Starting phenix.real_space_refine on Sat Aug 10 18:03:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1c_18807/08_2024/8r1c_18807.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1c_18807/08_2024/8r1c_18807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1c_18807/08_2024/8r1c_18807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1c_18807/08_2024/8r1c_18807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1c_18807/08_2024/8r1c_18807.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1c_18807/08_2024/8r1c_18807.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 19377 2.51 5 N 5010 2.21 5 O 5898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 50": "OD1" <-> "OD2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 27": "OD1" <-> "OD2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B GLU 658": "OE1" <-> "OE2" Residue "B PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 386": "OD1" <-> "OD2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 575": "OD1" <-> "OD2" Residue "C GLU 658": "OE1" <-> "OE2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 30426 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8276 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 6 Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 931 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 795 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 931 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 795 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "F" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 931 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 795 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "B" Number of atoms: 8276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8276 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 6 Chain: "C" Number of atoms: 8276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8276 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 6 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.44, per 1000 atoms: 0.54 Number of scatterers: 30426 At special positions: 0 Unit cell: (159.936, 152.633, 171.62, 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 141 16.00 O 5898 8.00 N 5010 7.00 C 19377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.04 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.04 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 103 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.04 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.04 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.04 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 654 " " NAG A1302 " - " ASN A 714 " " NAG A1303 " - " ASN A 798 " " NAG A1304 " - " ASN A1131 " " NAG A1305 " - " ASN A 706 " " NAG A1306 " - " ASN A 613 " " NAG A1307 " - " ASN A1095 " " NAG A1308 " - " ASN A 279 " " NAG A1309 " - " ASN A1071 " " NAG A1310 " - " ASN A 231 " " NAG B1301 " - " ASN B 654 " " NAG B1302 " - " ASN B 714 " " NAG B1303 " - " ASN B 798 " " NAG B1304 " - " ASN B1131 " " NAG B1305 " - " ASN B 706 " " NAG B1306 " - " ASN B 613 " " NAG B1307 " - " ASN B1095 " " NAG B1308 " - " ASN B 279 " " NAG B1309 " - " ASN B1071 " " NAG B1310 " - " ASN B 231 " " NAG C1301 " - " ASN C 654 " " NAG C1302 " - " ASN C 714 " " NAG C1303 " - " ASN C 798 " " NAG C1304 " - " ASN C1131 " " NAG C1305 " - " ASN C 706 " " NAG C1306 " - " ASN C 613 " " NAG C1307 " - " ASN C1095 " " NAG C1308 " - " ASN C 279 " " NAG C1309 " - " ASN C1071 " " NAG C1310 " - " ASN C 231 " Time building additional restraints: 11.16 Conformation dependent library (CDL) restraints added in 5.5 seconds 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7194 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 69 sheets defined 22.9% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.05 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.750A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.759A pdb=" N VAL A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.526A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.669A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.649A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 845 through 853 removed outlier: 3.893A pdb=" N ALA A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.820A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 909 through 916 removed outlier: 3.951A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.033A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 63 through 66 removed outlier: 3.505A pdb=" N LYS D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 63 through 66 removed outlier: 3.509A pdb=" N LYS F 66 " --> pdb=" O PRO F 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 63 through 66' Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.750A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 3.759A pdb=" N VAL B 364 " --> pdb=" O ASP B 361 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR B 366 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 386 removed outlier: 4.526A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.669A pdb=" N SER B 405 " --> pdb=" O ASN B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 613 through 617 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.649A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 845 through 853 removed outlier: 3.893A pdb=" N ALA B 849 " --> pdb=" O ASP B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.820A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 909 through 916 removed outlier: 3.952A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.034A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.750A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.759A pdb=" N VAL C 364 " --> pdb=" O ASP C 361 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 366 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 386 removed outlier: 4.526A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.669A