016 (m-80) REVERT: B 363 ILE cc_start: 0.8598 (tp) cc_final: 0.7611 (tp) REVERT: B 385 PHE cc_start: 0.8010 (m-80) cc_final: 0.7523 (m-80) REVERT: B 460 HIS cc_start: 0.8353 (m170) cc_final: 0.8035 (m90) REVERT: B 461 LEU cc_start: 0.8613 (mp) cc_final: 0.8282 (tp) REVERT: B 500 MET cc_start: 0.6861 (tmm) cc_final: 0.6256 (ttt) REVERT: B 531 LYS cc_start: 0.8285 (pttm) cc_final: 0.7904 (tttt) REVERT: B 557 LYS cc_start: 0.8587 (pttt) cc_final: 0.8152 (pttt) REVERT: B 571 SER cc_start: 0.8565 (t) cc_final: 0.8084 (p) REVERT: B 586 ARG cc_start: 0.7522 (mtp85) cc_final: 0.6703 (mtp180) REVERT: B 619 TYR cc_start: 0.8023 (m-10) cc_final: 0.6960 (m-10) REVERT: B 666 MET cc_start: 0.7762 (ttp) cc_final: 0.7017 (ttp) REVERT: B 977 MET cc_start: 0.9026 (mmp) cc_final: 0.8764 (mmp) REVERT: B 1012 TYR cc_start: 0.8058 (t80) cc_final: 0.7649 (t80) REVERT: B 1163 ARG cc_start: 0.6963 (tpt-90) cc_final: 0.6065 (tpt170) REVERT: C 101 MET cc_start: 0.8118 (mpp) cc_final: 0.7709 (mpp) REVERT: C 189 GLN cc_start: 0.8437 (pm20) cc_final: 0.8156 (tt0) REVERT: C 373 ASP cc_start: 0.8309 (t70) cc_final: 0.7852 (m-30) REVERT: C 540 LEU cc_start: 0.9104 (tp) cc_final: 0.8802 (mt) REVERT: C 945 ARG cc_start: 0.7888 (tmt170) cc_final: 0.7049 (ttt180) REVERT: C 977 MET cc_start: 0.6206 (ptt) cc_final: 0.5661 (ptt) REVERT: C 1028 PHE cc_start: 0.8602 (m-80) cc_final: 0.8064 (m-10) REVERT: C 1104 TYR cc_start: 0.5711 (t80) cc_final: 0.4352 (t80) REVERT: C 1126 PHE cc_start: 0.9009 (m-80) cc_final: 0.8744 (m-80) REVERT: D 181 PHE cc_start: 0.6408 (p90) cc_final: 0.5888 (p90) REVERT: D 214 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.7768 (ttt90) REVERT: D 359 PHE cc_start: 0.8026 (p90) cc_final: 0.7799 (p90) REVERT: D 385 PHE cc_start: 0.8081 (m-80) cc_final: 0.7776 (m-80) REVERT: D 393 TYR cc_start: 0.8600 (t80) cc_final: 0.8222 (t80) REVERT: D 446 HIS cc_start: 0.6567 (t70) cc_final: 0.6348 (t70) REVERT: D 449 TYR cc_start: 0.7384 (m-80) cc_final: 0.6870 (m-80) REVERT: D 546 LEU cc_start: 0.7535 (tp) cc_final: 0.7103 (tp) REVERT: D 550 ASP cc_start: 0.8036 (t0) cc_final: 0.7648 (t0) REVERT: D 554 ASP cc_start: 0.9082 (p0) cc_final: 0.8764 (p0) REVERT: D 567 LYS cc_start: 0.9064 (tmtt) cc_final: 0.8824 (tptp) REVERT: D 662 ASN cc_start: 0.9373 (p0) cc_final: 0.8984 (p0) REVERT: D 963 GLN cc_start: 0.7559 (tm-30) cc_final: 0.6940 (tt0) REVERT: D 968 MET cc_start: -0.1800 (tpt) cc_final: -0.2406 (ttt) REVERT: D 1007 TYR cc_start: 0.6576 (m-80) cc_final: 0.5832 (t80) REVERT: D 1378 MET cc_start: 0.7792 (mmt) cc_final: 0.6048 (tpp) outliers start: 5 outliers final: 0 residues processed: 536 average time/residue: 0.5244 time to fit residues: 462.5406 Evaluate side-chains 415 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 413 time to evaluate : 5.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 169 optimal weight: 6.9990 chunk 453 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 295 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 504 optimal weight: 20.0000 chunk 418 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 264 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN ** C1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN ** D 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1358 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 42374 Z= 0.285 Angle : 0.888 15.030 57572 Z= 0.447 Chirality : 0.053 0.415 6686 Planarity : 0.006 0.147 7358 Dihedral : 8.956 59.496 6502 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 31.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.79 % Favored : 84.06 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.10), residues: 5220 helix: -1.52 (0.16), residues: 808 sheet: -2.63 (0.13), residues: 1305 loop : -3.73 (0.09), residues: 3107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C1132 HIS 0.008 0.001 HIS A1259 PHE 0.054 0.003 PHE D1049 TYR 0.062 0.002 TYR A1152 ARG 0.011 0.001 ARG C1163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 4.