Starting phenix.real_space_refine on Tue Feb 20 07:56:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6h_23696/02_2024/7m6h_23696_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6h_23696/02_2024/7m6h_23696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6h_23696/02_2024/7m6h_23696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6h_23696/02_2024/7m6h_23696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6h_23696/02_2024/7m6h_23696_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6h_23696/02_2024/7m6h_23696_neut.pdb" } resolution = 4.0 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= -0.001 sd= 0.017 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 127 5.16 5 C 17404 2.51 5 N 4534 2.21 5 O 5314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27379 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "D" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "F" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "G" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 13.14, per 1000 atoms: 0.48 Number of scatterers: 27379 At special positions: 0 Unit cell: (134.695, 143.385, 191.18, 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 127 16.00 O 5314 8.00 N 4534 7.00 C 17404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=1.45 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=1.99 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " 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=1, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 331 " " NAG C1301 " - " ASN A 282 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C 331 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.45 Conformation dependent library (CDL) restraints added in 5.0 seconds 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6458 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 21.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.529A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.581A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.560A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.902A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.378A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.638A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.528A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.191A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.681A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.688A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.707A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.124A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.297A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.102A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.875A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.792A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.142A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.127A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.640A pdb=" N ASP D 86 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 87' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.796A pdb=" N SER E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.815A pdb=" N ASP E 86 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 83 through 87' Processing helix chain 'F' and resid 26 through 30 removed outlier: 4.088A pdb=" N ALA F 29 " --> pdb=" O SER F 27A" (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1452 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: 6.05 Time building geometry restraints manager: 12.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4474 1.31 - 1.44: 7794 1.44 - 1.57: 15557 1.57 - 1.70: 1 1.70 - 1.83: 161 Bond restraints: 27987 Sorted by residual: bond pdb=" C VAL A 320 " pdb=" N GLN A 321 " ideal model delta sigma weight residual 1.326 1.237 0.090 1.84e-02 2.95e+03 2.37e+01 bond pdb=" C ARG C 357 " pdb=" O ARG C 357 " ideal model delta sigma weight residual 1.234 1.175 0.059 1.26e-02 6.30e+03 2.19e+01 bond pdb=" N PRO D 112 " pdb=" CD PRO D 112 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.24e+01 bond pdb=" N PRO E 112 " pdb=" CD PRO E 112 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" N ILE C 402 " pdb=" CA ILE C 402 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.18e+01 ... (remaining 27982 not shown) Histogram of bond angle deviations from ideal: 95.88 - 104.27: 433 104.27 - 112.67: 14341 112.67 - 121.07: 14744 121.07 - 129.47: 8435 129.47 - 137.87: 120 Bond angle restraints: 38073 Sorted by residual: angle pdb=" CA PRO D 112 " pdb=" N PRO D 112 " pdb=" CD PRO D 112 " ideal model delta