pdb=" N SER C 405 " --> pdb=" O ASN C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 613 through 617 Processing helix chain 'C' and resid 734 through 741 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.650A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 845 through 853 removed outlier: 3.893A pdb=" N ALA C 849 " --> pdb=" O ASP C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.820A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 916 removed outlier: 3.952A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1030 Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.033A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27 removed outlier: 7.666A pdb=" N ASN A 58 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR A 266 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.866A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 132 removed outlier: 5.949A pdb=" N GLU A 129 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA A 160 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN A 131 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 140 removed outlier: 3.990A pdb=" N ASP A 139 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 4.397A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.204A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.567A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.145A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 701 removed outlier: 6.460A pdb=" N ASN A 700 " --> pdb=" O LYS B 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.857A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 725 removed outlier: 5.904A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.464A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.231A pdb=" N TRP H 36 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.988A pdb=" N ILE H 113 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP H 101 " --> pdb=" O PHE H 111 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE H 111 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.411A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 12 removed outlier: 5.877A pdb=" N THR L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.595A pdb=" N GLY D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG D 40 " --> pdb=" O TRP D 49 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TRP D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.996A pdb=" N ILE D 113 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP D 101 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE D 111 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.416A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 9 through 12 removed outlier: 5.914A pdb=" N THR E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AD4, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.597A pdb=" N GLY F 51 " --> pdb=" O TRP F 38 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG F 40 " --> pdb=" O TRP F 49 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP F 49 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.001A pdb=" N ILE F 113 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP F 101 " --> pdb=" O PHE F 111 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE F 111 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.436A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 9 through 12 removed outlier: 5.894A pdb=" N THR G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AE1, first strand: chain 'B' and resid 23 through 27 removed outlier: 7.666A pdb=" N ASN B 58 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR B 266 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 44 through 52 removed outlier: 3.866A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'B' and resid 129 through 132 removed outlier: 5.950A pdb=" N GLU B 129 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA B 160 " --> pdb=" O GLU B 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN B 131 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 139 through 140 removed outlier: 3.990A pdb=" N ASP B 139 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 308 through 316 removed outlier: 4.397A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.203A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AE9, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.567A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AF2, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AF3, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.145A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 699 through 701 removed outlier: 6.460A pdb=" N ASN B 700 " --> pdb=" O LYS C 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.856A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 715 through 725 removed outlier: 5.903A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.464A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AF9, first strand: chain 'C' and resid 23 through 27 removed outlier: 7.666A pdb=" N ASN C 58 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR C 266 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 44 through 52 removed outlier: 3.866A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AG3, first strand: chain 'C' and resid 129 through 132 removed outlier: 5.948A pdb=" N GLU C 129 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA C 160 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN C 131 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 139 through 140 removed outlier: 3.990A pdb=" N ASP C 139 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 308 through 316 removed outlier: 4.397A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 321 through 325 removed outlier: 4.204A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AG8, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.567A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AH1, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AH2, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.145A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.857A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 715 through 725 removed outlier: 5.904A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.464A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 1117 through 1119 1322 hydrogen bonds defined for protein. 3486 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: 16.23 Time building geometry restraints manager: 12.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.76 - 1.01: 2 1.01 - 1.26: 4921 1.26 - 1.50: 13997 1.50 - 1.75: 12030 1.75 - 2.00: 175 Bond restraints: 31125 Sorted by residual: bond pdb=" CG PRO F 9 " pdb=" CD PRO F 9 " ideal model delta sigma weight residual 1.503 0.759 0.744 3.40e-02 8.65e+02 4.78e+02 bond pdb=" CG PRO D 9 " pdb=" CD PRO D 9 " ideal model delta sigma weight residual 1.503 0.894 0.609 3.40e-02 8.65e+02 3.21e+02 bond pdb=" CB PRO F 9 " pdb=" CG PRO F 9 " ideal model delta sigma weight residual 1.492 2.001 -0.509 5.00e-02 4.00e+02 1.04e+02 bond pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 1.468 1.564 -0.096 1.20e-02 6.94e+03 6.44e+01 bond pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 1.492 1.105 0.387 5.00e-02 4.00e+02 6.00e+01 ... (remaining 31120 not shown) Histogram of bond angle deviations from ideal: 51.20 - 76.96: 7 76.96 - 102.71: 81 102.71 - 128.46: 42121 128.46 - 154.21: 147 154.21 - 179.97: 1 Bond angle restraints: 42357 Sorted by residual: angle pdb=" N PRO D 9 " pdb=" CD PRO D 9 " pdb=" CG PRO D 9 " ideal model delta sigma weight residual 103.20 51.20 52.00 1.50e+00 4.44e-01 1.20e+03 angle pdb=" N PRO F 9 " pdb=" CD PRO F 9 " pdb=" CG PRO F 9 " ideal model delta sigma weight residual 103.20 62.65 40.55 1.50e+00 4.44e-01 7.31e+02 angle pdb=" N PRO H 9 " pdb=" CD PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 103.20 67.36 35.84 1.50e+00 4.44e-01 5.71e+02 angle pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 106.10 179.97 -73.87 3.20e+00 9.77e-02 5.33e+02 angle pdb=" CA PRO D 9 " pdb=" CB PRO D 9 " pdb=" CG PRO D 9 " ideal model delta sigma weight residual 104.50 61.12 43.38 1.90e+00 2.77e-01 5.21e+02 ... (remaining 42352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 17724 22.75 - 45.50: 896 45.50 - 68.25: 160 68.25 - 91.00: 70 91.00 - 113.75: 2 Dihedral angle restraints: 18852 sinusoidal: 7632 harmonic: 11220 Sorted by residual: dihedral pdb=" N PRO F 9 " pdb=" C PRO F 9 " pdb=" CA PRO F 9 " pdb=" CB PRO F 9 " ideal model delta harmonic sigma weight residual 115.10 97.53 17.57 0 2.50e+00 1.60e-01 4.94e+01 dihedral pdb=" CA PRO D 9 " pdb=" CB PRO D 9 " pdb=" CG PRO D 9 " pdb=" CD PRO D 9 " ideal model delta sinusoidal sigma weight residual 38.00 151.75 -113.75 1 2.00e+01 2.50e-03 3.37e+01 dihedral pdb=" N PRO D 9 " pdb=" CG PRO D 9 " pdb=" CD PRO D 9 " pdb=" CB PRO D 9 " ideal model delta sinusoidal sigma weight residual 30.00 107.23 -77.23 1 1.50e+01 4.44e-03 3.32e+01 ... (remaining 18849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3625 0.048 - 0.096: 974 0.096 - 0.144: 276 0.144 - 0.192: 10 0.192 - 0.240: 2 Chirality restraints: 4887 Sorted by residual: chirality pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CB PRO H 9 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA PRO D 9 " pdb=" N PRO D 9 " pdb=" C PRO D 9 " pdb=" CB PRO D 9 " both_signs ideal model delta sigma weight residual False 2.72 2.95 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO F 9 " pdb=" N PRO F 9 " pdb=" C PRO F 9 " pdb=" CB PRO F 9 " both_signs ideal model delta sigma weight residual False 2.72 2.89 -0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 4884 not shown) Planarity restraints: 5436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 8 " -0.106 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO H 9 " 0.262 5.00e-02 4.00e+02 pdb=" CA PRO H 9 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO H 9 " -0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 8 " 0.086 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO D 9 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO D 9 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO D 9 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS L 41 " 0.072 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO L 42 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " 0.057 5.00e-02 4.00e+02 ... (remaining 5433 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 255 2.65 - 3.22: 26987 3.22 - 3.78: 46994 3.78 - 4.34: 69218 4.34 - 4.90: 110180 Nonbonded interactions: 253634 Sorted by model distance: nonbonded pdb=" OG1 THR C 596 " pdb=" O PRO C 597 " model vdw 2.093 3.040 nonbonded pdb=" OG1 THR A 596 " pdb=" O PRO A 597 " model vdw 2.093 3.040 nonbonded pdb=" OG1 THR B 596 " pdb=" O PRO B 597 " model vdw 2.094 3.040 nonbonded pdb=" O THR B 390 " pdb=" OG1 THR B 520 " model vdw 2.112 3.040 nonbonded pdb=" O THR C 390 " pdb=" OG1 THR C 520 " model vdw 2.112 3.040 ... (remaining 253629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.460 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 85.440 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.008 0.744 31125 Z= 0.509 Angle : 0.869 73.867 42357 Z= 0.471 Chirality : 0.046 0.240 4887 Planarity : 0.005 0.152 5406 Dihedral : 14.579 113.749 11505 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.07 % Allowed : 10.53 % Favored : 88.39 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 3813 helix: 1.93 (0.20), residues: 714 sheet: 0.29 (0.15), residues: 1023 loop : -0.61 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.007 0.001 HIS A 516 PHE 0.015 0.001 PHE B 895 TYR 0.018 0.001 TYR C1064 ARG 0.002 0.000 ARG C1016 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 243 time to evaluate : 3.213 Fit side-chains REVERT: H 40 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7339 (ptt180) REVERT: F 9 PRO cc_start: 0.6117 (OUTLIER) cc_final: 0.5888 (Cg_exo) REVERT: F 101 ASP cc_start: 0.8005 (t0) cc_final: 0.7804 (t0) REVERT: F 119 MET cc_start: 0.6791 (mtt) cc_final: 0.6381 (mpp) REVERT: B 118 ASN cc_start: 0.7095 (t0) cc_final: 0.6701 (m110) REVERT: B 150 MET cc_start: 0.6046 (tmm) cc_final: 0.5601 (pp-130) REVERT: B 776 GLN cc_start: 0.8858 (tt0) cc_final: 0.8581 (tp40) REVERT: B 897 MET cc_start: 0.9325 (mtp) cc_final: 0.9092 (mtp) REVERT: B 932 GLN cc_start: 0.7847 (tt0) cc_final: 0.7640 (tt0) REVERT: B 1070 LYS cc_start: 0.8608 (mttt) cc_final: 0.8290 (mtpp) REVERT: C 150 MET cc_start: 0.6036 (tmm) cc_final: 0.5403 (pp-130) REVERT: C 742 ASP cc_start: 0.8132 (p0) cc_final: 0.7931 (p0) REVERT: C 776 GLN cc_start: 0.8888 (tt0) cc_final: 0.8672 (tp40) REVERT: C 1070 LYS cc_start: 0.8632 (mttt) cc_final: 0.8244 (mtpp) outliers start: 36 outliers final: 23 residues processed: 273 average time/residue: 1.2406 time to fit residues: 408.2519 Evaluate side-chains 249 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 224 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 9 PRO Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 298 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 181 optimal weight: 40.0000 chunk 222 optimal weight: 8.9990 chunk 345 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 999 GLN H 116 GLN B 447 ASN B 561 GLN B 910 GLN B 999 GLN C 23 GLN C 118 ASN C 561 GLN C 610 GLN C 910 GLN C 999 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 31125 Z= 0.275 Angle : 0.580 14.835 42357 Z= 0.314 Chirality : 0.047 0.188 4887 Planarity : 0.004 0.046 5406 Dihedral : 5.514 43.188 4806 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.88 % Allowed : 10.03 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 3813 helix: 2.12 (0.20), residues: 693 sheet: 0.33 (0.15), residues: 1005 loop : -0.56 (0.12), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 36 HIS 0.008 0.001 HIS C 516 PHE 0.020 0.002 PHE B 895 TYR 0.019 0.002 TYR A1064 ARG 0.006 0.001 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 236 time to evaluate : 3.065 Fit side-chains REVERT: A 455 LYS cc_start: 0.8385 (mmtt) cc_final: 0.7838 (mtmm) REVERT: A 643 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8070 (mtp180) REVERT: L 87 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7291 (t0) REVERT: D 40 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7556 (ptt180) REVERT: E 40 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6769 (tt0) REVERT: E 87 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.6960 (m-30) REVERT: F 119 MET cc_start: 0.6801 (mtt) cc_final: 0.6386 (mpp) REVERT: B 118 ASN cc_start: 0.7136 (t0) cc_final: 0.6726 (m110) REVERT: B 150 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.5440 (pp-130) REVERT: B 332 LEU cc_start: 0.7978 (mm) cc_final: 0.7693 (mm) REVERT: B 455 LYS cc_start: 0.8325 (mmtt) cc_final: 0.7776 (mtmt) REVERT: B 643 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7206 (mpp-170) REVERT: B 776 GLN cc_start: 0.8789 (tt0) cc_final: 0.8519 (tp40) REVERT: B 847 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7881 (mp) REVERT: B 932 GLN cc_start: 0.7876 (tt0) cc_final: 0.7660 (tt0) REVERT: B 1070 LYS cc_start: 0.8639 (mttt) cc_final: 0.8163 (mptt) REVERT: C 150 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.5484 (pp-130) REVERT: C 643 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7645 (mtp180) REVERT: C 1070 LYS cc_start: 0.8634 (mttt) cc_final: 0.8269 (mtpp) outliers start: 63 outliers final: 21 residues processed: 281 average time/residue: 1.3358 time to fit residues: 451.9027 Evaluate side-chains 264 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 233 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 192 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 287 optimal weight: 50.0000 chunk 235 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 346 optimal weight: 0.1980 chunk 374 optimal weight: 0.6980 chunk 308 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 447 ASN B 561 GLN B 999 GLN C 118 ASN C 561 GLN C 999 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31125 Z= 0.199 Angle : 0.513 6.401 42357 Z= 0.277 Chirality : 0.045 0.166 4887 Planarity : 0.004 0.036 5406 Dihedral : 5.088 45.336 4780 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.55 % Allowed : 10.24 % Favored : 88.21 % 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: 0.36 (0.13), residues: 3813 helix: 2.41 (0.20), residues: 672 sheet: 0.40 (0.16), residues: 972 loop : -0.53 (0.12), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.006 0.001 HIS A 516 PHE 0.016 0.001 PHE B 895 TYR 0.018 0.001 TYR A1064 ARG 0.005 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 243 time to evaluate : 3.237 Fit side-chains REVERT: A 169 SER cc_start: 0.7251 (OUTLIER) cc_final: 0.6995 (m) REVERT: A 455 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7826 (mtmm) REVERT: A 643 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7697 (mtp180) REVERT: D 40 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7509 (ptt180) REVERT: E 40 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.6529 (tt0) REVERT: E 87 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: F 119 MET cc_start: 0.6810 (mtt) cc_final: 0.6384 (mpp) REVERT: B 118 ASN cc_start: 0.7105 (t0) cc_final: 0.6704 (m110) REVERT: B 150 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5970 (mpt) REVERT: B 455 LYS cc_start: 0.8357 (mmtt) cc_final: 0.7766 (mtmt) REVERT: B 643 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7215 (mpp-170) REVERT: B 776 GLN cc_start: 0.8780 (tt0) cc_final: 0.8470 (tp40) REVERT: B 847 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7901 (mp) REVERT: B 932 GLN cc_start: 0.7882 (tt0) cc_final: 0.7666 (tt0) REVERT: B 1070 LYS cc_start: 0.8632 (mttt) cc_final: 0.8161 (mptt) REVERT: C 150 MET cc_start: 0.6318 (tmm) cc_final: 0.5428 (pp-130) REVERT: C 169 SER cc_start: 0.7325 (OUTLIER) cc_final: 0.7114 (m) REVERT: C 332 LEU cc_start: 0.7878 (mm) cc_final: 0.7602 (mm) REVERT: C 643 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7619 (mtp180) REVERT: C 1070 LYS cc_start: 0.8624 (mttt) cc_final: 0.8262 (mtpp) outliers start: 52 outliers final: 15 residues processed: 281 average time/residue: 1.2782 time to fit residues: 435.3037 Evaluate side-chains 257 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 232 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 342 optimal weight: 8.9990 chunk 260 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 232 optimal weight: 8.9990 chunk 347 optimal weight: 1.9990 chunk 368 optimal weight: 9.9990 chunk 181 optimal weight: 30.0000 chunk 329 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 447 ASN B 561 GLN B 999 GLN C 118 ASN C 561 GLN C 999 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31125 Z= 0.242 Angle : 0.542 7.233 42357 Z= 0.293 Chirality : 0.046 0.176 4887 Planarity : 0.004 0.041 5406 Dihedral : 5.209 46.719 4779 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.76 % Allowed : 10.38 % Favored : 87.85 % 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: 0.33 (0.13), residues: 3813 helix: 2.30 (0.20), residues: 675 sheet: 0.36 (0.16), residues: 978 loop : -0.51 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.006 0.001 HIS C 516 PHE 0.019 0.002 PHE B 895 TYR 0.019 0.002 TYR A1064 ARG 0.006 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 234 time to evaluate : 3.000 Fit side-chains REVERT: A 455 LYS cc_start: 0.8404 (mmtt) cc_final: 0.7819 (mtmm) REVERT: A 643 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8070 (mtp180) REVERT: A 961 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8193 (mtpt) REVERT: L 40 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.5970 (tp40) REVERT: D 40 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7549 (ptt180) REVERT: E 40 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.6514 (tt0) REVERT: E 87 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7029 (m-30) REVERT: B 118 ASN cc_start: 0.7127 (t0) cc_final: 0.6745 (m110) REVERT: B 150 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.5919 (mpt) REVERT: B 332 LEU cc_start: 0.7940 (mm) cc_final: 0.7686 (mm) REVERT: B 643 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7212 (mpp-170) REVERT: B 776 GLN cc_start: 0.8813 (tt0) cc_final: 0.8494 (tp40) REVERT: B 847 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7892 (mp) REVERT: B 932 GLN cc_start: 0.7940 (tt0) cc_final: 0.7695 (tt0) REVERT: B 961 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8020 (mppt) REVERT: B 1070 LYS cc_start: 0.8636 (mttt) cc_final: 0.8160 (mptt) REVERT: C 118 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6839 (m110) REVERT: C 138 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6841 (mp) REVERT: C 150 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5391 (pp-130) REVERT: C 169 SER cc_start: 0.7317 (OUTLIER) cc_final: 0.7102 (m) REVERT: C 332 LEU cc_start: 0.7832 (mm) cc_final: 0.7534 (mm) REVERT: C 643 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7629 (mtp180) REVERT: C 776 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8565 (tt0) REVERT: C 1070 LYS cc_start: 0.8637 (mttt) cc_final: 0.8270 (mtpp) outliers start: 59 outliers final: 22 residues processed: 276 average time/residue: 1.2893 time to fit residues: 428.0424 Evaluate side-chains 269 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 231 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 961 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 306 optimal weight: 30.0000 chunk 209 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 274 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 188 optimal weight: 30.0000 chunk 330 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31125 Z= 0.290 Angle : 0.570 8.599 42357 Z= 0.308 Chirality : 0.047 0.183 4887 Planarity : 0.004 0.047 5406 Dihedral : 5.356 48.104 4779 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.85 % Allowed : 10.89 % Favored : 87.26 % 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: 0.22 (0.13), residues: 3813 helix: 2.20 (0.20), residues: 675 sheet: 0.25 (0.15), residues: 1014 loop : -0.56 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.007 0.001 HIS A 516 PHE 0.021 0.002 PHE B 895 TYR 0.020 0.002 TYR A 753 ARG 0.007 0.001 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 235 time to evaluate : 3.641 Fit side-chains REVERT: A 455 LYS cc_start: 0.8417 (mmtt) cc_final: 0.7826 (mtmm) REVERT: A 520 THR cc_start: 0.8608 (p) cc_final: 0.8403 (p) REVERT: A 643 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.8008 (mtp180) REVERT: A 961 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8202 (mtpt) REVERT: L 40 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.6262 (tp40) REVERT: D 40 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7549 (ptt180) REVERT: E 40 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.6442 (tt0) REVERT: E 87 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7045 (m-30) REVERT: B 118 ASN cc_start: 0.7166 (t0) cc_final: 0.6807 (m110) REVERT: B 150 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5714 (mpt) REVERT: B 332 LEU cc_start: 0.7952 (mm) cc_final: 0.7689 (mm) REVERT: B 437 LYS cc_start: 0.8120 (mttt) cc_final: 0.7885 (mtpt) REVERT: B 643 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7202 (mpp-170) REVERT: B 776 GLN cc_start: 0.8830 (tt0) cc_final: 0.8499 (tp40) REVERT: B 847 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7895 (mp) REVERT: B 932 GLN cc_start: 0.7947 (tt0) cc_final: 0.7695 (tt0) REVERT: B 961 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8010 (mppt) REVERT: B 1070 LYS cc_start: 0.8649 (mttt) cc_final: 0.8174 (mptt) REVERT: C 118 ASN cc_start: 0.7190 (t0) cc_final: 0.6814 (m110) REVERT: C 138 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6711 (mp) REVERT: C 150 MET cc_start: 0.6290 (OUTLIER) cc_final: 0.5387 (pp-130) REVERT: C 332 LEU cc_start: 0.7849 (mm) cc_final: 0.7511 (mm) REVERT: C 643 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7652 (mtp180) REVERT: C 1070 LYS cc_start: 0.8628 (mttt) cc_final: 0.8273 (mtpp) outliers start: 62 outliers final: 29 residues processed: 280 average time/residue: 1.3383 time to fit residues: 453.9097 Evaluate side-chains 271 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 229 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 961 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 123 optimal weight: 5.9990 chunk 331 optimal weight: 9.9990 chunk 72 optimal weight: 0.0770 chunk 216 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 368 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 121 optimal weight: 40.0000 chunk 193 optimal weight: 4.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31125 Z= 0.227 Angle : 0.534 8.122 42357 Z= 0.287 Chirality : 0.046 0.170 4887 Planarity : 0.004 0.037 5406 Dihedral : 5.203 48.537 4779 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.79 % Allowed : 11.13 % Favored : 87.08 % 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: 0.30 (0.13), residues: 3813 helix: 2.16 (0.20), residues: 693 sheet: 0.36 (0.16), residues: 975 loop : -0.51 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 36 HIS 0.006 0.001 HIS A 516 PHE 0.017 0.001 PHE B 895 TYR 0.018 0.001 TYR A1064 ARG 0.005 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 238 time to evaluate : 3.182 Fit side-chains REVERT: A 316 ARG cc_start: 0.7462 (mtt-85) cc_final: 0.7171 (mpt90) REVERT: A 437 LYS cc_start: 0.8158 (mttt) cc_final: 0.7905 (mtpt) REVERT: A 455 LYS cc_start: 0.8425 (mmtt) cc_final: 0.7817 (mtmm) REVERT: A 643 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7696 (mtp180) REVERT: A 792 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.6203 (tmtt) REVERT: L 40 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.6051 (tp40) REVERT: D 40 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7527 (ptt180) REVERT: E 40 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.6392 (tt0) REVERT: E 87 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7043 (m-30) REVERT: B 118 ASN cc_start: 0.7150 (t0) cc_final: 0.6779 (m110) REVERT: B 150 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.5863 (mpt) REVERT: B 437 LYS cc_start: 0.8078 (mttt) cc_final: 0.7838 (mtpt) REVERT: B 455 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7759 (mtmt) REVERT: B 643 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7169 (mpp-170) REVERT: B 776 GLN cc_start: 0.8826 (tt0) cc_final: 0.8495 (tp40) REVERT: B 847 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7895 (mp) REVERT: B 932 GLN cc_start: 0.7960 (tt0) cc_final: 0.7706 (tt0) REVERT: B 961 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7991 (mppt) REVERT: B 1070 LYS cc_start: 0.8640 (mttt) cc_final: 0.8173 (mptt) REVERT: C 138 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6800 (mp) REVERT: C 150 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.5410 (pp-130) REVERT: C 169 SER cc_start: 0.7353 (OUTLIER) cc_final: 0.7146 (m) REVERT: C 332 LEU cc_start: 0.7820 (mm) cc_final: 0.7475 (mm) REVERT: C 643 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7634 (mtp180) REVERT: C 1070 LYS cc_start: 0.8639 (mttt) cc_final: 0.8275 (mtpp) outliers start: 60 outliers final: 30 residues processed: 282 average time/residue: 1.2466 time to fit residues: 425.1012 Evaluate side-chains 277 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 233 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 355 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 210 optimal weight: 0.0670 chunk 269 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 205 optimal weight: 0.7980 chunk 367 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 169 optimal weight: 30.0000 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 31125 Z= 0.153 Angle : 0.487 8.707 42357 Z= 0.260 Chirality : 0.044 0.156 4887 Planarity : 0.003 0.036 5406 Dihedral : 4.863 48.127 4779 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.37 % Allowed : 11.79 % Favored : 86.84 % 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: 0.47 (0.13), residues: 3813 helix: 2.37 (0.20), residues: 693 sheet: 0.47 (0.16), residues: 969 loop : -0.44 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 36 HIS 0.004 0.001 HIS A 516 PHE 0.014 0.001 PHE C 562 TYR 0.016 0.001 TYR A1064 ARG 0.002 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 243 time to evaluate : 3.087 Fit side-chains REVERT: A 316 ARG cc_start: 0.7440 (mtt-85) cc_final: 0.7176 (mpt90) REVERT: A 437 LYS cc_start: 0.8142 (mttt) cc_final: 0.7904 (mtpt) REVERT: A 455 LYS cc_start: 0.8395 (mmtt) cc_final: 0.7782 (mtmm) REVERT: A 643 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7666 (mtp180) REVERT: A 792 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.6199 (tmtt) REVERT: L 40 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.5823 (tp40) REVERT: E 40 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6228 (tt0) REVERT: E 87 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7030 (m-30) REVERT: B 150 MET cc_start: 0.6338 (OUTLIER) cc_final: 0.5910 (mpt) REVERT: B 318 GLN cc_start: 0.8144 (mm110) cc_final: 0.7887 (mm110) REVERT: B 332 LEU cc_start: 0.7947 (mm) cc_final: 0.7712 (mm) REVERT: B 437 LYS cc_start: 0.8057 (mttt) cc_final: 0.7809 (mtpt) REVERT: B 455 LYS cc_start: 0.8347 (mmtt) cc_final: 0.7745 (mtmt) REVERT: B 643 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7198 (mpp-170) REVERT: B 776 GLN cc_start: 0.8816 (tt0) cc_final: 0.8473 (tp40) REVERT: B 805 ASP cc_start: 0.7402 (t0) cc_final: 0.7175 (t0) REVERT: B 932 GLN cc_start: 0.7956 (tt0) cc_final: 0.7703 (tt0) REVERT: B 1070 LYS cc_start: 0.8631 (mttt) cc_final: 0.8161 (mptt) REVERT: B 1098 HIS cc_start: 0.8639 (m90) cc_final: 0.8275 (m90) REVERT: C 138 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6799 (mp) REVERT: C 150 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.5475 (pp-130) REVERT: C 318 GLN cc_start: 0.8225 (mm110) cc_final: 0.8003 (mm110) REVERT: C 332 LEU cc_start: 0.7770 (mm) cc_final: 0.7414 (mm) REVERT: C 437 LYS cc_start: 0.8068 (mttt) cc_final: 0.7866 (mtpt) REVERT: C 643 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7613 (mtp180) REVERT: C 1070 LYS cc_start: 0.8619 (mttt) cc_final: 0.8255 (mtpp) outliers start: 46 outliers final: 19 residues processed: 275 average time/residue: 1.2559 time to fit residues: 414.7613 Evaluate side-chains 263 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 234 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 792 LYS Chi-restraints excluded: chain A residue 983 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 227 optimal weight: 7.9990 chunk 146 optimal weight: 50.0000 chunk 219 optimal weight: 10.0000 chunk 110 optimal weight: 50.0000 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 233 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 181 optimal weight: 30.0000 chunk 34 optimal weight: 40.0000 chunk 288 optimal weight: 40.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN C 625 GLN C 999 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31125 Z= 0.254 Angle : 0.550 9.761 42357 Z= 0.296 Chirality : 0.046 0.170 4887 Planarity : 0.004 0.040 5406 Dihedral : 5.213 49.361 4779 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.46 % Allowed : 11.82 % Favored : 86.72 % 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: 0.35 (0.13), residues: 3813 helix: 2.18 (0.20), residues: 693 sheet: 0.41 (0.16), residues: 975 loop : -0.48 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.006 0.001 HIS C 516 PHE 0.019 0.002 PHE B 895 TYR 0.019 0.002 TYR A1064 ARG 0.004 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 230 time to evaluate : 3.066 Fit side-chains REVERT: A 316 ARG cc_start: 0.7421 (mtt-85) cc_final: 0.7116 (mpt90) REVERT: A 437 LYS cc_start: 0.8183 (mttt) cc_final: 0.7928 (mtpt) REVERT: A 455 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7796 (mtmm) REVERT: A 643 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8054 (mtp180) REVERT: A 792 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.6222 (tmtt) REVERT: A 961 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8193 (mtpt) REVERT: A 983 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7062 (ttpt) REVERT: L 40 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.6065 (tp40) REVERT: D 40 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7560 (ptt180) REVERT: E 40 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.6282 (tt0) REVERT: E 87 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7032 (m-30) REVERT: B 118 ASN cc_start: 0.7163 (t0) cc_final: 0.6790 (m110) REVERT: B 150 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.5867 (mpt) REVERT: B 332 LEU cc_start: 0.7936 (mm) cc_final: 0.7688 (mm) REVERT: B 437 LYS cc_start: 0.8101 (mttt) cc_final: 0.7845 (mtpt) REVERT: B 643 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7204 (mpp-170) REVERT: B 776 GLN cc_start: 0.8819 (tt0) cc_final: 0.8479 (tp40) REVERT: B 847 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7916 (mp) REVERT: B 932 GLN cc_start: 0.7972 (tt0) cc_final: 0.7710 (tt0) REVERT: B 1070 LYS cc_start: 0.8640 (mttt) cc_final: 0.8162 (mptt) REVERT: C 138 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6824 (mp) REVERT: C 150 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.5454 (pp-130) REVERT: C 332 LEU cc_start: 0.7798 (mm) cc_final: 0.7432 (mm) REVERT: C 437 LYS cc_start: 0.8092 (mttt) cc_final: 0.7888 (mtpt) REVERT: C 643 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7632 (mtp180) REVERT: C 1070 LYS cc_start: 0.8645 (mttt) cc_final: 0.8278 (mtpp) outliers start: 49 outliers final: 27 residues processed: 265 average time/residue: 1.3400 time to fit residues: 424.8838 Evaluate side-chains 269 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 228 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LYS Chi-restraints excluded: chain A residue 961 LYS Chi-restraints excluded: chain A residue 983 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 334 optimal weight: 5.9990 chunk 351 optimal weight: 1.9990 chunk 320 optimal weight: 20.0000 chunk 342 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 309 optimal weight: 7.9990 chunk 323 optimal weight: 0.0770 chunk 341 optimal weight: 5.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31125 Z= 0.167 Angle : 0.502 10.278 42357 Z= 0.269 Chirality : 0.044 0.157 4887 Planarity : 0.003 0.035 5406 Dihedral : 4.946 49.167 4779 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.25 % Allowed : 11.94 % Favored : 86.81 % 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: 0.46 (0.13), residues: 3813 helix: 2.32 (0.20), residues: 693 sheet: 0.44 (0.16), residues: 975 loop : -0.42 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.005 0.001 HIS C 516 PHE 0.015 0.001 PHE C 562 TYR 0.017 0.001 TYR A1064 ARG 0.009 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 238 time to evaluate : 3.286 Fit side-chains REVERT: A 316 ARG cc_start: 0.7428 (mtt-85) cc_final: 0.7141 (mpt90) REVERT: A 437 LYS cc_start: 0.8147 (mttt) cc_final: 0.7909 (mtpt) REVERT: A 455 LYS cc_start: 0.8411 (mmtt) cc_final: 0.7787 (mtmm) REVERT: A 643 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7672 (mtp180) REVERT: A 792 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.6178 (tmtt) REVERT: L 40 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.5752 (tp40) REVERT: E 40 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6219 (tt0) REVERT: E 87 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7028 (m-30) REVERT: B 150 MET cc_start: 0.6346 (OUTLIER) cc_final: 0.5901 (mpt) REVERT: B 318 GLN cc_start: 0.8243 (mm110) cc_final: 0.7998 (mm110) REVERT: B 332 LEU cc_start: 0.7945 (mm) cc_final: 0.7715 (mm) REVERT: B 437 LYS cc_start: 0.8124 (mttt) cc_final: 0.7879 (mtpt) REVERT: B 643 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7175 (mpp-170) REVERT: B 776 GLN cc_start: 0.8821 (tt0) cc_final: 0.8479 (tp40) REVERT: B 805 ASP cc_start: 0.7330 (t0) cc_final: 0.7079 (t0) REVERT: B 932 GLN cc_start: 0.7952 (tt0) cc_final: 0.7693 (tt0) REVERT: B 1070 LYS cc_start: 0.8633 (mttt) cc_final: 0.8160 (mptt) REVERT: C 138 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6876 (mp) REVERT: C 150 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.5430 (pp-130) REVERT: C 332 LEU cc_start: 0.7755 (mm) cc_final: 0.7381 (mm) REVERT: C 437 LYS cc_start: 0.8069 (mttt) cc_final: 0.7866 (mtpt) REVERT: C 564 ARG cc_start: 0.7446 (mtt-85) cc_final: 0.7152 (mtt-85) REVERT: C 643 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7621 (mtp180) REVERT: C 1070 LYS cc_start: 0.8624 (mttt) cc_final: 0.8261 (mtpp) outliers start: 42 outliers final: 24 residues processed: 268 average time/residue: 1.2795 time to fit residues: 412.0833 Evaluate side-chains 267 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 233 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 792 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 224 optimal weight: 4.9990 chunk 361 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 379 optimal weight: 6.9990 chunk 349 optimal weight: 7.9990 chunk 302 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 233 optimal weight: 0.7980 chunk 185 optimal weight: 9.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 23 GLN B 561 GLN B 999 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31125 Z= 0.238 Angle : 0.542 10.654 42357 Z= 0.291 Chirality : 0.046 0.164 4887 Planarity : 0.004 0.038 5406 Dihedral : 5.187 49.995 4779 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.34 % Allowed : 11.94 % Favored : 86.72 % 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: 0.37 (0.13), residues: 3813 helix: 2.20 (0.20), residues: 693 sheet: 0.42 (0.16), residues: 975 loop : -0.47 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.006 0.001 HIS C 516 PHE 0.018 0.001 PHE B 895 TYR 0.019 0.002 TYR A1064 ARG 0.010 0.000 ARG B 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 230 time to evaluate : 3.274 Fit side-chains REVERT: A 316 ARG cc_start: 0.7408 (mtt-85) cc_final: 0.7107 (mpt90) REVERT: A 437 LYS cc_start: 0.8141 (mttt) cc_final: 0.7911 (mtpt) REVERT: A 455 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7793 (mtmm) REVERT: A 490 ARG cc_start: 0.7173 (mmt90) cc_final: 0.6883 (tpp-160) REVERT: A 643 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8059 (mtp180) REVERT: A 792 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.6215 (tmtt) REVERT: A 961 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8184 (mtpt) REVERT: L 40 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.5950 (tp40) REVERT: D 40 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7553 (ptt180) REVERT: E 40 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6266 (tt0) REVERT: E 87 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7044 (m-30) REVERT: B 118 ASN cc_start: 0.7165 (t0) cc_final: 0.6791 (m110) REVERT: B 150 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.5903 (mpt) REVERT: B 318 GLN cc_start: 0.8232 (mm110) cc_final: 0.7981 (mm110) REVERT: B 332 LEU cc_start: 0.7951 (mm) cc_final: 0.7713 (mm) REVERT: B 437 LYS cc_start: 0.8151 (mttt) cc_final: 0.7902 (mtpt) REVERT: B 643 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7207 (mpp-170) REVERT: B 776 GLN cc_start: 0.8819 (tt0) cc_final: 0.8480 (tp40) REVERT: B 847 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7916 (mp) REVERT: B 932 GLN cc_start: 0.7976 (tt0) cc_final: 0.7718 (tt0) REVERT: B 961 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8006 (mppt) REVERT: B 1070 LYS cc_start: 0.8637 (mttt) cc_final: 0.8159 (mptt) REVERT: C 138 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6901 (mp) REVERT: C 150 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.5495 (pp-130) REVERT: C 332 LEU cc_start: 0.7766 (mm) cc_final: 0.7396 (mm) REVERT: C 437 LYS cc_start: 0.8094 (mttt) cc_final: 0.7889 (mtpt) REVERT: C 643 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7628 (mtp180) REVERT: C 1070 LYS cc_start: 0.8640 (mttt) cc_final: 0.8276 (mtpp) outliers start: 45 outliers final: 27 residues processed: 263 average time/residue: 1.3456 time to fit residues: 425.5776 Evaluate side-chains 268 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 227 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LYS Chi-restraints excluded: chain A residue 961 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 240 optimal weight: 2.9990 chunk 321 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 44 optimal weight: 0.3980 chunk 83 optimal weight: 9.9990 chunk 302 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 310 optimal weight: 9.9990 chunk 38 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.188073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114981 restraints weight = 27865.633| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.11 r_work: 0.3083 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31125 Z= 0.196 Angle : 0.518 10.625 42357 Z= 0.278 Chirality : 0.045 0.158 4887 Planarity : 0.004 0.035 5406 Dihedral : 5.067 50.025 4779 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.22 % Allowed : 12.06 % Favored : 86.72 % 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: 0.42 (0.13), residues: 3813 helix: 2.26 (0.20), residues: 693 sheet: 0.43 (0.16), residues: 975 loop : -0.44 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.005 0.001 HIS C 516 PHE 0.016 0.001 PHE C 562 TYR 0.018 0.001 TYR A1064 ARG 0.009 0.000 ARG B 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9815.07 seconds wall clock time: 174 minutes 14.10 seconds (10454.10 seconds total)