Starting phenix.real_space_refine (version: dev) on Tue Dec 20 21:48:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/12_2022/7o7r_12754.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/12_2022/7o7r_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_12754/12_2022/7o7r_12754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/12_2022/7o7r_12754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/12_2022/7o7r_12754.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/12_2022/7o7r_12754.pdb" } resolution = 3.9 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 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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 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: 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: 22.18, per 1000 atoms: 0.55 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: 17.56 Conformation dependent library (CDL) restraints added in 6.0 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: 0.77 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: 9.62 Time building geometry restraints manager: 18.90 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=" C2 NAG L 1 " pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 109.64 118.04 -8.40 5.38e-01 3.45e+00 2.44e+02 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=" C2 NAG H 1 " pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 109.64 116.05 -6.41 5.38e-01 3.45e+00 1.42e+02 ... (remaining 56265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 21542 17.84 - 35.69: 2817 35.69 - 53.53: 490 53.53 - 71.37: 92 71.37 - 89.22: 45 Dihedral angle restraints: 24986 sinusoidal: 10072 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 24983 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 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. 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: 1.170 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: 0.030 Extract box with map and model: 9.990 Check model and map are aligned: 0.540 Convert atoms to be neutral: 0.320 Process input model: 96.000 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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= 0.865 Angle : 1.325 19.221 56270 Z= 0.780 Chirality : 0.073 1.142 6514 Planarity : 0.013 0.301 7202 Dihedral : 16.255 89.217 15254 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.33 % Allowed : 18.28 % Favored : 81.39 % Rotamer Outliers : 1.07 % 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 *********************** 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 : 4.898 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: 48 outliers final: 26 residues processed: 946 average time/residue: 0.5019 time to fit residues: 786.9070 Evaluate side-chains 647 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 621 time to evaluate : 4.790 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3599 time to fit residues: 24.2460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 214 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 chunk 399 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 297 optimal weight: 6.9990 chunk 463 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 159 ASN A 177 GLN A 217 HIS A 232 GLN A 361 GLN ** 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 ** 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 ** 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 790 GLN B 827 GLN B 938 ASN ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1035 ASN B1179 ASN ** B1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN C 200 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C1259 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 GLN D 310 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN 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 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 ** 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: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.075 41420 Z= 0.437 Angle : 0.970 12.669 56270 Z= 0.507 Chirality : 0.055 0.383 6514 Planarity : 0.007 0.074 7202 Dihedral : 7.885 35.794 5726 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 28.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.03 % Favored : 86.77 % Rotamer Outliers : 4.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -4.90 (0.10), residues: 5110 helix: -1.92 (0.15), residues: 798 sheet: -3.29 (0.11), residues: 1482 loop : -3.75 (0.10), residues: 2830 *********************** REFINEMENT MACRO_CYCLE 2 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 937 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 736 time to evaluate : 4.525 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: 201 outliers final: 116 residues processed: 868 average time/residue: 0.4787 time to fit residues: 700.5573 Evaluate side-chains 723 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 607 time to evaluate : 4.377 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 0 residues processed: 116 average time/residue: 0.3693 time to fit residues: 85.1583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 385 optimal weight: 0.9980 chunk 315 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 463 optimal weight: 4.9990 chunk 501 optimal weight: 10.0000 chunk 413 optimal weight: 4.9990 chunk 460 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 372 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 424 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 GLN B 938 ASN B 960 GLN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1325 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 GLN D 85 HIS ** 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 310 GLN D 368 GLN D 424 ASN D 511 HIS D 592 GLN ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN ** D1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 41420 Z= 0.278 Angle : 0.832 12.594 56270 Z= 0.429 Chirality : 0.051 0.356 6514 Planarity : 0.006 0.068 7202 Dihedral : 7.066 36.251 5726 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.70 % Favored : 88.18 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -4.29 (0.10), residues: 5110 helix: -1.12 (0.16), residues: 820 sheet: -2.86 (0.12), residues: 1470 loop : -3.49 (0.10), residues: 2820 *********************** REFINEMENT MACRO_CYCLE 3 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 843 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 714 time to evaluate : 