sigma weight residual 112.00 99.50 12.50 1.40e+00 5.10e-01 7.97e+01 angle pdb=" CA PRO E 112 " pdb=" N PRO E 112 " pdb=" CD PRO E 112 " ideal model delta sigma weight residual 112.00 99.58 12.42 1.40e+00 5.10e-01 7.87e+01 angle pdb=" N ILE E 75 " pdb=" CA ILE E 75 " pdb=" C ILE E 75 " ideal model delta sigma weight residual 113.20 105.05 8.15 9.60e-01 1.09e+00 7.20e+01 angle pdb=" N VAL A 826 " pdb=" CA VAL A 826 " pdb=" C VAL A 826 " ideal model delta sigma weight residual 112.29 105.56 6.73 9.40e-01 1.13e+00 5.13e+01 angle pdb=" C PRO G 15 " pdb=" CA PRO G 15 " pdb=" CB PRO G 15 " ideal model delta sigma weight residual 112.64 100.60 12.04 1.74e+00 3.30e-01 4.79e+01 ... (remaining 38068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15405 17.94 - 35.88: 1281 35.88 - 53.82: 215 53.82 - 71.76: 66 71.76 - 89.70: 24 Dihedral angle restraints: 16991 sinusoidal: 6930 harmonic: 10061 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.32 -84.32 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -161.65 75.65 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 92 " pdb=" CB CYS E 92 " ideal model delta sinusoidal sigma weight residual 93.00 168.07 -75.07 1 1.00e+01 1.00e-02 7.13e+01 ... (remaining 16988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 4268 0.158 - 0.317: 116 0.317 - 0.475: 9 0.475 - 0.634: 5 0.634 - 0.792: 2 Chirality restraints: 4400 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.82e+00 ... (remaining 4397 not shown) Planarity restraints: 4917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1310 " 0.320 2.00e-02 2.50e+03 2.80e-01 9.77e+02 pdb=" C7 NAG C1310 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG C1310 " 0.091 2.00e-02 2.50e+03 pdb=" N2 NAG C1310 " -0.500 2.00e-02 2.50e+03 pdb=" O7 NAG C1310 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.013 2.00e-02 2.50e+03 6.35e-02 5.03e+01 pdb=" CG ASN C 234 " 0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" CG ASN C 234 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.026 2.00e-02 2.50e+03 ... (remaining 4914 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1647 2.72 - 3.26: 27978 3.26 - 3.81: 46939 3.81 - 4.35: 56702 4.35 - 4.90: 91334 Nonbonded interactions: 224600 Sorted by model distance: nonbonded pdb=" O ASN A 125 " pdb=" O6 NAG A1302 " model vdw 2.170 2.440 nonbonded pdb=" O GLN A 804 " pdb=" OG SER A 816 " model vdw 2.188 2.440 nonbonded pdb=" OD1 ASN B 370 " pdb=" OG1 THR E 100B" model vdw 2.226 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.231 2.440 nonbonded pdb=" OE1 GLN G 6 " pdb=" OG1 THR G 103 " model vdw 2.241 2.440 ... (remaining 224595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 1147 or resid 1301 through 1308)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 1147 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 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: 19.350 Check model and map are aligned: 0.930 Set scattering table: 0.300 Process input model: 66.860 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.170 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 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 : 0.006 0.095 27987 Z= 0.424 Angle : 1.130 21.570 38073 Z= 0.639 Chirality : 0.071 0.792 4400 Planarity : 0.009 0.280 4890 Dihedral : 13.704 89.695 10404 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.05 % Favored : 92.87 % Rotamer: Outliers : 0.27 % Allowed : 1.03 % Favored : 98.70 % Cbeta Deviations : 0.22 % 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: -2.57 (0.13), residues: 3420 helix: -1.66 (0.18), residues: 622 sheet: -1.41 (0.22), residues: 493 loop : -1.87 (0.12), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 47 HIS 0.017 0.002 HIS A 49 PHE 0.054 0.003 PHE A 201 TYR 0.043 0.003 TYR C 917 ARG 0.015 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 329 time to evaluate : 3.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.5971 (m-10) cc_final: 0.5603 (m-80) REVERT: A 515 PHE cc_start: 0.8932 (m-80) cc_final: 0.8574 (m-80) REVERT: A 562 PHE cc_start: 0.8679 (t80) cc_final: 0.8236 (t80) REVERT: A 960 ASN cc_start: 0.8586 (t0) cc_final: 0.8374 (t0) REVERT: A 1095 PHE cc_start: 0.7622 (m-10) cc_final: 0.7277 (m-10) REVERT: B 864 LEU cc_start: 0.7323 (tt) cc_final: 0.6518 (mm) REVERT: B 976 VAL cc_start: 0.8844 (t) cc_final: 0.8284 (t) REVERT: C 271 GLN cc_start: 0.5800 (mm-40) cc_final: 0.5508 (mm-40) REVERT: C 336 CYS cc_start: 0.2353 (OUTLIER) cc_final: 0.1802 (t) REVERT: E 51 MET cc_start: 0.5989 (tpt) cc_final: 0.5537 (tpt) REVERT: E 100 MET cc_start: 0.8810 (tpt) cc_final: 