Starting phenix.real_space_refine on Tue Apr 16 19:11:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/04_2024/7o7r_12754.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/04_2024/7o7r_12754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/04_2024/7o7r_12754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/04_2024/7o7r_12754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/04_2024/7o7r_12754.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/04_2024/7o7r_12754.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 172 5.16 5 C 25734 2.51 5 N 6746 2.21 5 O 7878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 184": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A GLU 886": "OE1" <-> "OE2" Residue "A GLU 911": "OE1" <-> "OE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A GLU 1096": "OE1" <-> "OE2" Residue "A GLU 1165": "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 GLU 439": "OE1" <-> "OE2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "B GLU 624": "OE1" <-> "OE2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B GLU 753": "OE1" <-> "OE2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B GLU 806": "OE1" <-> "OE2" Residue "B GLU 842": "OE1" <-> "OE2" Residue "B GLU 892": "OE1" <-> "OE2" Residue "B GLU 906": "OE1" <-> "OE2" Residue "B GLU 908": "OE1" <-> "OE2" Residue "B GLU 911": "OE1" <-> "OE2" Residue "B GLU 930": "OE1" <-> "OE2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B GLU 999": "OE1" <-> "OE2" Residue "B GLU 1030": "OE1" <-> "OE2" Residue "B GLU 1165": "OE1" <-> "OE2" Residue "B GLU 1337": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 737": "OE1" <-> "OE2" Residue "C GLU 753": "OE1" <-> "OE2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C GLU 840": "OE1" <-> "OE2" Residue "C GLU 908": "OE1" <-> "OE2" Residue "C GLU 999": "OE1" <-> "OE2" Residue "C GLU 1030": "OE1" <-> "OE2" Residue "C GLU 1198": "OE1" <-> "OE2" Residue "C GLU 1337": "OE1" <-> "OE2" Residue "C GLU 1338": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D GLU 612": "OE1" <-> "OE2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D GLU 737": "OE1" <-> "OE2" Residue "D GLU 753": "OE1" <-> "OE2" Residue "D PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 806": "OE1" <-> "OE2" Residue "D GLU 842": "OE1" <-> "OE2" Residue "D GLU 886": "OE1" <-> "OE2" Residue "D GLU 906": "OE1" <-> "OE2" Residue "D GLU 930": "OE1" <-> "OE2" Residue "D GLU 1098": "OE1" <-> "OE2" Residue "D GLU 1137": "OE1" <-> "OE2" Residue "D GLU 1337": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40530 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10023 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 67, 'TRANS': 1217} Chain breaks: 1 Chain: "B" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} Chain breaks: 1 Chain: "C" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10023 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 67, 'TRANS': 1217} Chain breaks: 1 Chain: "D" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 21.14, per 1000 atoms: 0.52 Number of scatterers: 40530 At special positions: 0 Unit cell: (213.556, 152.54, 158.852, 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 172 16.00 O 7878 8.00 N 6746 7.00 C 25734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, 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=2.01 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS B 278 " distance=2.02 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.03 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 689 " distance=2.04 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.02 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 86 " distance=2.04 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 299 " distance=2.02 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 287 " distance=2.02 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 563 " distance=2.04 