4.494 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: 129 outliers final: 62 residues processed: 814 average time/residue: 0.4898 time to fit residues: 678.5048 Evaluate side-chains 662 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 600 time to evaluate : 4.183 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.3424 time to fit residues: 46.4443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 8.9990 chunk 348 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 465 optimal weight: 0.0470 chunk 492 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 441 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN A 566 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS ** B 293 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 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS C 680 ASN ** C1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 177 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 GLN ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 41420 Z= 0.310 Angle : 0.843 18.229 56270 Z= 0.430 Chirality : 0.052 0.394 6514 Planarity : 0.006 0.093 7202 Dihedral : 6.837 35.928 5726 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 26.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.23 % Favored : 87.69 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -4.05 (0.11), residues: 5110 helix: -0.79 (0.17), residues: 780 sheet: -2.70 (0.11), residues: 1622 loop : -3.34 (0.11), residues: 2708 *********************** REFINEMENT MACRO_CYCLE 4 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 816 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 658 time to evaluate : 4.458 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: 158 outliers final: 86 residues processed: 769 average time/residue: 0.5010 time to fit residues: 658.0593 Evaluate side-chains 672 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 586 time to evaluate : 4.980 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 0.3904 time to fit residues: 67.7738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 367 optimal weight: 0.0370 chunk 203 optimal weight: 7.9990 chunk 420 optimal weight: 0.6980 chunk 340 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 442 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1017 ASN ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 ASN ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS ** C1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 983 ASN ** D1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 41420 Z= 0.237 Angle : 0.810 12.936 56270 Z= 0.407 Chirality : 0.051 0.380 6514 Planarity : 0.005 0.073 7202 Dihedral : 6.427 34.906 5726 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.65 % Favored : 89.30 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.11), residues: 5110 helix: -0.30 (0.17), residues: 786 sheet: -2.50 (0.12), residues: 1628 loop : -3.20 (0.11), residues: 2696 *********************** REFINEMENT MACRO_CYCLE 5 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 786 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 691 time to evaluate : 5.311 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 outliers start: 95 outliers final: 48 residues processed: 755 average time/residue: 0.4757 time to fit residues: 609.0140 Evaluate side-chains 641 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 593 time to evaluate : 4.463 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.3808 time to fit residues: 40.4542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 6.9990 chunk 443 optimal weight: 0.0970 chunk 97 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 493 optimal weight: 5.9990 chunk 409 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN A 368 GLN A 413 ASN A 460 HIS A 566 ASN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 GLN ** B 293 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 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** B1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN C 132 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 ASN ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 ASN ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 ASN ** C1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 GLN ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 41420 Z= 0.405 Angle : 0.898 13.276 56270 Z= 0.461 Chirality : 0.053 0.565 6514 Planarity : 0.006 0.065 7202 Dihedral : 6.837 34.916 5726 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 33.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.31 % Favored : 86.58 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.02 % 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: -3.92 (0.11), residues: 5110 helix: -0.78 (0.17), residues: 786 sheet: -2.61 (0.12), residues: 1574 loop : -3.22 (0.11), residues: 2750 *********************** REFINEMENT MACRO_CYCLE 6 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 772 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 615 time to evaluate : 4.590 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 outliers start: 157 outliers final: 97 residues processed: 719 average time/residue: 0.4950 time to fit residues: 612.5245 Evaluate side-chains 652 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 555 time to evaluate : 4.632 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 0.3745 time to fit residues: 74.3721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 281 optimal weight: 10.0000 chunk 360 optimal weight: 0.7980 chunk 279 optimal weight: 0.9990 chunk 415 optimal weight: 7.9990 chunk 275 optimal weight: 6.9990 chunk 491 optimal weight: 7.9990 chunk 307 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1017 ASN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 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 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 GLN ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 ASN ** C1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 41420 Z= 0.238 Angle : 0.829 14.213 56270 Z= 0.412 Chirality : 0.052 0.598 6514 Planarity : 0.005 0.077 7202 Dihedral : 6.394 33.180 5726 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.49 % Favored : 89.45 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -3.55 (0.11), residues: 5110 helix: -0.21 (0.18), residues: 788 sheet: -2.36 (0.12), residues: 1510 loop : -3.09 (0.11), residues: 2812 *********************** REFINEMENT MACRO_CYCLE 7 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 704 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 636 time to evaluate : 4.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 34 residues processed: 685 average time/residue: 0.4906 time to fit residues: 572.4447 Evaluate side-chains 611 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 577 time to evaluate : 5.082 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3755 time to fit residues: 30.6827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 293 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 312 optimal weight: 4.9990 chunk 334 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 386 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 ASN ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 41420 Z= 0.257 Angle : 0.826 13.895 56270 Z= 0.413 Chirality : 0.052 0.571 6514 Planarity : 0.005 0.070 7202 Dihedral : 6.297 31.953 5726 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 25.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.57 % Favored : 88.38 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.02 % 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: -3.51 (0.11), residues: 5110 helix: -0.19 (0.18), residues: 794 sheet: -2.32 (0.12), residues: 1544 loop : -3.08 (0.11), residues: 2772 *********************** REFINEMENT MACRO_CYCLE 8 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 670 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 617 time to evaluate : 4.253 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 outliers start: 53 outliers final: 30 residues processed: 647 average time/residue: 0.4872 time to fit residues: 535.0583 Evaluate side-chains 610 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 580 time to evaluate : 5.064 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3677 time to fit residues: 27.8814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 7.9990 chunk 470 optimal weight: 0.0980 chunk 429 optimal weight: 0.0970 chunk 458 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 359 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 413 optimal weight: 0.1980 chunk 433 optimal weight: 0.5980 chunk 456 optimal weight: 4.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 ASN ** A 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN A1159 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 ASN ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** C1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1242 GLN ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 41420 Z= 0.217 Angle : 0.833 16.192 56270 Z= 0.408 Chirality : 0.051 0.445 6514 Planarity : 0.005 0.062 7202 Dihedral : 6.018 30.934 5726 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.51 % Favored : 90.43 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.02 % 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: -3.30 (0.11), residues: 5110 helix: -0.07 (0.18), residues: 804 sheet: -2.03 (0.12), residues: 1536 loop : -3.03 (0.11), residues: 2770 *********************** REFINEMENT MACRO_CYCLE 9 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 695 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 670 time to evaluate : 5.235 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 outliers start: 25 outliers final: 9 residues processed: 684 average time/residue: 0.4969 time to fit residues: 577.7440 Evaluate side-chains 629 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 620 time to evaluate : 4.666 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3759 time to fit residues: 13.2290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 5.9990 chunk 484 optimal weight: 1.9990 chunk 295 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 336 optimal weight: 30.0000 chunk 508 optimal weight: 8.9990 chunk 467 optimal weight: 3.9990 chunk 404 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 312 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 ASN C 106 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 41420 Z= 0.334 Angle : 0.882 16.009 56270 Z= 0.443 Chirality : 0.052 0.434 6514 Planarity : 0.005 0.074 7202 Dihedral : 6.300 29.953 5726 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 30.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.04 % Favored : 87.89 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.11), residues: 5110 helix: -0.35 (0.18), residues: 790 sheet: -2.17 (0.12), residues: 1498 loop : -3.11 (0.11), residues: 2822 ********************** REFINEMENT MACRO_CYCLE 10 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 641 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 609 time to evaluate : 4.768 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 outliers start: 32 outliers final: 22 residues processed: 627 average time/residue: 0.4985 time to fit residues: 533.6811 Evaluate side-chains 600 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 578 time to evaluate : 4.784 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4189 time to fit residues: 23.6241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 0.6980 chunk 430 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 373 optimal weight: 8.9990 chunk 59 optimal weight: 0.0470 chunk 112 optimal weight: 6.9990 chunk 405 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 416 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 GLN A 938 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 ASN ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 GLN D 983 ASN ** D1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.105517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.082421 restraints weight = 140821.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.085592 restraints weight = 86050.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.087841 restraints weight = 59858.002| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 41420 Z= 0.228 Angle : 0.865 16.304 56270 Z= 0.422 Chirality : 0.051 0.471 6514 Planarity : 0.005 0.096 7202 Dihedral : 6.032 29.596 5726 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.73 % Favored : 90.22 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.11), residues: 5110 helix: -0.14 (0.18), residues: 792 sheet: -1.99 (0.13), residues: 1536 loop : -3.03 (0.11), residues: 2782 =============================================================================== Job complete usr+sys time: 10458.88 seconds wall clock time: 192 minutes 16.89 seconds (11536.89 seconds total)