0.8606 (tpt) REVERT: G 32 ASP cc_start: 0.4368 (m-30) cc_final: 0.3951 (t0) outliers start: 8 outliers final: 1 residues processed: 336 average time/residue: 0.3728 time to fit residues: 204.1920 Evaluate side-chains 226 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 144 optimal weight: 0.4980 chunk 89 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 139 optimal weight: 0.0010 chunk 269 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 312 optimal weight: 10.0000 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 317 ASN A 506 GLN A 655 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 49 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27987 Z= 0.182 Angle : 0.665 11.943 38073 Z= 0.339 Chirality : 0.048 0.500 4400 Planarity : 0.005 0.058 4890 Dihedral : 8.233 59.948 4310 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 1.16 % Allowed : 9.04 % Favored : 89.79 % 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: -2.25 (0.13), residues: 3420 helix: -1.09 (0.19), residues: 637 sheet: -1.15 (0.24), residues: 451 loop : -1.78 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.006 0.001 HIS C1048 PHE 0.026 0.002 PHE C 338 TYR 0.017 0.001 TYR B 200 ARG 0.006 0.000 ARG B1091 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 259 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.6799 (t-90) cc_final: 0.6422 (t-90) REVERT: A 516 GLU cc_start: 0.7861 (pm20) cc_final: 0.7471 (pm20) REVERT: A 562 PHE cc_start: 0.8746 (t80) cc_final: 0.8493 (t80) REVERT: A 824 ASN cc_start: 0.8209 (t0) cc_final: 0.7860 (t0) REVERT: A 960 ASN cc_start: 0.8622 (t0) cc_final: 0.8360 (t0) REVERT: A 978 ASN cc_start: 0.8349 (m-40) cc_final: 0.7978 (p0) REVERT: A 1037 SER cc_start: 0.8635 (t) cc_final: 0.8391 (m) REVERT: A 1095 PHE cc_start: 0.7618 (m-10) cc_final: 0.7336 (m-10) REVERT: A 1103 PHE cc_start: 0.7097 (m-10) cc_final: 0.6828 (m-10) REVERT: B 201 PHE cc_start: 0.6850 (t80) cc_final: 0.6549 (t80) REVERT: B 402 ILE cc_start: 0.3265 (tp) cc_final: 0.3011 (tp) REVERT: B 996 LEU cc_start: 0.8840 (tt) cc_final: 0.8635 (tt) REVERT: C 336 CYS cc_start: 0.2249 (OUTLIER) cc_final: 0.1541 (t) REVERT: C 346 ARG cc_start: 0.4420 (tpt-90) cc_final: 0.3952 (tpt-90) REVERT: E 48 MET cc_start: 0.8068 (mpp) cc_final: 0.7235 (mpp) REVERT: E 51 MET cc_start: 0.5884 (tpt) cc_final: 0.5586 (tpt) REVERT: E 69 MET cc_start: 0.3708 (mpp) cc_final: 0.3377 (mmm) REVERT: E 80 MET cc_start: 0.6898 (tpt) cc_final: 0.6664 (tpt) REVERT: G 32 ASP cc_start: 0.4263 (m-30) cc_final: 0.3641 (t0) REVERT: G 45 LYS cc_start: 0.7737 (mmtp) cc_final: 0.7513 (mmtm) REVERT: G 47 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8044 (pp) outliers start: 35 outliers final: 21 residues processed: 280 average time/residue: 0.3494 time to fit residues: 164.4527 Evaluate side-chains 243 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 220 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 212 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 312 optimal weight: 9.9990 chunk 338 optimal weight: 0.0020 chunk 278 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 106 optimal weight: 0.0000 chunk 251 optimal weight: 9.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27987 Z= 0.199 Angle : 0.627 10.292 38073 Z= 0.321 Chirality : 0.046 0.432 4400 Planarity : 0.004 0.052 4890 Dihedral : 7.599 59.787 4310 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.96 % Favored : 93.01 % Rotamer: Outliers : 2.03 % Allowed : 12.43 % Favored : 85.54 % 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: -2.07 (0.13), residues: 3420 helix: -0.76 (0.19), residues: 644 sheet: -1.10 (0.24), residues: 447 loop : -1.70 (0.12), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 103 HIS 0.006 0.001 HIS C1048 PHE 0.018 0.001 PHE B1052 TYR 0.017 0.001 TYR C 365 ARG 0.005 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 239 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: -0.1557 (OUTLIER) cc_final: -0.2446 (tt0) REVERT: A 515 PHE cc_start: 0.8414 (m-80) cc_final: 0.8117 (m-80) REVERT: A 516 GLU cc_start: 0.7821 (pm20) cc_final: 0.7523 (pm20) REVERT: A 562 PHE cc_start: 0.8670 (t80) cc_final: 0.8381 (t80) REVERT: A 824 ASN cc_start: 0.8261 (t0) cc_final: 0.7955 (t0) REVERT: A 978 ASN cc_start: 0.8275 (m-40) cc_final: 0.8022 (p0) REVERT: A 1095 PHE cc_start: 0.7650 (m-10) cc_final: 0.7364 (m-10) REVERT: A 1103 PHE cc_start: 0.7290 (m-10) cc_final: 0.7032 (m-10) REVERT: B 402 ILE cc_start: 0.3739 (tp) cc_final: 0.3472 (tp) REVERT: B 697 MET cc_start: 0.7476 (ppp) cc_final: 0.7021 (ppp) REVERT: B 996 