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS D 431 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1127 " distance=2.01 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 86 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 771 " distance=2.04 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 689 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS D 921 " - pdb=" SG CYS D1321 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1127 " distance=2.04 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 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-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 247 " " NAG D2004 " - " ASN D 396 " " NAG D2005 " - " ASN D 410 " " 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 869 " " NAG L 1 " - " ASN D 991 " Time building additional restraints: 18.75 Conformation dependent library (CDL) restraints added in 8.5 seconds 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9600 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 16.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 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: 6.241A pdb=" N SER A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N MET A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 993 Proline residue: A 982 - end of helix removed outlier: 4.023A 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 removed outlier: 3.541A pdb=" N LEU B 606 " --> pdb=" O GLN B 602 " (cutoff:3.500A) 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: 6.830A pdb=" N SER B 957 " --> pdb=" O ASP B 953 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA B 958 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N MET B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLN B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 963 " --> pdb=" O MET B 959 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 965 " --> pdb=" O ASN B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 993 removed outlier: 3.502A pdb=" N MET B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 982 - end of helix removed outlier: 4.345A pdb=" N TYR B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 988 " --> pdb=" O ILE B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1017 removed outlier: 4.061A pdb=" N TYR B1007 " --> pdb=" O LYS B1003 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN B1017 " --> pdb=" O GLN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1055 removed outlier: 3.860A pdb=" N TYR B1055 " --> pdb=" O GLN B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1073 removed outlier: 4.472A pdb=" N ALA B1066 " --> pdb=" O HIS B1062 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TRP B1069 " --> pdb=" O GLN B1065 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B1070 " --> pdb=" O ALA B1066 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B1071 " --> pdb=" O LEU B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1111 removed outlier: 3.520A pdb=" N ILE B1107 " --> pdb=" O ALA B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1137 removed outlier: 4.088A pdb=" N PHE B1126 " --> pdb=" O ARG B1122 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B1135 " --> pdb=" O ALA B1131 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B1137 " --> pdb=" O LYS B1133 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1157 removed outlier: 3.542A pdb=" N TYR B1152 " --> pdb=" O ALA B1148 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B1153 " --> pdb=" O LEU B1149 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B1157 " --> pdb=" O ALA B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1160 through 1172 removed outlier: 4.680A pdb=" N LYS B1164 " --> pdb=" O GLN B1160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B1165 " --> pdb=" O ASP B1161 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B1166 " --> pdb=" O LYS B1162 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B1169 " --> pdb=" O GLU B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1225 through 1241 removed outlier: 3.568A pdb=" N SER B1230 " --> pdb=" O GLU B1226 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B1235 " --> pdb=" O ALA B1231 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP B1237 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B1240 " --> pdb=" O LYS B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1251 through 1268 removed outlier: 4.422A pdb=" N LEU B1258 " --> pdb=" O THR B1254 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS B1259 " --> pdb=" O VAL B1255 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) 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: 6.323A pdb=" N SER C 957 " --> pdb=" O ASP C 953 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA C 958 " --> pdb=" O ILE C 954 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN C 960 " --> pdb=" O GLY C 956 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.731A 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: 4.043A 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 Processing helix chain 'D' and resid 953 through 965 removed outlier: 6.995A pdb=" N SER D 957 " --> pdb=" O ASP D 953 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA D 958 " --> pdb=" O ILE D 954 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET D 959 " --> pdb=" O LEU D 955 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLN D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN D 961 " --> pdb=" O SER D 957 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN D 963 " --> pdb=" O MET D 959 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 965 " --> pdb=" O ASN D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 973 through 993 removed outlier: 3.696A pdb=" N MET D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 982 - end of helix removed outlier: 3.931A pdb=" N TYR D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 986 " --> pdb=" O PRO D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1017 removed outlier: 3.669A pdb=" N THR D1010 " --> pdb=" O GLY D1006 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN D1017 " --> pdb=" O GLN D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1055 removed outlier: 3.595A pdb=" N GLN D1051 " --> pdb=" O LYS D1047 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D1054 " --> pdb=" O ALA D1050 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR D1055 " --> pdb=" O GLN D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1060 through 1073 removed outlier: 3.670A pdb=" N THR D1064 " --> pdb=" O GLU D1060 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TRP D1069 " --> pdb=" O GLN D1065 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D1070 " --> pdb=" O ALA D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1098 through 1111 Processing helix chain 'D' and resid 1119 through 1137 removed outlier: 3.850A pdb=" N PHE D1126 " --> pdb=" O ARG D1122 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N CYS D1127 " --> pdb=" O ASN D1123 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D1135 " --> pdb=" O ALA D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1157 removed outlier: 4.007A pdb=" N LEU D1156 " --> pdb=" O TYR D1152 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA D1157 " --> pdb=" O ALA D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1172 removed outlier: 4.689A pdb=" N LYS D1164 " --> pdb=" O GLN D1160 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU D1165 " --> pdb=" O ASP D1161 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL D1166 " --> pdb=" O LYS D1162 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1241 removed outlier: 3.619A pdb=" N THR D1229 " --> pdb=" O SER D1225 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D1230 " --> pdb=" O GLU D1226 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP D1237 " --> pdb=" O ASN D1233 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D1240 " --> pdb=" O LYS D1236 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D1241 " --> pdb=" O TRP D1237 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1268 removed outlier: 3.614A pdb=" N LYS D1263 " --> pdb=" O HIS D1259 " (cutoff:3.500A) removed outlier: 3.732A 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' 480 hydrogen bonds defined for protein. 