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 38 LEU cc_start: 0.8280 (tt) cc_final: 0.7881 (tp) REVERT: A 82 ASP cc_start: 0.9553 (m-30) cc_final: 0.9279 (m-30) REVERT: A 209 LYS cc_start: 0.8388 (mttt) cc_final: 0.7961 (mttt) REVERT: A 229 PHE cc_start: 0.7872 (p90) cc_final: 0.6567 (p90) REVERT: A 237 LYS cc_start: 0.8810 (tmtt) cc_final: 0.8564 (tmtt) REVERT: A 310 GLN cc_start: 0.8276 (mp10) cc_final: 0.7973 (mp10) REVERT: A 384 ILE cc_start: 0.9375 (pt) cc_final: 0.9073 (mm) REVERT: A 415 MET cc_start: 0.3664 (ttt) cc_final: 0.3111 (ttt) REVERT: A 440 GLU cc_start: 0.6130 (tt0) cc_final: 0.5345 (mp0) REVERT: A 464 MET cc_start: 0.8780 (ttt) cc_final: 0.8512 (ttt) REVERT: A 514 LEU cc_start: 0.8972 (mm) cc_final: 0.8582 (mt) REVERT: A 673 MET cc_start: 0.8490 (tpt) cc_final: 0.8087 (tpp) REVERT: A 959 MET cc_start: 0.5826 (mtt) cc_final: 0.5566 (ptt) REVERT: A 1112 ILE cc_start: 0.8047 (mt) cc_final: 0.7846 (mt) REVERT: A 1122 ARG cc_start: 0.8730 (mtp180) cc_final: 0.8506 (mmm160) REVERT: A 1216 TYR cc_start: 0.8428 (m-10) cc_final: 0.8203 (m-10) REVERT: A 1263 LYS cc_start: 0.8591 (mmpt) cc_final: 0.8357 (mmmt) REVERT: B 151 MET cc_start: -0.0046 (mtm) cc_final: -0.0514 (ttp) REVERT: B 256 TYR cc_start: 0.8422 (t80) cc_final: 0.8015 (t80) REVERT: B 309 PHE cc_start: 0.8229 (m-80) cc_final: 0.7944 (m-80) REVERT: B 348 THR cc_start: 0.8534 (m) cc_final: 0.7629 (p) REVERT: B 363 ILE cc_start: 0.8597 (tp) cc_final: 0.7833 (tp) REVERT: B 385 PHE cc_start: 0.8045 (m-80) cc_final: 0.7569 (m-80) REVERT: B 456 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8400 (mmtt) REVERT: B 460 HIS cc_start: 0.8322 (m170) cc_final: 0.8069 (m90) REVERT: B 461 LEU cc_start: 0.8859 (mp) cc_final: 0.8390 (tp) REVERT: B 500 MET cc_start: 0.6593 (tmm) cc_final: 0.5927 (ttt) REVERT: B 531 LYS cc_start: 0.8237 (pttm) cc_final: 0.7920 (tttt) REVERT: B 552 ILE cc_start: 0.9409 (pt) cc_final: 0.8871 (pt) REVERT: B 557 LYS cc_start: 0.8591 (pttt) cc_final: 0.8354 (pttt) REVERT: B 571 SER cc_start: 0.8543 (t) cc_final: 0.8090 (p) REVERT: B 586 ARG cc_start: 0.7511 (mtp85) cc_final: 0.6669 (mtp180) REVERT: B 619 TYR cc_start: 0.7861 (m-10) cc_final: 0.6733 (m-10) REVERT: B 666 MET cc_start: 0.7878 (ttp) cc_final: 0.7471 (tpt) REVERT: B 977 MET cc_start: 0.9008 (mmp) cc_final: 0.8772 (mmp) REVERT: B 1126 PHE cc_start: 0.8114 (t80) cc_final: 0.7732 (t80) REVERT: B 1184 GLU cc_start: 0.7312 (pt0) cc_final: 0.6711 (mt-10) REVERT: B 1328 LEU cc_start: 0.9661 (tp) cc_final: 0.9076 (tp) REVERT: C 101 MET cc_start: 0.8016 (mpp) cc_final: 0.7772 (mpp) REVERT: C 189 GLN cc_start: 0.8384 (pm20) cc_final: 0.8104 (tt0) REVERT: C 323 GLU cc_start: 0.8699 (mp0) cc_final: 0.8327 (mp0) REVERT: C 373 ASP cc_start: 0.8383 (t70) cc_final: 0.7989 (m-30) REVERT: C 415 MET cc_start: 0.6039 (ppp) cc_final: 0.5816 (ptt) REVERT: C 1005 ILE cc_start: 0.4862 (mt) cc_final: 0.4619 (mt) REVERT: C 1104 TYR cc_start: 0.5586 (t80) cc_final: 0.4302 (t80) REVERT: C 1126 PHE cc_start: 0.9019 (m-80) cc_final: 0.8732 (m-80) REVERT: D 181 PHE cc_start: 0.6346 (p90) cc_final: 0.5828 (p90) REVERT: D 214 ARG cc_start: 0.8342 (mtp-110) cc_final: 0.8085 (mtp-110) REVERT: D 246 MET cc_start: 0.0261 (ttm) cc_final: -0.0492 (mtt) REVERT: D 284 GLN cc_start: 0.8689 (pp30) cc_final: 0.8434 (pm20) REVERT: D 359 PHE cc_start: 0.8015 (p90) cc_final: 0.7801 (p90) REVERT: D 385 PHE cc_start: 0.8106 (m-80) cc_final: 0.7662 (m-80) REVERT: D 393 TYR cc_start: 0.8586 (t80) cc_final: 0.8365 (t80) REVERT: D 446 HIS cc_start: 0.6449 (t70) cc_final: 0.6244 (t70) REVERT: D 449 TYR cc_start: 0.7355 (m-80) cc_final: 0.6875 (m-80) REVERT: D 483 ASN cc_start: 0.7777 (m110) cc_final: 0.7076 (p0) REVERT: D 491 LYS cc_start: 0.9400 (ptpp) cc_final: 0.9186 (ptpp) REVERT: D 546 LEU cc_start: 0.7650 (tp) cc_final: 0.7205 (tp) REVERT: D 550 ASP cc_start: 0.7946 (t0) cc_final: 0.7506 (t0) REVERT: D 567 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8822 (tptp) REVERT: D 662 ASN cc_start: 0.9354 (p0) cc_final: 0.8933 (p0) REVERT: D 963 GLN cc_start: 0.7316 (tm-30) cc_final: 0.6736 (tt0) REVERT: D 968 MET cc_start: -0.1726 (tpt) cc_final: -0.2398 (ttt) REVERT: D 1007 TYR cc_start: 0.6590 (m-80) cc_final: 0.5969 (t80) REVERT: D 1378 MET cc_start: 0.7940 (mmt) cc_final: 0.6280 (tpp) outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.5321 time to fit residues: 446.1077 Evaluate side-chains 412 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 486 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 287 optimal weight: 10.0000 chunk 368 optimal weight: 3.9990 chunk 285 optimal weight: 8.9990 chunk 424 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 chunk 502 optimal weight: 40.0000 chunk 314 optimal weight: 2.9990 chunk 306 optimal weight: 0.6980 chunk 231 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 HIS ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 GLN B 106 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN C 368 GLN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS D 279 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN ** D 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 42374 Z= 0.241 Angle : 0.835 14.519 57572 Z= 0.419 Chirality : 0.051 0.389 6686 Planarity : 0.006 0.094 7358 Dihedral : 8.641 59.885 6502 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 27.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.31 % Favored : 85.54 % Rotamer: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.55 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.10), residues: 5220 helix: -1.25 (0.17), residues: 810 sheet: -2.52 (0.13), residues: 1337 loop : -3.60 (0.10), residues: 3073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C1132 HIS 0.010 0.001 HIS B 446 PHE 0.041 0.002 PHE B1126 TYR 0.043 0.002 TYR A1152 ARG 0.012 0.001 ARG B1163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 527 time to evaluate : 4.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8463 (tt) cc_final: 0.7665 (tt) REVERT: A 82 ASP cc_start: 0.9506 (m-30) cc_final: 0.8837 (m-30) REVERT: A 121 MET cc_start: 0.8869 (ttt) cc_final: 0.8660 (ttt) REVERT: A 126 ASP cc_start: 0.8415 (p0) cc_final: 0.8189 (p0) REVERT: A 229 PHE cc_start: 0.7877 (p90) cc_final: 0.7268 (p90) REVERT: A 310 GLN cc_start: 0.8290 (mp10) cc_final: 0.8024 (mp10) REVERT: A 384 ILE cc_start: 0.9351 (pt) cc_final: 0.9048 (mm) REVERT: A 399 THR cc_start: 0.8209 (p) cc_final: 0.7804 (t) REVERT: A 415 MET cc_start: 0.3418 (ttt) cc_final: 0.2957 (ttt) REVERT: A 440 GLU cc_start: 0.5985 (tt0) cc_final: 0.5197 (mp0) REVERT: A 464 MET cc_start: 0.8808 (ttt) cc_final: 0.8515 (ttt) REVERT: A 520 MET cc_start: 0.6976 (mmp) cc_final: 0.6646 (mmt) REVERT: A 567 LYS cc_start: 0.8923 (tttt) cc_final: 0.8624 (mptt) REVERT: A 926 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7357 (tm-30) REVERT: A 931 LEU cc_start: 0.8790 (tp) cc_final: 0.8023 (tp) REVERT: A 959 MET cc_start: 0.5872 (mtt) cc_final: 0.5614 (ptt) REVERT: A 1112 ILE cc_start: 0.7938 (mt) cc_final: 0.7723 (mt) REVERT: A 1122 ARG cc_start: 0.8744 (mtp180) cc_final: 0.8536 (mmm160) REVERT: A 1216 TYR cc_start: 0.8350 (m-10) cc_final: 0.8148 (m-10) REVERT: A 1263 LYS cc_start: 0.8567 (mmpt) cc_final: 0.8274 (mmmt) REVERT: A 1325 GLN cc_start: 0.6221 (tt0) cc_final: 0.5941 (tt0) REVERT: B 99 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7183 (mt-10) REVERT: B 256 TYR cc_start: 0.8428 (t80) cc_final: 0.7980 (t80) REVERT: B 309 PHE cc_start: 0.8141 (m-80) cc_final: 0.7773 (m-80) REVERT: B 318 MET cc_start: 0.8270 (mmm) cc_final: 0.7962 (mmm) REVERT: B 348 THR cc_start: 0.8542 (m) cc_final: 0.7843 (p) REVERT: B 363 ILE cc_start: 0.8609 (tp) cc_final: 0.7990 (tp) REVERT: B 385 PHE cc_start: 0.7966 (m-80) cc_final: 0.7532 (m-80) REVERT: B 409 ILE cc_start: 0.7730 (mp) cc_final: 0.6805 (tp) REVERT: B 461 LEU cc_start: 0.8903 (mp) cc_final: 0.8438 (tp) REVERT: B 531 LYS cc_start: 0.8245 (pttm) cc_final: 0.7890 (tttt) REVERT: B 545 VAL cc_start: 0.7830 (m) cc_final: 0.7513 (p) REVERT: B 552 ILE cc_start: 0.9424 (pt) cc_final: 0.8892 (pt) REVERT: B 557 LYS cc_start: 0.8592 (pttt) cc_final: 0.8313 (pttt) REVERT: B 571 SER cc_start: 0.8467 (t) cc_final: 0.8137 (p) REVERT: B 586 ARG cc_start: 0.7393 (mtp85) cc_final: 0.6651 (mtp180) REVERT: B 619 TYR cc_start: 0.7647 (m-10) cc_final: 0.6624 (m-10) REVERT: B 666 MET cc_start: 0.8081 (ttp) cc_final: 0.7601 (tpt) REVERT: B 977 MET cc_start: 0.9023 (mmt) cc_final: 0.8756 (mmp) REVERT: B 1184 GLU cc_start: 0.7254 (pt0) cc_final: 0.6659 (mt-10) REVERT: C 32 MET cc_start: 0.3807 (tmm) cc_final: 0.3484 (tmm) REVERT: C 189 GLN cc_start: 0.8389 (pm20) cc_final: 0.8169 (tt0) REVERT: C 323 GLU cc_start: 0.8794 (mp0) cc_final: 0.8468 (mp0) REVERT: C 361 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6946 (pp30) REVERT: C 373 ASP cc_start: 0.8345 (t70) cc_final: 0.7946 (m-30) REVERT: C 558 TYR cc_start: 0.7656 (m-80) cc_final: 0.7082 (m-80) REVERT: C 670 LEU cc_start: 0.9309 (pp) cc_final: 0.8952 (pp) REVERT: C 673 MET cc_start: 0.7530 (mtt) cc_final: 0.7311 (mtt) REVERT: C 977 MET cc_start: 0.5912 (ptt) cc_final: 0.5659 (ptt) REVERT: C 1104 TYR cc_start: 0.5305 (t80) cc_final: 0.4077 (t80) REVERT: C 1126 PHE cc_start: 0.9008 (m-80) cc_final: 0.8684 (m-80) REVERT: C 1208 MET cc_start: 0.8449 (ppp) cc_final: 0.8164 (ppp) REVERT: D 151 MET cc_start: 0.4381 (tpp) cc_final: 0.3990 (tpp) REVERT: D 181 PHE cc_start: 0.6351 (p90) cc_final: 0.5821 (p90) REVERT: D 246 MET cc_start: -0.0145 (ttm) cc_final: -0.0968 (mtm) REVERT: D 284 GLN cc_start: 0.8592 (pp30) cc_final: 0.8330 (pm20) REVERT: D 359 PHE cc_start: 0.7941 (p90) cc_final: 0.7678 (p90) REVERT: D 393 TYR cc_start: 0.8562 (t80) cc_final: 0.8346 (t80) REVERT: D 394 TYR cc_start: 0.8775 (t80) cc_final: 0.8573 (t80) REVERT: D 449 TYR cc_start: 0.7242 (m-80) cc_final: 0.6798 (m-80) REVERT: D 464 MET cc_start: 0.8482 (ptt) cc_final: 0.8236 (ptt) REVERT: D 483 ASN cc_start: 0.7647 (m110) cc_final: 0.7144 (p0) REVERT: D 491 LYS cc_start: 0.9403 (ptpp) cc_final: 0.8940 (ttmm) REVERT: D 531 LYS cc_start: 0.7516 (pttp) cc_final: 0.7114 (pttp) REVERT: D 546 LEU cc_start: 0.7723 (tp) cc_final: 0.7283 (tp) REVERT: D 550 ASP cc_start: 0.7942 (t0) cc_final: 0.7530 (t0) REVERT: D 567 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8852 (tptp) REVERT: D 662 ASN cc_start: 0.9356 (p0) cc_final: 0.8898 (p0) REVERT: D 963 GLN cc_start: 0.7167 (tm-30) cc_final: 0.6592 (tt0) REVERT: D 968 MET cc_start: -0.1949 (tpt) cc_final: -0.2649 (ttt) REVERT: D 1007 TYR cc_start: 0.6663 (m-80) cc_final: 0.6073 (t80) REVERT: D 1378 MET cc_start: 0.7924 (mmt) cc_final: 0.6195 (tpp) outliers start: 3 outliers final: 0 residues processed: 530 average time/residue: 0.5505 time to fit residues: 479.9842 Evaluate side-chains 423 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 422 time to evaluate : 4.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 310 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 319 optimal weight: 8.9990 chunk 342 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 394 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 GLN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1241 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN ** D 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1089 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 42374 Z= 0.284 Angle : 0.867 13.163 57572 Z= 0.436 Chirality : 0.052 0.487 6686 Planarity : 0.006 0.068 7358 Dihedral : 8.623 59.934 6502 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 31.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.65 % Favored : 84.20 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.10), residues: 5220 helix: -1.28 (0.17), residues: 812 sheet: -2.54 (0.13), residues: 1345 loop : -3.58 (0.10), residues: 3063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C1132 HIS 0.017 0.002 HIS A1195 PHE 0.037 0.002 PHE D1049 TYR 0.044 0.002 TYR D1216 ARG 0.011 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 4.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8538 (tt) cc_final: 0.7632 (tt) REVERT: A 53 TYR cc_start: 0.8844 (m-10) cc_final: 0.8637 (m-10) REVERT: A 121 MET cc_start: 0.8973 (ttt) cc_final: 0.8702 (ttt) REVERT: A 126 ASP cc_start: 0.8499 (p0) cc_final: 0.8191 (p0) REVERT: A 229 PHE cc_start: 0.7883 (p90) cc_final: 0.6524 (p90) REVERT: A 310 GLN cc_start: 0.8381 (mp10) cc_final: 0.8077 (mp10) REVERT: A 384 ILE cc_start: 0.9320 (pt) cc_final: 0.9052 (mm) REVERT: A 415 MET cc_start: 0.3953 (ttt) cc_final: 0.3375 (ttt) REVERT: A 440 GLU cc_start: 0.6087 (tt0) cc_final: 0.5346 (mp0) REVERT: A 464 MET cc_start: 0.8808 (ttt) cc_final: 0.8504 (ttt) REVERT: A 480 TYR cc_start: 0.7315 (p90) cc_final: 0.7043 (p90) REVERT: A 490 LEU cc_start: 0.8766 (mp) cc_final: 0.8435 (tt) REVERT: A 520 MET cc_start: 0.7305 (mmp) cc_final: 0.6916 (mmt) REVERT: A 673 MET cc_start: 0.8427 (tpt) cc_final: 0.7893 (tpp) REVERT: A 1112 ILE cc_start: 0.7965 (mt) cc_final: 0.7759 (mt) REVERT: A 1211 TYR cc_start: 0.6701 (m-80) cc_final: 0.6285 (m-80) REVERT: A 1263 LYS cc_start: 0.8491 (mmpt) cc_final: 0.8221 (mmmt) REVERT: A 1308 LEU cc_start: 0.8341 (mp) cc_final: 0.8086 (mm) REVERT: A 1314 MET cc_start: 0.8267 (mpp) cc_final: 0.7929 (mpp) REVERT: A 1325 GLN cc_start: 0.6132 (tt0) cc_final: 0.5929 (tt0) REVERT: A 1326 THR cc_start: 0.9017 (m) cc_final: 0.8794 (m) REVERT: B 99 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6887 (mt-10) REVERT: B 164 LEU cc_start: 0.8601 (tp) cc_final: 0.8392 (tp) REVERT: B 256 TYR cc_start: 0.8257 (t80) cc_final: 0.7790 (t80) REVERT: B 309 PHE cc_start: 0.8250 (m-80) cc_final: 0.7993 (m-80) REVERT: B 363 ILE cc_start: 0.8738 (tp) cc_final: 0.8170 (tp) REVERT: B 385 PHE cc_start: 0.8082 (m-80) cc_final: 0.7669 (m-80) REVERT: B 409 ILE cc_start: 0.7759 (mp) cc_final: 0.6814 (tp) REVERT: B 460 HIS cc_start: 0.8541 (m90) cc_final: 0.7965 (m90) REVERT: B 461 LEU cc_start: 0.9083 (mp) cc_final: 0.8800 (tp) REVERT: B 500 MET cc_start: 0.6729 (tmm) cc_final: 0.6029 (ttt) REVERT: B 531 LYS cc_start: 0.8236 (pttm) cc_final: 0.7887 (tttt) REVERT: B 552 ILE cc_start: 0.9424 (pt) cc_final: 0.8938 (pt) REVERT: B 557 LYS cc_start: 0.8647 (pttt) cc_final: 0.8370 (pttt) REVERT: B 571 SER cc_start: 0.8459 (t) cc_final: 0.8035 (p) REVERT: B 586 ARG cc_start: 0.7580 (mtp85) cc_final: 0.6796 (mtp180) REVERT: B 619 TYR cc_start: 0.7724 (m-10) cc_final: 0.6746 (m-10) REVERT: B 808 PHE cc_start: 0.8571 (p90) cc_final: 0.8198 (p90) REVERT: B 977 MET cc_start: 0.9049 (mmt) cc_final: 0.8818 (mmp) REVERT: B 1184 GLU cc_start: 0.7307 (pt0) cc_final: 0.6651 (mt-10) REVERT: C 101 MET cc_start: 0.8319 (mpp) cc_final: 0.8006 (mpp) REVERT: C 323 GLU cc_start: 0.8803 (mp0) cc_final: 0.8488 (mp0) REVERT: C 373 ASP cc_start: 0.8443 (t70) cc_final: 0.8026 (m-30) REVERT: C 977 MET cc_start: 0.6069 (ptt) cc_final: 0.5756 (ptt) REVERT: C 1126 PHE cc_start: 0.9045 (m-80) cc_final: 0.8745 (m-80) REVERT: D 151 MET cc_start: 0.4568 (tpp) cc_final: 0.3870 (tpp) REVERT: D 158 LEU cc_start: 0.8389 (tt) cc_final: 0.7610 (mp) REVERT: D 181 PHE cc_start: 0.6319 (p90) cc_final: 0.5796 (p90) REVERT: D 284 GLN cc_start: 0.8726 (pp30) cc_final: 0.8443 (pm20) REVERT: D 359 PHE cc_start: 0.7990 (p90) cc_final: 0.7777 (p90) REVERT: D 449 TYR cc_start: 0.7488 (m-80) cc_final: 0.7043 (m-80) REVERT: D 464 MET cc_start: 0.8508 (ptt) cc_final: 0.8266 (ptt) REVERT: D 483 ASN cc_start: 0.7694 (m110) cc_final: 0.7188 (p0) REVERT: D 491 LYS cc_start: 0.9426 (ptpp) cc_final: 0.8968 (ttmm) REVERT: D 531 LYS cc_start: 0.7711 (pttp) cc_final: 0.7256 (pttp) REVERT: D 546 LEU cc_start: 0.7712 (tp) cc_final: 0.7303 (tp) REVERT: D 550 ASP cc_start: 0.7996 (t0) cc_final: 0.7588 (t0) REVERT: D 567 LYS cc_start: 0.9047 (tmtt) cc_final: 0.8825 (tptp) REVERT: D 662 ASN cc_start: 0.9369 (p0) cc_final: 0.8923 (p0) REVERT: D 963 GLN cc_start: 0.7000 (tm-30) cc_final: 0.6575 (tt0) REVERT: D 968 MET cc_start: -0.1982 (tpt) cc_final: -0.2717 (ttt) REVERT: D 1007 TYR cc_start: 0.6688 (m-80) cc_final: 0.6119 (t80) REVERT: D 1378 MET cc_start: 0.7914 (mmt) cc_final: 0.6165 (tpp) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.5442 time to fit residues: 455.4154 Evaluate side-chains 409 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 4.