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8671 (tt) REVERT: C 336 CYS cc_start: 0.2186 (OUTLIER) cc_final: 0.1508 (t) REVERT: C 346 ARG cc_start: 0.4448 (tpt-90) cc_final: 0.3973 (tpt-90) REVERT: C 1005 GLN cc_start: 0.8370 (mp10) cc_final: 0.8166 (mp10) REVERT: E 51 MET cc_start: 0.6032 (tpt) cc_final: 0.5749 (tpt) REVERT: E 69 MET cc_start: 0.3778 (mpp) cc_final: 0.3203 (mmp) REVERT: G 32 ASP cc_start: 0.4192 (m-30) cc_final: 0.3775 (t0) outliers start: 61 outliers final: 34 residues processed: 286 average time/residue: 0.3342 time to fit residues: 161.6526 Evaluate side-chains 247 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 210 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 314 optimal weight: 20.0000 chunk 332 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 297 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 448 ASN A 580 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 360 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C1011 GLN C1054 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27BASN ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 27987 Z= 0.308 Angle : 0.689 9.613 38073 Z= 0.357 Chirality : 0.048 0.470 4400 Planarity : 0.005 0.053 4890 Dihedral : 7.543 59.222 4310 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.54 % Favored : 92.43 % Rotamer: Outliers : 3.32 % Allowed : 14.36 % Favored : 82.31 % 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: -2.06 (0.13), residues: 3420 helix: -0.59 (0.20), residues: 643 sheet: -1.16 (0.23), residues: 489 loop : -1.73 (0.12), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1102 HIS 0.015 0.002 HIS B1048 PHE 0.021 0.002 PHE B 55 TYR 0.018 0.002 TYR E 98 ARG 0.006 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 231 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7475 (m-10) cc_final: 0.7225 (m-10) REVERT: A 201 PHE cc_start: 0.7942 (m-80) cc_final: 0.7627 (m-10) REVERT: A 393 THR cc_start: 0.4134 (OUTLIER) cc_final: 0.3869 (m) REVERT: A 515 PHE cc_start: 0.8426 (m-80) cc_final: 0.8149 (m-80) REVERT: A 516 GLU cc_start: 0.8033 (pm20) cc_final: 0.7547 (pm20) REVERT: A 562 PHE cc_start: 0.8560 (t80) cc_final: 0.8260 (t80) REVERT: A 731 MET cc_start: 0.8641 (ptm) cc_final: 0.8417 (ptm) REVERT: A 824 ASN cc_start: 0.8250 (t0) cc_final: 0.7959 (t0) REVERT: A 950 ASP cc_start: 0.8509 (p0) cc_final: 0.7985 (p0) REVERT: A 960 ASN cc_start: 0.8643 (t0) cc_final: 0.8383 (t0) REVERT: A 1095 PHE cc_start: 0.7729 (m-10) cc_final: 0.7321 (m-10) REVERT: B 196 ASN cc_start: 0.3352 (OUTLIER) cc_final: 0.2946 (t0) REVERT: B 697 MET cc_start: 0.7435 (ppp) cc_final: 0.7145 (ppp) REVERT: B 764 ASN cc_start: 0.8719 (t0) cc_final: 0.8404 (t0) REVERT: B 765 ARG cc_start: 0.8805 (ttm110) cc_final: 0.8402 (ttm110) REVERT: C 346 ARG cc_start: 0.4391 (tpt-90) cc_final: 0.3921 (tpt170) REVERT: C 391 CYS cc_start: 0.3503 (OUTLIER) cc_final: 0.2996 (t) REVERT: E 23 LYS cc_start: 0.8341 (tppt) cc_final: 0.8080 (tppt) REVERT: E 69 MET cc_start: 0.4062 (mpp) cc_final: 0.3592 (tpp) REVERT: G 32 ASP cc_start: 0.4203 (m-30) cc_final: 0.3705 (t70) REVERT: G 45 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7882 (mmtm) REVERT: G 47 LEU cc_start: 0.8535 (mt) cc_final: 0.8182 (pp) outliers start: 100 outliers final: 59 residues processed: 305 average time/residue: 0.3562 time to fit residues: 182.6062 Evaluate side-chains 259 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 197 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 0.7980 chunk 188 optimal weight: 0.1980 chunk 4 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 283 optimal weight: 9.9990 chunk 229 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 955 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27987 Z= 0.308 Angle : 0.676 10.803 38073 Z= 0.350 Chirality : 0.048 0.464 4400 Planarity : 0.005 0.052 4890 Dihedral : 7.356 59.672 4309 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.78 % Favored : 92.19 % Rotamer: Outliers : 3.46 % Allowed : 16.52 % Favored : 80.02 % 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: -2.17 (0.13), residues: 3420 helix: -0.68 (0.19), residues: 647 sheet: -1.21 (0.23), residues: 486 loop : -1.81 (0.12), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1102 HIS 0.012 0.001 HIS B1048 PHE 0.020 0.002 PHE B 927 TYR 0.021 0.002 TYR C 365 ARG 0.005 0.001 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 224 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: -0.1208 (OUTLIER) cc_final: -0.1983 (tt0) REVERT: A 201 PHE cc_start: 0.7946 (m-80) cc_final: 0.7623 (m-10) REVERT: A 515 PHE cc_start: 0.8488 (m-80) cc_final: 0.8228 (m-80) REVERT: A 516 GLU cc_start: 0.8123 (pm20) cc_final: 0.7670 (pm20) REVERT: A 562 PHE cc_start: 0.8513 (t80) cc_final: 0.8139 (t80) REVERT: A 824 ASN cc_start: 0.8272 (t0) cc_final: 0.7957 (t0) REVERT: A 950 ASP cc_start: 0.8533 (p0) cc_final: 0.8144 (p0) REVERT: A 960 ASN cc_start: 0.8685 (t0) cc_final: 0.8409 (t0) REVERT: A 978 ASN cc_start: 0.8202 (p0) cc_final: 0.7974 (p0) REVERT: A 1095 PHE cc_start: 0.7790 (m-10) cc_final: 0.7381 (m-10) REVERT: A 1125 ASN cc_start: 0.7859 (p0) cc_final: 0.7461 (t0) REVERT: B 196 ASN cc_start: 0.3469 (OUTLIER) cc_final: 0.2987 (t0) REVERT: B 697 MET cc_start: 0.7303 (ppp) cc_final: 0.7052 (ppp) REVERT: B 764 ASN cc_start: 0.8800 (t0) cc_final: 0.8394 (t0) REVERT: B 765 ARG cc_start: 0.8821 (ttm110) cc_final: 0.8375 (ttm110) REVERT: B 873 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7525 (t80) REVERT: B 902 MET cc_start: 0.8121 (mmm) cc_final: 0.7715 (tpt) REVERT: B 984 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8237 (mm) REVERT: C 1138 TYR cc_start: 0.7115 (t80) cc_final: 0.6904 (t80) REVERT: D 91 PHE cc_start: 0.5777 (OUTLIER) cc_final: 0.5429 (t80) REVERT: E 69 MET cc_start: 0.4099 (mpp) cc_final: 0.3719 (tpp) REVERT: G 32 ASP cc_start: 0.4033 (m-30) cc_final: 0.3516 (t70) REVERT: G 36 TYR cc_start: 0.6539 (OUTLIER) cc_final: 0.5279 (m-80) outliers start: 104 outliers final: 68 residues processed: 305 average time/residue: 0.3402 time to fit residues: 176.8416 Evaluate side-chains 267 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 193 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 36 TYR Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 5.9990 chunk 299 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 276 optimal weight: 0.9980 chunk 154 optimal weight: 0.0370 chunk 27 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27987 Z= 0.204 Angle : 0.640 10.480 38073 Z= 0.326 Chirality : 0.047 0.437 4400 Planarity : 0.004 0.053 4890 Dihedral : 7.099 59.610 4309 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.31 % Favored : 92.66 % Rotamer: Outliers : 3.06 % Allowed : 18.09 % Favored : 78.86 % 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: -2.07 (0.14), residues: 3420 helix: -0.59 (0.19), residues: 645 sheet: -1.23 (0.24), residues: 464 loop : -1.72 (0.12), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.008 0.001 HIS C1048 PHE 0.036 0.002 PHE F 62 TYR 0.020 0.001 TYR B 37 ARG 0.004 0.000 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 231 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7748 (m-10) cc_final: 0.7520 (m-10) REVERT: A 115 GLN cc_start: -0.1143 (OUTLIER) cc_final: -0.1924 (tt0) REVERT: A 201 PHE cc_start: 0.7851 (m-80) cc_final: 0.7532 (m-10) REVERT: A 515 PHE cc_start: 0.8453 (m-80) cc_final: 0.8147 (m-80) REVERT: A 562 PHE cc_start: 0.8270 (t80) cc_final: 0.7961 (t80) REVERT: A 589 PRO cc_start: 0.6525 (Cg_exo) cc_final: 0.6295 (Cg_endo) REVERT: A 824 ASN cc_start: 0.8210 (t0) cc_final: 0.7937 (t0) REVERT: A 960 ASN cc_start: 0.8614 (t0) cc_final: 0.8359 (t0) REVERT: A 1095 PHE cc_start: 0.7671 (m-10) cc_final: 0.7245 (m-10) REVERT: A 1125 ASN cc_start: 0.7746 (p0) cc_final: 0.7478 (t0) REVERT: B 697 MET cc_start: 0.7296 (ppp) cc_final: 0.7079 (ppp) REVERT: B 764 ASN cc_start: 0.8737 (t0) cc_final: 0.8352 (t0) REVERT: B 765 ARG cc_start: 0.8805 (ttm110) cc_final: 0.8437 (ttm110) REVERT: B 873 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.7309 (t80) REVERT: B 902 MET cc_start: 0.8149 (mmm) cc_final: 0.7846 (tpt) REVERT: B 984 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8196 (mm) REVERT: C 220 PHE cc_start: 0.6098 (t80) cc_final: 0.5890 (t80) REVERT: C 346 ARG cc_start: 0.4403 (tpt-90) cc_final: 0.3917 (tpt170) REVERT: C 612 TYR cc_start: 0.7546 (m-80) cc_final: 0.7150 (m-80) REVERT: D 91 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.5541 (t80) REVERT: E 69 MET cc_start: 0.4014 (mpp) cc_final: 0.3624 (tpp) REVERT: G 32 ASP cc_start: 0.3934 (m-30) cc_final: 0.3428 (t70) REVERT: G 45 LYS cc_start: 0.8013 (mppt) cc_final: 0.7780 (mppt) REVERT: G 47 LEU cc_start: 0.8423 (mt) cc_final: 0.8034 (pp) outliers start: 92 outliers final: 64 residues processed: 304 average time/residue: 0.3423 time to fit residues: 176.6360 Evaluate side-chains 277 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 209 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 280 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 chunk 331 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27987 Z= 0.195 Angle : 0.622 14.232 38073 Z= 0.316 Chirality : 0.046 0.427 4400 Planarity : 0.004 0.050 4890 Dihedral : 6.865 59.919 4309 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 3.62 % Allowed : 18.25 % Favored : 78.12 % 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: -1.98 (0.14), residues: 3420 helix: -0.48 (0.20), residues: 646 sheet: -1.26 (0.23), residues: 479 loop : -1.66 (0.13), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.008 0.001 HIS C1048 PHE 0.022 0.001 PHE F 62 TYR 0.020 0.001 TYR C 170 ARG 0.008 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 237 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7811 (m-10) cc_final: 0.7573 (m-10) REVERT: A 115 GLN cc_start: -0.1031 (OUTLIER) cc_final: -0.1917 (tt0) REVERT: A 201 PHE cc_start: 0.7835 (m-80) cc_final: 0.7523 (m-10) REVERT: A 515 PHE cc_start: 0.8595 (m-80) cc_final: 0.8368 (m-80) REVERT: A 562 PHE cc_start: 0.8215 (t80) cc_final: 0.7946 (t80) REVERT: A 761 THR cc_start: 0.8590 (m) cc_final: 0.8263 (t) REVERT: A 824 ASN cc_start: 0.8206 (t0) cc_final: 0.7957 (t0) REVERT: A 954 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8024 (mp10) REVERT: A 960 ASN cc_start: 0.8657 (t0) cc_final: 0.8425 (t0) REVERT: A 1095 PHE cc_start: 0.7672 (m-10) cc_final: 0.7283 (m-10) REVERT: A 1125 ASN cc_start: 0.7758 (p0) cc_final: 0.7547 (t0) REVERT: B 198 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7299 (t0) REVERT: B 697 MET cc_start: 0.7250 (ppp) cc_final: 0.7049 (ppp) REVERT: B 762 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8642 (pm20) REVERT: B 764 ASN cc_start: 0.8721 (t0) cc_final: 0.8319 (t0) REVERT: B 765 ARG cc_start: 0.8787 (ttm110) cc_final: 0.8467 (ttm110) REVERT: B 873 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.7436 (t80) REVERT: B 902 MET cc_start: 0.8228 (mmm) cc_final: 0.7991 (tpt) REVERT: B 984 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8182 (mm) REVERT: C 271 GLN cc_start: 0.6362 (mm-40) cc_final: 0.6149 (mm-40) REVERT: C 346 ARG cc_start: 0.4349 (tpt-90) cc_final: 0.3812 (tpt170) REVERT: C 396 TYR cc_start: 0.3264 (OUTLIER) cc_final: 0.3047 (m-80) REVERT: C 1138 TYR cc_start: 0.6780 (t80) cc_final: 0.6567 (t80) REVERT: D 91 PHE cc_start: 0.5949 (OUTLIER) cc_final: 0.5570 (t80) REVERT: E 69 MET cc_start: 0.3999 (mpp) cc_final: 0.3688 (tpp) REVERT: F 54 ARG cc_start: 0.3530 (OUTLIER) cc_final: 0.3242 (mpt-90) REVERT: G 32 ASP cc_start: 0.3908 (m-30) cc_final: 0.3407 (t70) REVERT: G 36 TYR cc_start: 0.6525 (OUTLIER) cc_final: 0.6157 (m-80) REVERT: G 45 LYS cc_start: 0.8061 (mppt) cc_final: 0.7830 (mppt) REVERT: G 47 LEU cc_start: 0.8450 (mt) cc_final: 0.8047 (pp) outliers start: 109 outliers final: 69 residues processed: 322 average time/residue: 0.3398 time to fit residues: 185.1189 Evaluate side-chains 288 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 209 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 36 TYR Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 210 optimal weight: 8.9990 chunk 225 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 260 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27987 Z= 0.202 Angle : 0.625 10.650 38073 Z= 0.317 Chirality : 0.046 0.423 4400 Planarity : 0.004 0.052 4890 Dihedral : 6.784 59.847 4309 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.22 % Favored : 92.75 % Rotamer: Outliers : 3.19 % Allowed : 19.28 % Favored : 77.53 % 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: -1.91 (0.14), residues: 3420 helix: -0.41 (0.20), residues: 647 sheet: -1.11 (0.24), residues: 483 loop : -1.64 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.008 0.001 HIS C1048 PHE 0.028 0.002 PHE F 62 TYR 0.017 0.001 TYR C 365 ARG 0.007 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 220 time to evaluate : 3.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7905 (m-10) cc_final: 0.7641 (m-10) REVERT: A 115 GLN cc_start: -0.0898 (OUTLIER) cc_final: -0.1806 (tt0) REVERT: A 201 PHE cc_start: 0.7794 (m-80) cc_final: 0.7484 (m-10) REVERT: A 357 ARG cc_start: 0.7245 (mtt180) cc_final: 0.6985 (mtt180) REVERT: A 515 PHE cc_start: 0.8620 (m-80) cc_final: 0.8405 (m-80) REVERT: A 562 PHE cc_start: 0.8177 (t80) cc_final: 0.7875 (t80) REVERT: A 761 THR cc_start: 0.8649 (m) cc_final: 0.8413 (t) REVERT: A 824 ASN cc_start: 0.8160 (t0) cc_final: 0.7940 (t0) REVERT: A 960 ASN cc_start: 0.8625 (t0) cc_final: 0.8413 (t0) REVERT: A 1031 GLU cc_start: 0.7880 (pm20) cc_final: 0.7592 (pt0) REVERT: A 1095 PHE cc_start: 0.7646 (m-10) cc_final: 0.7198 (m-10) REVERT: B 198 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7403 (t0) REVERT: B 762 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8649 (pm20) REVERT: B 764 ASN cc_start: 0.8715 (t0) cc_final: 0.8327 (t0) REVERT: B 765 ARG cc_start: 0.8750 (ttm110) cc_final: 0.8450 (ttm110) REVERT: B 873 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.7430 (t80) REVERT: B 902 MET cc_start: 0.8235 (mmm) cc_final: 0.8004 (tpt) REVERT: B 984 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8186 (mm) REVERT: C 346 ARG cc_start: 0.4288 (tpt-90) cc_final: 0.3769 (tpt170) REVERT: C 396 TYR cc_start: 0.3254 (OUTLIER) cc_final: 0.3005 (m-80) REVERT: C 497 PHE cc_start: 0.1877 (OUTLIER) cc_final: 0.1638 (m-80) REVERT: D 91 PHE cc_start: 0.5972 (OUTLIER) cc_final: 0.5592 (t80) REVERT: E 69 MET cc_start: 0.4065 (mpp) cc_final: 0.3770 (tpp) REVERT: F 54 ARG cc_start: 0.3546 (OUTLIER) cc_final: 0.3074 (mpt-90) REVERT: G 32 ASP cc_start: 0.3905 (m-30) cc_final: 0.3408 (t70) REVERT: G 36 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: G 45 LYS cc_start: 0.8042 (mppt) cc_final: 0.7815 (mppt) REVERT: G 47 LEU cc_start: 0.8465 (mt) cc_final: 0.8087 (pp) outliers start: 96 outliers final: 74 residues processed: 290 average time/residue: 0.3477 time to fit residues: 171.0495 Evaluate side-chains 294 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 210 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 36 TYR Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 3.9990 chunk 317 optimal weight: 10.0000 chunk 289 optimal weight: 0.4980 chunk 308 optimal weight: 20.0000 chunk 185 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 242 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 279 optimal weight: 10.0000 chunk 292 optimal weight: 4.9990 chunk 307 optimal weight: 0.1980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN D 3 GLN ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27987 Z= 0.231 Angle : 0.638 11.825 38073 Z= 0.324 Chirality : 0.046 0.432 4400 Planarity : 0.004 0.050 4890 Dihedral : 6.746 59.883 4309 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.78 % Favored : 92.13 % Rotamer: Outliers : 3.49 % Allowed : 19.28 % Favored : 77.23 % 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: -1.88 (0.14), residues: 3420 helix: -0.36 (0.20), residues: 648 sheet: -0.95 (0.23), residues: 496 loop : -1.67 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 353 HIS 0.009 0.001 HIS C1048 PHE 0.027 0.002 PHE C1052 TYR 0.016 0.001 TYR C 365 ARG 0.006 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 217 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7919 (m-10) cc_final: 0.7660 (m-10) REVERT: A 115 GLN cc_start: -0.0659 (OUTLIER) cc_final: -0.1531 (tt0) REVERT: A 201 PHE cc_start: 0.7848 (m-80) cc_final: 0.7514 (m-10) REVERT: A 515 PHE cc_start: 0.8699 (m-80) cc_final: 0.8450 (m-80) REVERT: A 562 PHE cc_start: 0.8076 (t80) cc_final: 0.7809 (t80) REVERT: A 761 THR cc_start: 0.8723 (m) cc_final: 0.8461 (t) REVERT: A 824 ASN cc_start: 0.8243 (t0) cc_final: 0.8006 (t0) REVERT: A 858 LEU cc_start: 0.8809 (pt) cc_final: 0.8505 (pp) REVERT: A 960 ASN cc_start: 0.8659 (t0) cc_final: 0.8439 (t0) REVERT: A 1031 GLU cc_start: 0.8023 (pm20) cc_final: 0.7764 (pt0) REVERT: A 1095 PHE cc_start: 0.7666 (m-10) cc_final: 0.7260 (m-10) REVERT: B 198 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7498 (t0) REVERT: B 762 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8745 (pm20) REVERT: B 764 ASN cc_start: 0.8744 (t0) cc_final: 0.8377 (t0) REVERT: B 765 ARG cc_start: 0.8783 (ttm110) cc_final: 0.8501 (ttm110) REVERT: B 900 MET cc_start: 0.6938 (mmt) cc_final: 0.5528 (mmt) REVERT: B 902 MET cc_start: 0.8277 (mmm) cc_final: 0.7959 (tpt) REVERT: B 984 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8216 (mm) REVERT: C 346 ARG cc_start: 0.4298 (tpt-90) cc_final: 0.3760 (tpt170) REVERT: C 396 TYR cc_start: 0.3374 (OUTLIER) cc_final: 0.3117 (m-80) REVERT: C 497 PHE cc_start: 0.1709 (OUTLIER) cc_final: 0.1480 (m-80) REVERT: D 91 PHE cc_start: 0.5929 (OUTLIER) cc_final: 0.5538 (t80) REVERT: E 69 MET cc_start: 0.4233 (mpp) cc_final: 0.3979 (tpp) REVERT: G 32 ASP cc_start: 0.3899 (m-30) cc_final: 0.3414 (t70) REVERT: G 36 TYR cc_start: 0.6556 (OUTLIER) cc_final: 0.5335 (m-80) REVERT: G 45 LYS cc_start: 0.8073 (mppt) cc_final: 0.7851 (mppt) REVERT: G 47 LEU cc_start: 0.8422 (mt) cc_final: 0.8028 (pp) outliers start: 105 outliers final: 82 residues processed: 298 average time/residue: 0.3565 time to fit residues: 180.0488 Evaluate side-chains 298 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 208 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 36 TYR Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 6.9990 chunk 326 optimal weight: 40.0000 chunk 199 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 342 optimal weight: 5.9990 chunk 315 optimal weight: 20.0000 chunk 272 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 167 optimal weight: 0.2980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 1 GLN D 3 GLN ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27987 Z= 0.296 Angle : 0.682 11.371 38073 Z= 0.350 Chirality : 0.047 0.458 4400 Planarity : 0.005 0.053 4890 Dihedral : 6.940 59.920 4309 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 26.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.04 % Favored : 91.87 % Rotamer: Outliers : 3.16 % Allowed : 19.68 % Favored : 77.16 % 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: -2.02 (0.14), residues: 3420 helix: -0.53 (0.20), residues: 653 sheet: -1.13 (0.22), residues: 525 loop : -1.73 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1102 HIS 0.010 0.001 HIS B1048 PHE 0.035 0.002 PHE F 62 TYR 0.018 0.002 TYR B1047 ARG 0.006 0.001 ARG F 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 205 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8201 (pm20) cc_final: 0.7994 (pp30) REVERT: A 58 PHE cc_start: 0.7920 (m-10) cc_final: 0.7665 (m-10) REVERT: A 115 GLN cc_start: -0.0574 (OUTLIER) cc_final: -0.1316 (tt0) REVERT: A 515 PHE cc_start: 0.8720 (m-80) cc_final: 0.8501 (m-80) REVERT: A 562 PHE cc_start: 0.8002 (t80) cc_final: 0.7737 (t80) REVERT: A 761 THR cc_start: 0.8866 (m) cc_final: 0.8633 (t) REVERT: A 824 ASN cc_start: 0.8300 (t0) cc_final: 0.8085 (t0) REVERT: A 858 LEU cc_start: 0.8854 (pt) cc_final: 0.8580 (pp) REVERT: A 960 ASN cc_start: 0.8636 (t0) cc_final: 0.8400 (t0) REVERT: A 1031 GLU cc_start: 0.8134 (pm20) cc_final: 0.7727 (pt0) REVERT: A 1095 PHE cc_start: 0.7709 (m-10) cc_final: 0.7229 (m-10) REVERT: B 198 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7533 (t0) REVERT: B 764 ASN cc_start: 0.8808 (t0) cc_final: 0.8483 (t0) REVERT: B 765 ARG cc_start: 0.8836 (ttm110) cc_final: 0.8553 (ttm110) REVERT: B 900 MET cc_start: 0.6995 (mmt) cc_final: 0.5593 (mmt) REVERT: B 902 MET cc_start: 0.8102 (mmm) cc_final: 0.7678 (tpp) REVERT: B 984 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8319 (mm) REVERT: C 346 ARG cc_start: 0.4349 (tpt-90) cc_final: 0.3801 (tpt170) REVERT: C 396 TYR cc_start: 0.3227 (OUTLIER) cc_final: 0.3013 (m-80) REVERT: C 497 PHE cc_start: 0.2164 (OUTLIER) cc_final: 0.1898 (m-80) REVERT: D 91 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.5610 (t80) REVERT: E 51 MET cc_start: 0.6134 (tpt) cc_final: 0.5834 (tpt) REVERT: E 69 MET cc_start: 0.4512 (mpp) cc_final: 0.4193 (tpp) REVERT: G 32 ASP cc_start: 0.3687 (m-30) cc_final: 0.3275 (t70) REVERT: G 36 TYR cc_start: 0.6596 (OUTLIER) cc_final: 0.5323 (m-80) REVERT: G 47 LEU cc_start: 0.8393 (mt) cc_final: 0.8052 (pp) outliers start: 95 outliers final: 83 residues processed: 280 average time/residue: 0.3712 time to fit residues: 177.9229 Evaluate side-chains 280 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 190 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 36 TYR Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 3.9990 chunk 290 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 251 optimal weight: 0.0270 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 280 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.097494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.073336 restraints weight = 125484.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.075171 restraints weight = 70105.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.076377 restraints weight = 45775.127| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 27987 Z= 0.339 Angle : 0.807 59.200 38073 Z= 0.434 Chirality : 0.047 0.456 4400 Planarity : 0.004 0.053 4890 Dihedral : 6.937 59.909 4309 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 27.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.01 % Favored : 91.90 % Rotamer: Outliers : 3.09 % Allowed : 20.05 % Favored : 76.86 % Cbeta Deviations : 0.03 % 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: -2.05 (0.14), residues: 3420 helix: -0.53 (0.20), residues: 653 sheet: -1.14 (0.23), residues: 508 loop : -1.75 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1102 HIS 0.010 0.001 HIS C1048 PHE 0.064 0.002 PHE A 168 TYR 0.032 0.002 TYR A 170 ARG 0.006 0.000 ARG F 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5052.48 seconds wall clock time: 95 minutes 17.04 seconds (5717.04 seconds total)