1440 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: 8.31 Time building geometry restraints manager: 19.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 6761 1.30 - 1.43: 10901 1.43 - 1.57: 23502 1.57 - 1.71: 3 1.71 - 1.84: 253 Bond restraints: 41420 Sorted by residual: bond pdb=" N PRO C 902 " pdb=" CA PRO C 902 " ideal model delta sigma weight residual 1.470 1.700 -0.230 1.01e-02 9.80e+03 5.18e+02 bond pdb=" N PRO B 29 " pdb=" CA PRO B 29 " ideal model delta sigma weight residual 1.469 1.710 -0.241 1.28e-02 6.10e+03 3.55e+02 bond pdb=" N PRO D 29 " pdb=" CA PRO D 29 " ideal model delta sigma weight residual 1.469 1.706 -0.237 1.28e-02 6.10e+03 3.44e+02 bond pdb=" C GLN D 168 " pdb=" N ASP D 169 " ideal model delta sigma weight residual 1.331 1.162 0.169 1.59e-02 3.96e+03 1.14e+02 bond pdb=" C GLN C 967 " pdb=" N MET C 968 " ideal model delta sigma weight residual 1.330 1.209 0.121 1.47e-02 4.63e+03 6.82e+01 ... (remaining 41415 not shown) Histogram of bond angle deviations from ideal: 98.35 - 106.68: 1542 106.68 - 115.02: 25230 115.02 - 123.35: 25899 123.35 - 131.68: 3540 131.68 - 140.01: 59 Bond angle restraints: 56270 Sorted by residual: angle pdb=" C LYS B 28 " pdb=" N PRO B 29 " pdb=" CA PRO B 29 " ideal model delta sigma weight residual 119.84 138.75 -18.91 1.25e+00 6.40e-01 2.29e+02 angle pdb=" C LYS D 28 " pdb=" N PRO D 29 " pdb=" CA PRO D 29 " ideal model delta sigma weight residual 119.84 138.61 -18.77 1.25e+00 6.40e-01 2.26e+02 angle pdb=" C LYS C 901 " pdb=" N PRO C 902 " pdb=" CA PRO C 902 " ideal model delta sigma weight residual 120.79 140.01 -19.22 1.30e+00 5.92e-01 2.19e+02 angle pdb=" CA PRO C 902 " pdb=" N PRO C 902 " pdb=" CD PRO C 902 " ideal model delta sigma weight residual 112.00 98.49 13.51 1.40e+00 5.10e-01 9.32e+01 angle pdb=" CA PRO B 29 " pdb=" N PRO B 29 " pdb=" CD PRO B 29 " ideal model delta sigma weight residual 112.00 100.84 11.16 1.40e+00 5.10e-01 6.36e+01 ... (remaining 56265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 22850 21.17 - 42.34: 2267 42.34 - 63.51: 336 63.51 - 84.68: 88 84.68 - 105.85: 21 Dihedral angle restraints: 25562 sinusoidal: 10648 harmonic: 14914 Sorted by residual: dihedral pdb=" C ASN B 991 " pdb=" N ASN B 991 " pdb=" CA ASN B 991 " pdb=" CB ASN B 991 " ideal model delta harmonic sigma weight residual -122.60 -144.63 22.03 0 2.50e+00 1.60e-01 7.76e+01 dihedral pdb=" CB CYS B 470 " pdb=" SG CYS B 470 " pdb=" SG CYS B 563 " pdb=" CB CYS B 563 " ideal model delta sinusoidal sigma weight residual 93.00 19.32 73.68 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS C 431 " pdb=" SG CYS C 431 " pdb=" SG CYS D 278 " pdb=" CB CYS D 278 " ideal model delta sinusoidal sigma weight residual 93.00 161.36 -68.36 1 1.00e+01 1.00e-02 6.06e+01 ... (remaining 25559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 6458 0.228 - 0.457: 48 0.457 - 0.685: 5 0.685 - 0.913: 1 0.913 - 1.142: 2 Chirality restraints: 6514 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.89e+01 chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.17e+01 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 -2.28 -0.12 2.00e-02 2.50e+03 3.71e+01 ... (remaining 6511 not shown) Planarity restraints: 7230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.351 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG E 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.314 2.00e-02 2.50e+03 2.70e-01 9.11e+02 pdb=" C7 NAG F 1 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.010 