Starting phenix.real_space_refine (version: dev) on Wed Dec 21 04:12:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7s_12755/12_2022/7o7s_12755.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7s_12755/12_2022/7o7s_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_12755/12_2022/7o7s_12755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7s_12755/12_2022/7o7s_12755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7s_12755/12_2022/7o7s_12755.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7s_12755/12_2022/7o7s_12755.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 Convert atoms to be neutral 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-4807/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 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: 1 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 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: 1 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 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: 1 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 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: 2 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: 1 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 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 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 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 chiralities: 5 Time building chain proxies: 22.79, per 1000 atoms: 0.55 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: 17.84 Conformation dependent library (CDL) restraints added in 6.4 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: 0.71 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: 8.80 Time building geometry restraints manager: 19.17 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=" C2 NAG H 1 " pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 109.64 113.68 -4.04 5.38e-01 3.45e+00 5.65e+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 ... (remaining 57567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 21926 17.93 - 35.87: 2962 35.87 - 53.80: 537 53.80 - 71.73: 105 71.73 - 89.66: 55 Dihedral angle restraints: 25585 sinusoidal: 10329 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 25582 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 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. 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: 2.240 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: 0.050 Extract box with map and model: 10.660 Check model and map are aligned: 0.660 Convert atoms to be neutral: 0.370 Process input model: 96.870 Find NCS groups from input model: 3.850 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5779 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= 0.591 Angle : 1.273 14.498 57572 Z= 0.730 Chirality : 0.074 1.958 6686 Planarity : 0.021 0.306 7358 Dihedral : 16.676 89.663 15624 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.69 % Allowed : 20.13 % Favored : 79.18 % Rotamer Outliers : 1.09 % 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 *********************** 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 : 4.577 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 outliers start: 50 outliers final: 12 residues processed: 677 average time/residue: 0.5420 time to fit residues: 603.9371 Evaluate side-chains 432 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 420 time to evaluate : 4.780 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.3811 time to fit residues: 15.0859 ------------------------------------------------------------------------------- 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: 0.9990 chunk 134 optimal weight: 4.9990 chunk 266 optimal weight: 0.5980 chunk 210 optimal weight: 8.9990 chunk 408 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 303 optimal weight: 8.9990 chunk 473 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 562 ASN 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 142 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B1296 ASN C 97 ASN C 173 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 HIS C 644 ASN ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1020 HIS C1035 ASN ** C1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1243 ASN ** 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 321 HIS ** 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 424 ASN D 477 GLN ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 HIS D 647 ASN D 843 GLN D 938 ASN D 964 ASN D1051 GLN D1062 HIS D1159 ASN D1331 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 42374 Z= 0.333 Angle : 0.951 11.117 57572 Z= 0.502 Chirality : 0.055 0.608 6686 Planarity : 0.007 0.087 7358 Dihedral : 8.763 35.903 5878 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 26.06 Ramachandran Plot: Outliers : 0.29 % Allowed : 16.13 % Favored : 83.58 % Rotamer Outliers : 0.68 % 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: -5.28 (0.09), residues: 5220 helix: -2.34 (0.15), residues: 796 sheet: -3.21 (0.13), residues: 1217 loop : -4.17 (0.09), residues: 3207 *********************** 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 588 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 557 time to evaluate : 4.669 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 outliers start: 31 outliers final: 13 residues processed: 588 average time/residue: 0.5173 time to fit residues: 504.6827 Evaluate side-chains 421 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 408 time to evaluate : 4.661 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.3689 time to fit residues: 15.4980 ------------------------------------------------------------------------------- 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: 4.9990 chunk 146 optimal weight: 0.0970 chunk 393 optimal weight: 1.9990 chunk 322 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 473 optimal weight: 5.9990 chunk 512 optimal weight: 30.0000 chunk 422 optimal weight: 0.0270 chunk 470 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 380 optimal weight: 3.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 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 ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 ASN A1171 ASN A1259 HIS ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 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** C 177 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 GLN ** 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** ** C1159 ASN ** 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 154 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 HIS ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 GLN ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 964 ASN D1062 HIS D1358 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 42374 Z= 0.252 Angle : 0.836 13.694 57572 Z= 0.437 Chirality : 0.052 0.529 6686 Planarity : 0.006 0.077 7358 Dihedral : 7.935 36.256 5878 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.39 % Favored : 85.38 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: -4.72 (0.10), residues: 5220 helix: -1.68 (0.16), residues: 794 sheet: -2.82 (0.13), residues: 1218 loop : -3.87 (0.09), residues: 3208 *********************** 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 579 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 571 time to evaluate : 4.665 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 outliers start: 8 outliers final: 5 residues processed: 578 average time/residue: 0.5240 time to fit residues: 501.7396 Evaluate side-chains 423 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 418 time to evaluate : 5.047 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3679 time to fit residues: 10.1391 ------------------------------------------------------------------------------- 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: 9.9990 chunk 356 optimal weight: 20.0000 chunk 245 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 318 optimal weight: 0.9990 chunk 475 optimal weight: 10.0000 chunk 503 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 450 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 182 GLN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 995 GLN ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN A1171 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** 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** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1296 ASN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN C 177 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 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 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1182 HIS C1242 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN ** D 310 GLN ** 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 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5951 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 42374 Z= 0.406 Angle : 0.991 12.917 57572 Z= 0.517 Chirality : 0.056 0.495 6686 Planarity : 0.007 0.085 7358 Dihedral : 8.137 34.186 5878 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 38.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.97 % Favored : 82.84 % Rotamer Outliers : 0.31 % 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: -4.83 (0.10), residues: 5220 helix: -1.96 (0.15), residues: 808 sheet: -2.80 (0.13), residues: 1235 loop : -3.94 (0.09), residues: 3177 *********************** 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 525 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 511 time to evaluate : 5.612 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 outliers start: 14 outliers final: 6 residues processed: 524 average time/residue: 0.5492 time to fit residues: 476.6665 Evaluate side-chains 400 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 394 time to evaluate : 4.681 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3638 time to fit residues: 10.6075 ------------------------------------------------------------------------------- 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: 9.9990 chunk 285 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 374 optimal weight: 0.5980 chunk 207 optimal weight: 8.9990 chunk 429 optimal weight: 8.9990 chunk 348 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 257 optimal weight: 9.9990 chunk 452 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 566 ASN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN A1171 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN B 132 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS ** B 406 GLN ** 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** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** 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 189 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 651 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1302 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 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 GLN D1062 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 42374 Z= 0.259 Angle : 0.846 12.550 57572 Z= 0.439 Chirality : 0.052 0.461 6686 Planarity : 0.006 0.090 7358 Dihedral : 7.635 35.616 5878 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 27.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.08 % Favored : 85.75 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % 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: -4.51 (0.10), residues: 5220 helix: -1.49 (0.16), residues: 804 sheet: -2.65 (0.13), residues: 1300 loop : -3.76 (0.09), residues: 3116 *********************** 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 535 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 528 time to evaluate : 4.793 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 outliers start: 7 outliers final: 2 residues processed: 535 average time/residue: 0.5385 time to fit residues: 475.5220 Evaluate side-chains 401 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 399 time to evaluate : 4.805 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3691 time to fit residues: 8.1349 ------------------------------------------------------------------------------- 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: 5.9990 chunk 453 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 295 optimal weight: 20.0000 chunk 124 optimal weight: 0.0000 chunk 504 optimal weight: 8.9990 chunk 418 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 264 optimal weight: 2.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- 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 177 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 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN A1171 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 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** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1259 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 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 651 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** 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 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 HIS ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 GLN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 42374 Z= 0.247 Angle : 0.819 12.727 57572 Z= 0.423 Chirality : 0.051 0.429 6686 Planarity : 0.006 0.221 7358 Dihedral : 7.331 39.781 5878 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.18 % Favored : 85.65 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.10), residues: 5220 helix: -1.21 (0.17), residues: 804 sheet: -2.49 (0.13), residues: 1298 loop : -3.62 (0.09), residues: 3118 *********************** 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 533 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 532 time to evaluate : 4.855 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 outliers start: 1 outliers final: 0 residues processed: 533 average time/residue: 0.5404 time to fit residues: 475.0958 Evaluate side-chains 394 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 4.462 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1985 ------------------------------------------------------------------------------- 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: 7.9990 chunk 285 optimal weight: 8.9990 chunk 424 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 chunk 502 optimal weight: 40.0000 chunk 314 optimal weight: 1.9990 chunk 306 optimal weight: 0.0870 chunk 231 optimal weight: 2.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- 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 177 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 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 GLN ** 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** B 106 GLN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 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 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 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 189 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 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** 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 177 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 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 42374 Z= 0.253 Angle : 0.827 14.127 57572 Z= 0.426 Chirality : 0.051 0.513 6686 Planarity : 0.006 0.174 7358 Dihedral : 7.144 37.439 5878 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.93 % Favored : 85.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.10), residues: 5220 helix: -1.10 (0.17), residues: 806 sheet: -2.28 (0.14), residues: 1308 loop : -3.53 (0.10), residues: 3106 *********************** 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 516 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 4.863 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 outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.5395 time to fit residues: 461.7557 Evaluate side-chains 393 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 4.692 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8442 ------------------------------------------------------------------------------- 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: 2.9990 chunk 200 optimal weight: 6.9990 chunk 299 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 319 optimal weight: 3.9990 chunk 342 optimal weight: 0.9980 chunk 248 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 394 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 GLN ** 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** B 106 GLN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 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** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS ** B1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** C 189 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 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 177 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 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5725 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 42374 Z= 0.221 Angle : 0.804 12.254 57572 Z= 0.411 Chirality : 0.050 0.427 6686 Planarity : 0.006 0.135 7358 Dihedral : 6.871 38.461 5878 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.33 % Favored : 86.53 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.02 % 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: -3.94 (0.10), residues: 5220 helix: -0.99 (0.17), residues: 819 sheet: -2.15 (0.14), residues: 1321 loop : -3.47 (0.10), residues: 3080 *********************** 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 524 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 523 time to evaluate : 5.028 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 outliers start: 1 outliers final: 0 residues processed: 524 average time/residue: 0.5601 time to fit residues: 482.1173 Evaluate side-chains 398 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 4.771 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.5972 ------------------------------------------------------------------------------- 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: 5.9990 chunk 438 optimal weight: 10.0000 chunk 467 optimal weight: 5.9990 chunk 480 optimal weight: 20.0000 chunk 281 optimal weight: 9.9990 chunk 203 optimal weight: 0.4980 chunk 367 optimal weight: 30.0000 chunk 143 optimal weight: 9.9990 chunk 422 optimal weight: 9.9990 chunk 442 optimal weight: 0.7980 overall best weight: 4.6586 ------------------------------------------------------------------------------- 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 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 GLN ** 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 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 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 644 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 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN ** C 189 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 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 177 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 413 ASN D 680 ASN ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1089 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.084 42374 Z= 0.367 Angle : 0.939 12.398 57572 Z= 0.486 Chirality : 0.054 0.390 6686 Planarity : 0.007 0.101 7358 Dihedral : 7.329 35.886 5878 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 37.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.96 % Favored : 83.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.10), residues: 5220 helix: -1.50 (0.16), residues: 825 sheet: -2.31 (0.14), residues: 1295 loop : -3.59 (0.09), residues: 3100 *********************** 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 493 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 4.812 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 outliers start: 0 outliers final: 0 residues processed: 493 average time/residue: 0.5494 time to fit residues: 451.1438 Evaluate side-chains 369 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 5.232 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0978 ------------------------------------------------------------------------------- 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: 0.9990 chunk 494 optimal weight: 7.9990 chunk 302 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 343 optimal weight: 10.0000 chunk 519 optimal weight: 30.0000 chunk 477 optimal weight: 30.0000 chunk 413 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 319 optimal weight: 0.3980 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 HIS ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 GLN ** 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** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 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** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 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 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** C 576 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 177 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 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS D1259 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 42374 Z= 0.251 Angle : 0.837 13.178 57572 Z= 0.430 Chirality : 0.051 0.383 6686 Planarity : 0.006 0.067 7358 Dihedral : 7.061 35.989 5878 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 28.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.60 % Favored : 86.26 % Rotamer Outliers : 0.00 % 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: -4.04 (0.10), residues: 5220 helix: -1.22 (0.17), residues: 826 sheet: -2.15 (0.14), residues: 1267 loop : -3.51 (0.09), residues: 3127 ********************** 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 486 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 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 outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.5413 time to fit residues: 442.0373 Evaluate side-chains 381 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 5.038 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9075 ------------------------------------------------------------------------------- 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: 4.9990 chunk 328 optimal weight: 10.0000 chunk 440 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 381 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 413 optimal weight: 0.9990 chunk 173 optimal weight: 20.0000 chunk 425 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 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 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 GLN ** 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** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS ** 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** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 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 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 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1123 ASN D 112 GLN ** 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 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1281 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.148726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.116633 restraints weight = 195411.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.120008 restraints weight = 145671.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.121626 restraints weight = 121037.616| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 42374 Z= 0.241 Angle : 0.819 12.251 57572 Z= 0.421 Chirality : 0.051 0.380 6686 Planarity : 0.006 0.067 7358 Dihedral : 6.883 35.188 5878 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.23 % Favored : 85.65 % Rotamer Outliers : 0.02 % 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: -3.94 (0.11), residues: 5220 helix: -1.01 (0.17), residues: 822 sheet: -2.14 (0.14), residues: 1308 loop : -3.47 (0.10), residues: 3090 =============================================================================== Job complete usr+sys time: 9241.97 seconds wall clock time: 169 minutes 7.58 seconds (10147.58 seconds total)