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 456 optimal weight: 20.0000 chunk 481 optimal weight: 20.0000 chunk 438 optimal weight: 0.9990 chunk 467 optimal weight: 8.9990 chunk 480 optimal weight: 0.9980 chunk 281 optimal weight: 9.9990 chunk 203 optimal weight: 30.0000 chunk 367 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 422 optimal weight: 3.9990 chunk 442 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN A 816 ASN ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 ASN ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 42374 Z= 0.258 Angle : 0.846 12.468 57572 Z= 0.423 Chirality : 0.051 0.700 6686 Planarity : 0.006 0.082 7358 Dihedral : 8.542 59.461 6502 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 29.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.83 % Favored : 85.04 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: -4.14 (0.10), residues: 5220 helix: -1.17 (0.17), residues: 816 sheet: -2.42 (0.14), residues: 1295 loop : -3.52 (0.10), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1132 HIS 0.018 0.001 HIS A1195 PHE 0.040 0.002 PHE B1126 TYR 0.044 0.002 TYR D1216 ARG 0.011 0.001 ARG B1122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 5.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8641 (tt) cc_final: 0.7700 (tt) REVERT: A 82 ASP cc_start: 0.9438 (m-30) cc_final: 0.8813 (m-30) REVERT: A 121 MET cc_start: 0.8963 (ttt) cc_final: 0.8725 (ttt) REVERT: A 126 ASP cc_start: 0.8484 (p0) cc_final: 0.8126 (p0) REVERT: A 229 PHE cc_start: 0.7861 (p90) cc_final: 0.6498 (p90) REVERT: A 245 GLU cc_start: 0.9106 (mp0) cc_final: 0.8877 (mp0) REVERT: A 440 GLU cc_start: 0.5997 (tt0) cc_final: 0.5203 (mp0) REVERT: A 464 MET cc_start: 0.8827 (ttt) cc_final: 0.8499 (ttt) REVERT: A 480 TYR cc_start: 0.7450 (p90) cc_final: 0.7150 (p90) REVERT: A 520 MET cc_start: 0.7274 (mmp) cc_final: 0.6852 (mmt) REVERT: A 931 LEU cc_start: 0.8937 (tp) cc_final: 0.8181 (tp) REVERT: A 1112 ILE cc_start: 0.7890 (mt) cc_final: 0.7667 (mt) REVERT: A 1122 ARG cc_start: 0.8709 (mtp180) cc_final: 0.8392 (mtp180) REVERT: A 1211 TYR cc_start: 0.6427 (m-80) cc_final: 0.6083 (m-80) REVERT: A 1263 LYS cc_start: 0.8467 (mmpt) cc_final: 0.8213 (mmmt) REVERT: A 1280 ILE cc_start: 0.8422 (mp) cc_final: 0.7777 (mp) REVERT: A 1308 LEU cc_start: 0.8364 (mp) cc_final: 0.8084 (mm) REVERT: A 1314 MET cc_start: 0.8220 (mpp) cc_final: 0.7914 (mpp) REVERT: A 1328 LEU cc_start: 0.9352 (tp) cc_final: 0.9143 (tp) REVERT: B 99 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6940 (mt-10) REVERT: B 164 LEU cc_start: 0.8651 (tp) cc_final: 0.8442 (tp) REVERT: B 255 THR cc_start: 0.9251 (p) cc_final: 0.8880 (p) REVERT: B 256 TYR cc_start: 0.8227 (t80) cc_final: 0.7757 (t80) REVERT: B 309 PHE cc_start: 0.8186 (m-80) cc_final: 0.7945 (m-80) REVERT: B 348 THR cc_start: 0.8173 (m) cc_final: 0.7931 (p) REVERT: B 363 ILE cc_start: 0.8510 (tp) cc_final: 0.7714 (tp) REVERT: B 385 PHE cc_start: 0.8085 (m-80) cc_final: 0.7674 (m-80) REVERT: B 409 ILE cc_start: 0.7828 (mp) cc_final: 0.6804 (tp) REVERT: B 460 HIS cc_start: 0.8544 (m90) cc_final: 0.7909 (m90) REVERT: B 461 LEU cc_start: 0.9123 (mp) cc_final: 0.8847 (tp) REVERT: B 500 MET cc_start: 0.6611 (tmm) cc_final: 0.5909 (ttt) REVERT: B 531 LYS cc_start: 0.8271 (pttm) cc_final: 0.7934 (tttt) REVERT: B 557 LYS cc_start: 0.8623 (pttt) cc_final: 0.8328 (pttt) REVERT: B 571 SER cc_start: 0.8414 (t) cc_final: 0.7357 (p) REVERT: B 586 ARG cc_start: 0.7543 (mtp85) cc_final: 0.6827 (mtp180) REVERT: B 619 TYR cc_start: 0.7662 (m-10) cc_final: 0.6604 (m-10) REVERT: B 808 PHE cc_start: 0.8644 (p90) cc_final: 0.8202 (p90) REVERT: B 977 MET cc_start: 0.9014 (mmt) cc_final: 0.8784 (mmp) REVERT: B 1184 GLU cc_start: 0.7172 (pt0) cc_final: 0.6508 (mt-10) REVERT: C 101 MET cc_start: 0.8098 (mpp) cc_final: 0.7843 (mpp) REVERT: C 161 LEU cc_start: 0.5450 (pt) cc_final: 0.5163 (mp) REVERT: C 229 PHE cc_start: 0.8882 (p90) cc_final: 0.8675 (p90) REVERT: C 323 GLU cc_start: 0.8806 (mp0) cc_final: 0.8500 (mp0) REVERT: C 373 ASP cc_start: 0.8392 (t70) cc_final: 0.8006 (m-30) REVERT: C 977 MET cc_start: 0.5940 (ptt) cc_final: 0.5625 (ptt) REVERT: C 1126 PHE cc_start: 0.9046 (m-80) cc_final: 0.8731 (m-80) REVERT: C 1208 MET cc_start: 0.8421 (ppp) cc_final: 0.7981 (ppp) REVERT: D 151 MET cc_start: 0.4455 (tpp) cc_final: 0.4209 (tpp) REVERT: D 246 MET cc_start: -0.0149 (ttm) cc_final: -0.0929 (mtm) REVERT: D 284 GLN cc_start: 0.8546 (pp30) cc_final: 0.8139 (pm20) REVERT: D 359 PHE cc_start: 0.7998 (p90) cc_final: 0.7650 (p90) REVERT: D 387 ARG cc_start: 0.9017 (mmp-170) cc_final: 0.8698 (mmp80) REVERT: D 393 TYR cc_start: 0.8420 (t80) cc_final: 0.8200 (t80) REVERT: D 446 HIS cc_start: 0.6366 (t70) cc_final: 0.6157 (t70) REVERT: D 449 TYR cc_start: 0.7418 (m-80) cc_final: 0.6999 (m-80) REVERT: D 483 ASN cc_start: 0.7639 (m110) cc_final: 0.7230 (p0) REVERT: D 491 LYS cc_start: 0.9421 (ptpp) cc_final: 0.8963 (ttmm) REVERT: D 531 LYS cc_start: 0.7589 (pttp) cc_final: 0.7163 (pttp) REVERT: D 546 LEU cc_start: 0.7909 (tp) cc_final: 0.7526 (tp) REVERT: D 550 ASP cc_start: 0.7954 (t0) cc_final: 0.7592 (t0) REVERT: D 567 LYS cc_start: 0.9036 (tmtt) cc_final: 0.8823 (tptp) REVERT: D 662 ASN cc_start: 0.9358 (p0) cc_final: 0.8878 (p0) REVERT: D 968 MET cc_start: -0.2161 (tpt) cc_final: -0.2885 (ttt) REVERT: D 1007 TYR cc_start: 0.6638 (m-80) cc_final: 0.6176 (t80) REVERT: D 1378 MET cc_start: 0.7858 (mmt) cc_final: 0.6158 (tpp) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.5421 time to fit residues: 454.2749 Evaluate side-chains 418 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 4.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 466 optimal weight: 0.9980 chunk 307 optimal weight: 6.9990 chunk 494 optimal weight: 30.0000 chunk 302 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 chunk 343 optimal weight: 9.9990 chunk 519 optimal weight: 30.0000 chunk 477 optimal weight: 40.0000 chunk 413 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 319 optimal weight: 0.3980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 42374 Z= 0.286 Angle : 0.871 12.880 57572 Z= 0.438 Chirality : 0.052 0.402 6686 Planarity : 0.006 0.068 7358 Dihedral : 8.587 59.310 6502 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 32.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.69 % Favored : 84.18 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.10), residues: 5220 helix: -1.22 (0.17), residues: 802 sheet: -2.45 (0.14), residues: 1270 loop : -3.54 (0.09), residues: 3148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 739 HIS 0.015 0.001 HIS A1195 PHE 0.067 0.002 PHE A1196 TYR 0.043 0.002 TYR D1216 ARG 0.010 0.001 ARG D 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 4.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8656 (tt) cc_final: 0.7689 (tt) REVERT: A 121 MET cc_start: 0.9011 (ttt) cc_final: 0.8772 (ttt) REVERT: A 229 PHE cc_start: 0.7971 (p90) cc_final: 0.6681 (p90) REVERT: A 385 PHE cc_start: 0.9189 (m-10) cc_final: 0.8939 (m-10) REVERT: A 415 MET cc_start: 0.4022 (ttt) cc_final: 0.1745 (ptp) REVERT: A 440 GLU cc_start: 0.5992 (tt0) cc_final: 0.5124 (mp0) REVERT: A 464 MET cc_start: 0.8812 (ttt) cc_final: 0.8469 (ttt) REVERT: A 480 TYR cc_start: 0.7414 (p90) cc_final: 0.7084 (p90) REVERT: A 491 LYS cc_start: 0.9019 (tptt) cc_final: 0.8687 (tppt) REVERT: A 500 MET cc_start: 0.2386 (ttt) cc_final: 0.2065 (ttt) REVERT: A 520 MET cc_start: 0.7338 (mmp) cc_final: 0.7080 (mmp) REVERT: A 619 TYR cc_start: 0.7531 (m-80) cc_final: 0.7285 (m-80) REVERT: A 1112 ILE cc_start: 0.7887 (mt) cc_final: 0.7654 (mt) REVERT: A 1122 ARG cc_start: 0.8727 (mtp180) cc_final: 0.8412 (mtp180) REVERT: A 1211 TYR cc_start: 0.6419 (m-80) cc_final: 0.6036 (m-80) REVERT: A 1263 LYS cc_start: 0.8550 (mmpt) cc_final: 0.8214 (mmmt) REVERT: A 1308 LEU cc_start: 0.8461 (mp) cc_final: 0.8206 (mm) REVERT: A 1314 MET cc_start: 0.8271 (mpp) cc_final: 0.8026 (mpp) REVERT: A 1326 THR cc_start: 0.9036 (m) cc_final: 0.8820 (m) REVERT: A 1328 LEU cc_start: 0.9376 (tp) cc_final: 0.9156 (tp) REVERT: B 99 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6886 (mt-10) REVERT: B 255 THR cc_start: 0.9273 (p) cc_final: 0.8952 (p) REVERT: B 256 TYR cc_start: 0.8446 (t80) cc_final: 0.7925 (t80) REVERT: B 309 PHE cc_start: 0.8230 (m-80) cc_final: 0.7895 (m-80) REVERT: B 310 GLN cc_start: 0.8588 (mp-120) cc_final: 0.8163 (mm110) REVERT: B 348 THR cc_start: 0.8675 (m) cc_final: 0.7808 (p) REVERT: B 363 ILE cc_start: 0.8388 (tp) cc_final: 0.7652 (tp) REVERT: B 385 PHE cc_start: 0.8111 (m-80) cc_final: 0.7706 (m-80) REVERT: B 409 ILE cc_start: 0.7924 (mp) cc_final: 0.6948 (tp) REVERT: B 460 HIS cc_start: 0.8570 (m90) cc_final: 0.7922 (m90) REVERT: B 461 LEU cc_start: 0.9224 (mp) cc_final: 0.8961 (tp) REVERT: B 500 MET cc_start: 0.6638 (tmm) cc_final: 0.5934 (ttt) REVERT: B 531 LYS cc_start: 0.8348 (pttm) cc_final: 0.7936 (tttt) REVERT: B 557 LYS cc_start: 0.8597 (pttt) cc_final: 0.8232 (pttt) REVERT: B 571 SER cc_start: 0.8269 (t) cc_final: 0.7361 (p) REVERT: B 586 ARG cc_start: 0.7570 (mtp85) cc_final: 0.6989 (mtp180) REVERT: B 619 TYR cc_start: 0.7782 (m-10) cc_final: 0.6751 (m-10) REVERT: B 808 PHE cc_start: 0.8672 (p90) cc_final: 0.8305 (p90) REVERT: B 977 MET cc_start: 0.9051 (mmt) cc_final: 0.8793 (mmp) REVERT: B 1126 PHE cc_start: 0.8269 (t80) cc_final: 0.7926 (t80) REVERT: B 1184 GLU cc_start: 0.7184 (pt0) cc_final: 0.6537 (mt-10) REVERT: C 101 MET cc_start: 0.8194 (mpp) cc_final: 0.7967 (mpp) REVERT: C 161 LEU cc_start: 0.5557 (pt) cc_final: 0.5231 (mp) REVERT: C 323 GLU cc_start: 0.8847 (mp0) cc_final: 0.8520 (mp0) REVERT: C 373 ASP cc_start: 0.8478 (t70) cc_final: 0.8117 (m-30) REVERT: C 977 MET cc_start: 0.5801 (ptt) cc_final: 0.5498 (ptt) REVERT: C 1014 ARG cc_start: 0.4830 (ttm170) cc_final: 0.4595 (tpp-160) REVERT: C 1126 PHE cc_start: 0.9057 (m-80) cc_final: 0.8745 (m-80) REVERT: C 1208 MET cc_start: 0.8356 (ppp) cc_final: 0.7961 (ppp) REVERT: D 151 MET cc_start: 0.4519 (tpp) cc_final: 0.4267 (tpp) REVERT: D 246 MET cc_start: -0.0130 (ttm) cc_final: -0.0864 (mtm) REVERT: D 359 PHE cc_start: 0.8098 (p90) cc_final: 0.7886 (p90) REVERT: D 387 ARG cc_start: 0.9092 (mmp-170) cc_final: 0.8703 (mmp80) REVERT: D 393 TYR cc_start: 0.8491 (t80) cc_final: 0.8235 (t80) REVERT: D 446 HIS cc_start: 0.6452 (t70) cc_final: 0.6214 (t70) REVERT: D 449 TYR cc_start: 0.7474 (m-80) cc_final: 0.7052 (m-80) REVERT: D 483 ASN cc_start: 0.7658 (m110) cc_final: 0.7249 (p0) REVERT: D 491 LYS cc_start: 0.9420 (ptpp) cc_final: 0.8975 (ttmm) REVERT: D 500 MET cc_start: 0.4642 (tpp) cc_final: 0.3170 (tpp) REVERT: D 531 LYS cc_start: 0.7787 (pttp) cc_final: 0.7342 (pttp) REVERT: D 662 ASN cc_start: 0.9361 (p0) cc_final: 0.8912 (p0) REVERT: D 968 MET cc_start: -0.2130 (tpt) cc_final: -0.2913 (ttt) REVERT: D 1007 TYR cc_start: 0.6563 (m-80) cc_final: 0.5976 (t80) REVERT: D 1378 MET cc_start: 0.7818 (mmt) cc_final: 0.6128 (tpp) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 0.5343 time to fit residues: 452.8007 Evaluate side-chains 412 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 4.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 253 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 440 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 381 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 413 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 425 optimal weight: 0.1980 chunk 52 optimal weight: 0.8980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN B 106 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1233 ASN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.149504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.118582 restraints weight = 194927.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.121326 restraints weight = 156193.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.123211 restraints weight = 125179.641| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 42374 Z= 0.220 Angle : 0.812 12.735 57572 Z= 0.404 Chirality : 0.050 0.374 6686 Planarity : 0.006 0.086 7358 Dihedral : 8.287 59.952 6502 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.68 % Favored : 86.19 % Rotamer: Outliers : 0.02 % Allowed : 0.68 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.10), residues: 5220 helix: -1.01 (0.17), residues: 821 sheet: -2.31 (0.14), residues: 1281 loop : -3.44 (0.10), residues: 3118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 765 HIS 0.017 0.001 HIS A1195 PHE 0.064 0.002 PHE A1196 TYR 0.044 0.002 TYR D1216 ARG 0.009 0.001 ARG C1163 =============================================================================== Job complete usr+sys time: 9443.29 seconds wall clock time: 172 minutes 54.14 seconds (10374.14 seconds total)