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.465 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.307 2.00e-02 2.50e+03 2.64e-01 8.72e+02 pdb=" C7 NAG L 1 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.004 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.454 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.211 2.00e-02 2.50e+03 ... (remaining 7227 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 832 2.51 - 3.11: 36462 3.11 - 3.70: 66679 3.70 - 4.30: 88971 4.30 - 4.90: 137942 Nonbonded interactions: 330886 Sorted by model distance: nonbonded pdb=" O PRO B 657 " pdb=" OG1 THR C 656 " model vdw 1.912 2.440 nonbonded pdb=" OG1 THR A 656 " pdb=" O PRO D 657 " model vdw 1.956 2.440 nonbonded pdb=" OG1 THR B 656 " pdb=" O PRO C 657 " model vdw 1.995 2.440 nonbonded pdb=" O GLN C1281 " pdb=" OG SER C1313 " model vdw 1.995 2.440 nonbonded pdb=" OG1 THR D1224 " pdb=" OD1 ASP D1227 " model vdw 2.021 2.440 ... (remaining 330881 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 26 through 1337 or resid 2001 through 2005)) selection = chain 'B' selection = (chain 'C' and (resid 26 through 1337 or resid 2001 through 2005)) selection = chain 'D' } 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 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 0.060 Extract box with map and model: 9.480 Check model and map are aligned: 0.640 Set scattering table: 0.370 Process input model: 101.110 Find NCS groups from input model: 4.130 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.013 0.241 41420 Z= 0.872 Angle : 1.333 19.221 56270 Z= 0.768 Chirality : 0.074 1.142 6514 Planarity : 0.013 0.301 7202 Dihedral : 16.898 105.849 15830 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.33 % Allowed : 18.28 % Favored : 81.39 % Rotamer: Outliers : 1.07 % Allowed : 10.51 % Favored : 88.41 % Cbeta Deviations : 0.17 % 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: -5.78 (0.09), residues: 5110 helix: -3.17 (0.12), residues: 808 sheet: -3.84 (0.11), residues: 1268 loop : -4.22 (0.09), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B1237 HIS 0.024 0.003 HIS C 321 PHE 0.039 0.004 PHE C 365 TYR 0.041 0.004 TYR D 166 ARG 0.018 0.002 ARG D 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 907 time to evaluate : 4.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ILE cc_start: 0.8475 (mt) cc_final: 0.8273 (tt) REVERT: A 216 GLU cc_start: 0.8327 (pm20) cc_final: 0.8066 (pm20) REVERT: A 256 TYR cc_start: 0.8364 (t80) cc_final: 0.7296 (t80) REVERT: A 290 PHE cc_start: 0.7461 (m-80) cc_final: 0.7240 (m-80) REVERT: A 393 TYR cc_start: 0.9212 (t80) cc_final: 0.8933 (t80) REVERT: A 436 TRP cc_start: 0.7475 (t-100) cc_final: 0.7247 (t-100) REVERT: A 496 TYR cc_start: 0.6104 (m-80) cc_final: 0.5881 (m-10) REVERT: A 514 LEU cc_start: 0.9051 (pt) cc_final: 0.8806 (mt) REVERT: A 543 TYR cc_start: 0.7987 (p90) cc_final: 0.7782 (p90) REVERT: A 612 GLU cc_start: 0.8087 (tt0) cc_final: 0.7736 (tt0) REVERT: A 669 PHE cc_start: 0.8863 (m-80) cc_final: 0.8554 (m-80) REVERT: A 787 ARG cc_start: 0.8321 (ptp90) cc_final: 0.8029 (ptp90) REVERT: A 829 GLU cc_start: 0.8581 (tp30) cc_final: 0.7750 (mp0) REVERT: A 975 GLN cc_start: 0.8503 (mm-40) cc_final: 0.7936 (mt0) REVERT: A 976 ASN cc_start: 0.9164 (t0) cc_final: 0.8756 (t0) REVERT: A 990 LEU cc_start: 0.9012 (mt) cc_final: 0.8639 (mm) REVERT: A 1015 GLN cc_start: 0.8445 (tp40) cc_final: 0.8173 (tp40) REVERT: A 1017 ASN cc_start: 0.8884 (m110) cc_final: 0.8508 (m-40) REVERT: A 1076 ASP cc_start: 0.7796 (p0) cc_final: 0.7573 (p0) REVERT: A 1087 LEU cc_start: 0.9553 (tt) cc_final: 0.9150 (mt) REVERT: A 1146 THR cc_start: 0.8870 (p) cc_final: 0.8665 (p) REVERT: A 1208 MET cc_start: 0.9205 (ppp) cc_final: 0.8787 (ppp) REVERT: A 1217 LEU cc_start: 0.9356 (mm) cc_final: 0.9097 (mm) REVERT: B 98 GLU cc_start: 0.8631 (tt0) cc_final: 0.8264 (tm-30) REVERT: B 113 GLU cc_start: 0.6589 (pt0) cc_final: 0.6369 (pm20) REVERT: B 121 MET cc_start: 0.8297 (tpp) cc_final: 0.7696 (tpp) REVERT: B 169 ASP cc_start: 0.6657 (t0) cc_final: 0.6457 (t0) REVERT: B 256 TYR cc_start: 0.8020 (t80) cc_final: 0.7509 (t80) REVERT: B 289 LYS cc_start: 0.9089 (mttm) cc_final: 0.8775 (mmtp) REVERT: B 318 MET cc_start: 0.8216 (mtt) cc_final: 0.7801 (tpt) REVERT: B 393 TYR cc_start: 0.9038 (t80) cc_final: 0.8475 (t80) REVERT: B 533 ASP cc_start: 0.8006 (t0) cc_final: 0.7635 (t0) REVERT: B 567 LYS cc_start: 0.9196 (tppt) cc_final: 0.8924 (mmtm) REVERT: B 635 ASN cc_start: 0.8299 (p0) cc_final: 0.8004 (p0) REVERT: B 637 GLN cc_start: 0.7364 (pp30) cc_final: 0.7086 (pp30) REVERT: B 669 PHE cc_start: 0.8552 (m-80) cc_final: 0.8020 (m-80) REVERT: B 673 MET cc_start: 0.8226 (tpp) cc_final: 0.7739 (tpp) REVERT: B 741 TRP cc_start: 0.8285 (t-100) cc_final: 0.7684 (t-100) REVERT: B 766 LYS cc_start: 0.8370 (tppt) cc_final: 0.8124 (tptp) REVERT: B 792 PHE cc_start: 0.7679 (t80) cc_final: 0.7471 (t80) REVERT: B 863 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8507 (ttpt) REVERT: B 951 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6438 (pp) REVERT: B 965 LEU cc_start: 0.9163 (tt) cc_final: 0.8770 (mm) REVERT: B 975 GLN cc_start: 0.9133 (mm110) cc_final: 0.8857 (mt0) REVERT: B 976 ASN cc_start: 0.9303 (t0) cc_final: 0.9028 (t0) REVERT: B 977 MET cc_start: 0.9403 (mmm) cc_final: 0.9173 (mmm) REVERT: B 1076 ASP cc_start: 0.7806 (p0) cc_final: 0.7432 (p0) REVERT: B 1123 ASN cc_start: 0.9196 (m110) cc_final: 0.8740 (m110) REVERT: B 1125 LEU cc_start: 0.9247 (mt) cc_final: 0.8861 (mm) REVERT: B 1133 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8913 (mmtm) REVERT: B 1161 ASP cc_start: 0.9028 (p0) cc_final: 0.8730 (p0) REVERT: B 1237 TRP cc_start: 0.7443 (t60) cc_final: 0.7238 (t60) REVERT: B 1245 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8680 (tm-30) REVERT: B 1323 TYR cc_start: 0.6543 (t80) cc_final: 0.5953 (t80) REVERT: B 1325 GLN cc_start: 0.7955 (tt0) cc_final: 0.6851 (tp40) REVERT: C 76 ASP cc_start: 0.8482 (p0) cc_final: 0.8036 (m-30) REVERT: C 101 MET cc_start: 0.8322 (mtp) cc_final: 0.7883 (mmm) REVERT: C 121 MET cc_start: 0.8165 (ttt) cc_final: 0.7396 (tpt) REVERT: C 368 GLN cc_start: 0.8870 (tt0) cc_final: 0.8565 (tm-30) REVERT: C 387 ARG cc_start: 0.8268 (mmt180) cc_final: 0.7846 (mmm160) REVERT: C 635 ASN cc_start: 0.8205 (p0) cc_final: 0.7651 (p0) REVERT: C 671 GLU cc_start: 0.9055 (tt0) cc_final: 0.8510 (tt0) REVERT: C 672 ASP cc_start: 0.8884 (t0) cc_final: 0.8614 (t0) REVERT: C 688 MET cc_start: 0.7528 (ppp) cc_final: 0.6947 (ppp) REVERT: C 737 GLU cc_start: 0.8116 (mp0) cc_final: 0.7814 (mp0) REVERT: C 787 ARG cc_start: 0.8445 (ptp90) cc_final: 0.8180 (mtp180) REVERT: C 800 TYR cc_start: 0.7696 (p90) cc_final: 0.7325 (p90) REVERT: C 916 PHE cc_start: 0.8655 (m-80) cc_final: 0.8368 (m-80) REVERT: C 967 GLN cc_start: 0.9051 (mt0) cc_final: 0.8803 (mp10) REVERT: C 977 MET cc_start: 0.9159 (mmm) cc_final: 0.8933 (mmm) REVERT: C 983 ASN cc_start: 0.9141 (m-40) cc_final: 0.8938 (m-40) REVERT: C 988 ASP cc_start: 0.8304 (t0) cc_final: 0.7823 (t70) REVERT: C 1015 GLN cc_start: 0.7744 (tp40) cc_final: 0.6655 (tp40) REVERT: C 1057 PHE cc_start: 0.8012 (t80) cc_final: 0.7607 (t80) REVERT: C 1072 GLN cc_start: 0.9096 (mt0) cc_final: 0.8838 (mt0) REVERT: C 1073 ARG cc_start: 0.9111 (mmt-90) cc_final: 0.8701 (mmp80) REVERT: C 1163 ARG cc_start: 0.8646 (tmm-80) cc_final: 0.8287 (ttt180) REVERT: C 1234 ILE cc_start: 0.8225 (pt) cc_final: 0.7967 (pt) REVERT: C 1254 THR cc_start: 0.9176 (m) cc_final: 0.8861 (m) REVERT: C 1312 TYR cc_start: 0.8946 (m-80) cc_final: 0.8580 (m-80) REVERT: C 1323 TYR cc_start: 0.6384 (t80) cc_final: 0.5971 (t80) REVERT: D 98 GLU cc_start: 0.8798 (tt0) cc_final: 0.8285 (tp30) REVERT: D 121 MET cc_start: 0.7942 (mmm) cc_final: 0.7687 (mmm) REVERT: D 175 ILE cc_start: 0.8719 (tp) cc_final: 0.8440 (tp) REVERT: D 203 TYR cc_start: 0.7078 (m-80) cc_final: 0.6177 (m-80) REVERT: D 256 TYR cc_start: 0.7275 (t80) cc_final: 0.6346 (t80) REVERT: D 381 ASN cc_start: 0.9115 (m-40) cc_final: 0.8717 (p0) REVERT: D 399 THR cc_start: 0.8561 (p) cc_final: 0.8262 (p) REVERT: D 669 PHE cc_start: 0.8667 (m-80) cc_final: 0.8184 (m-80) REVERT: D 671 GLU cc_start: 0.8752 (tt0) cc_final: 0.8463 (tt0) REVERT: D 682 LYS cc_start: 0.8717 (mttt) cc_final: 0.8376 (mmtp) REVERT: D 737 GLU cc_start: 0.8108 (mp0) cc_final: 0.7793 (mp0) REVERT: D 766 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7563 (mmmt) REVERT: D 783 THR cc_start: 0.9490 (p) cc_final: 0.8727 (p) REVERT: D 976 ASN cc_start: 0.9274 (t0) cc_final: 0.8895 (t0) REVERT: D 992 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: D 1003 LYS cc_start: 0.9495 (tptt) cc_final: 0.9241 (tptp) REVERT: D 1089 ASN cc_start: 0.8828 (p0) cc_final: 0.8511 (p0) REVERT: D 1133 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8660 (mmtm) REVERT: D 1144 VAL cc_start: 0.8648 (m) cc_final: 0.7788 (m) REVERT: D 1147 LYS cc_start: 0.9306 (mttp) cc_final: 0.8874 (mttp) REVERT: D 1150 LEU cc_start: 0.9590 (mm) cc_final: 0.9385 (mm) REVERT: D 1154 PHE cc_start: 0.8721 (m-80) cc_final: 0.8456 (m-80) REVERT: D 1208 MET cc_start: 0.9467 (ppp) cc_final: 0.8995 (ppp) REVERT: D 1243 ASN cc_start: 0.9266 (t0) cc_final: 0.8980 (t0) REVERT: D 1245 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8656 (tm-30) REVERT: D 1269 PHE cc_start: 0.8709 (t80) cc_final: 0.8258 (t80) REVERT: D 1312 TYR cc_start: 0.9088 (m-80) cc_final: 0.8718 (m-80) outliers start: 48 outliers final: 26 residues processed: 946 average time/residue: 0.5278 time to fit residues: 823.4347 Evaluate side-chains 687 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 659 time to evaluate : 4.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1056 ILE Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1056 ILE Chi-restraints excluded: chain D residue 1214 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 7.9990 chunk 386 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 260 optimal weight: 20.0000 chunk 206 optimal weight: 20.0000 chunk 399 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 297 optimal weight: 6.9990 chunk 463 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 106 GLN ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 217 HIS ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 413 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 479 HIS A 511 HIS A 517 GLN A 523 HIS ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 ASN A 963 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1017 ASN ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN A1072 GLN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 132 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 381 ASN ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 483 ASN B 511 HIS B 592 GLN B 637 GLN B 790 GLN B 827 GLN ** B 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 ASN B1035 ASN B1179 ASN ** B1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN C 200 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN C 413 ASN ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 HIS ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 ASN C 680 ASN C 694 GLN C 790 GLN ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1259 HIS D 132 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 GLN D 310 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** D 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 592 GLN D 637 GLN D 662 ASN D 827 GLN ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1035 ASN ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 GLN ** D1182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1187 GLN ** D1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1241 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2496 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: