Starting phenix.real_space_refine on Wed Jul 24 22:33:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhy_34807/07_2024/8hhy_34807.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhy_34807/07_2024/8hhy_34807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhy_34807/07_2024/8hhy_34807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhy_34807/07_2024/8hhy_34807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhy_34807/07_2024/8hhy_34807.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhy_34807/07_2024/8hhy_34807.cif" } resolution = 2.77 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= 0.077 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 123 5.16 5 C 17431 2.51 5 N 4528 2.21 5 O 5338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 27420 Number of models: 1 Model: "" Number of chains: 16 Chain: "F" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 955 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "W" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 675 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 82} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 753 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "H" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 819 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 82 Chain: "L" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 660 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 86} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 7454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7454 Classifications: {'peptide': 957} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 45, 'TRANS': 911} Chain breaks: 10 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 7574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7574 Classifications: {'peptide': 971} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 924} Chain breaks: 9 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 7264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 7264 Classifications: {'peptide': 934} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 44, 'TRANS': 889} Chain breaks: 9 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "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: 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 Time building chain proxies: 15.86, per 1000 atoms: 0.58 Number of scatterers: 27420 At special positions: 0 Unit cell: (157.7, 158.53, 182.6, 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 123 16.00 O 5338 8.00 N 4528 7.00 C 17431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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=2.03 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=2.02 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=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 122 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A 717 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 122 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 717 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 122 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1098 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 801 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN B 331 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN C 717 " Time building additional restraints: 11.80 Conformation dependent library (CDL) restraints added in 5.3 seconds 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6496 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 62 sheets defined 22.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'W' and resid 79 through 83 removed outlier: 4.079A pdb=" N ILE W 83 " --> pdb=" O PRO W 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.872A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.045A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.847A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 759 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 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 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.644A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.765A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.593A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.003A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.024A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.873A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.504A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 759 through 782 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.115A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) 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 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.552A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.830A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.672A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.595A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.754A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.807A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.926A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 940 removed outlier: 4.267A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 977 through 984 removed outlier: 3.508A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.546A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.564A pdb=" N TRP F 33 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 18 through 23 removed outlier: 3.602A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR F 80 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER F 71 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN F 82 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR F 69 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'W' and resid 48 through 49 removed outlier: 3.947A pdb=" N TYR W 49 " --> pdb=" O ASN W 53 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN W 53 " --> pdb=" O TYR W 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'W' and resid 66 through 67 removed outlier: 3.748A pdb=" N SER W 67 " --> pdb=" O ASP W 70 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP W 70 " --> pdb=" O SER W 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'W' and resid 89 through 91 removed outlier: 4.651A pdb=" N GLN W 90 " --> pdb=" O THR W 97 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR W 97 " --> pdb=" O GLN W 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 32 through 34 removed outlier: 5.995A pdb=" N TRP G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY G 99 " --> pdb=" O TRP G 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AA8, first strand: chain 'G' and resid 49 through 52 removed outlier: 3.738A pdb=" N ARG G 50 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN G 59 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR G 57 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 68 through 73 removed outlier: 4.151A pdb=" N THR G 69 " --> pdb=" O GLN G 82 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN G 82 " --> pdb=" O THR G 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 36 through 37 removed outlier: 4.424A pdb=" N GLN I 37 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS I 45 " --> pdb=" O GLN I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 48 through 49 removed outlier: 4.168A pdb=" N TYR I 49 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN I 53 " --> pdb=" O TYR I 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 90 through 91 removed outlier: 4.604A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 46 through 51 removed outlier: 4.145A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 46 through 51 removed outlier: 4.145A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 6 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 36 through 38 Processing sheet with id=AB8, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.538A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.675A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.530A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AC4, first strand: chain 'A' and resid 190 through 191 removed outlier: 6.777A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.384A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.614A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.673A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 654 through 656 removed outlier: 5.550A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AD1, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.914A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.549A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AD5, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.716A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.701A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.584A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.584A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.344A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.950A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AE4, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.287A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AE6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.901A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AE8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.756A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.552A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 50 through 52 removed outlier: 7.878A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=AF4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AF5, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AF6, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AF7, first strand: chain 'C' and resid 190 through 191 removed outlier: 6.723A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AF9, first strand: chain 'C' and resid 318 through 319 removed outlier: 3.605A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AG2, first strand: chain 'C' and resid 354 through 357 removed outlier: 4.981A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 565 through 566 removed outlier: 4.115A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.365A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AG6, first strand: chain 'C' and resid 718 through 727 Processing sheet with id=AG7, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AG8, first strand: chain 'C' and resid 1094 through 1096 removed outlier: 3.699A pdb=" N VAL C1096 " --> pdb=" O PHE C1103 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE C1103 " --> pdb=" O VAL C1096 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2358 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: 11.67 Time building geometry restraints manager: 12.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8766 1.35 - 1.47: 7212 1.47 - 1.60: 11871 1.60 - 1.73: 1 1.73 - 1.85: 159 Bond restraints: 28009 Sorted by residual: bond pdb=" CG PRO B 272 " pdb=" CD PRO B 272 " ideal model delta sigma weight residual 1.503 1.367 0.136 3.40e-02 8.65e+02 1.60e+01 bond pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.28e+01 bond pdb=" CB PRO B 272 " pdb=" CG PRO B 272 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.65e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" C MET H 40 " pdb=" N PRO H 41 " ideal model delta sigma weight residual 1.332 1.359 -0.027 1.12e-02 7.97e+03 5.66e+00 ... (remaining 28004 not shown) Histogram of bond angle deviations from ideal: 92.46 - 100.78: 22 100.78 - 109.10: 2047 109.10 - 117.42: 18537 117.42 - 125.74: 17144 125.74 - 134.06: 334 Bond angle restraints: 38084 Sorted by residual: angle pdb=" N PRO B 272 " pdb=" CD PRO B 272 " pdb=" CG PRO B 272 " ideal model delta sigma weight residual 103.20 92.64 10.56 1.50e+00 4.44e-01 4.96e+01 angle pdb=" CA PRO B 272 " pdb=" N PRO B 272 " pdb=" CD PRO B 272 " ideal model delta sigma weight residual 112.00 102.66 9.34 1.40e+00 5.10e-01 4.45e+01 angle pdb=" CG1 ILE L 29 " pdb=" CB ILE L 29 " pdb=" CG2 ILE L 29 " ideal model delta sigma weight residual 110.70 125.10 -14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" C ILE L 29 " pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 angle pdb=" N PRO C1090 " pdb=" CD PRO C1090 " pdb=" CG PRO C1090 " ideal model delta sigma weight residual 103.20 96.50 6.70 1.50e+00 4.44e-01 1.99e+01 ... (remaining 38079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.84: 15947 21.84 - 43.69: 922 43.69 - 65.53: 138 65.53 - 87.37: 61 87.37 - 109.21: 7 Dihedral angle restraints: 17075 sinusoidal: 6978 harmonic: 10097 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 169.36 -76.36 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 167.77 -74.77 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 165.71 -72.71 1 1.00e+01 1.00e-02 6.75e+01 ... (remaining 17072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 4402 0.148 - 0.295: 18 0.295 - 0.443: 0 0.443 - 0.591: 0 0.591 - 0.738: 2 Chirality restraints: 4422 Sorted by residual: chirality pdb=" CB ILE L 29 " pdb=" CA ILE L 29 " pdb=" CG1 ILE L 29 " pdb=" CG2 ILE L 29 " both_signs ideal model delta sigma weight residual False 2.64 1.91 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.77e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 4419 not shown) Planarity restraints: 4900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " -0.000 2.00e-02 2.50e+03 3.70e-02 1.71e+01 pdb=" CG ASN B 616 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " -0.040 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 9 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ALA H 9 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA H 9 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU H 10 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C1078 " 0.063 5.00e-02 4.00e+02 9.60e-02 1.47e+01 pdb=" N PRO C1079 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO C1079 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C1079 " 0.051 5.00e-02 4.00e+02 ... (remaining 4897 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 386 2.64 - 3.20: 24988 3.20 - 3.77: 41071 3.77 - 4.33: 57633 4.33 - 4.90: 92203 Nonbonded interactions: 216281 Sorted by model distance: nonbonded pdb=" O PHE B 106 " pdb=" OG SER B 116 " model vdw 2.074 2.440 nonbonded pdb=" OE2 GLU B 819 " pdb=" OG SER B1055 " model vdw 2.082 2.440 nonbonded pdb=" OE2 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.111 2.440 nonbonded pdb=" O ALA B 879 " pdb=" OG1 THR B 883 " model vdw 2.128 2.440 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.129 2.520 ... (remaining 216276 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 141 or (resid 142 and (name N or name CA or nam \ e C or name O or name CB )) or resid 166 through 442 or resid 502 through 1120 o \ r (resid 1121 and (name N or name CA or name C or name O or name CB )) or resid \ 1122 through 1145 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 68 or resid 80 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 142 or resi \ d 166 through 209 or resid 216 through 243 or resid 263 through 442 or resid 502 \ through 1145 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 96 or (resid 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 through 141 or (resid 142 and (name N or n \ ame CA or name C or name O or name CB )) or resid 166 through 209 or resid 216 t \ hrough 1120 or (resid 1121 and (name N or name CA or name C or name O or name CB \ )) or resid 1122 through 1145 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'F' and (resid 3 through 10 or (resid 11 through 13 and (name N or name C \ A or name C or name O or name CB )) or resid 14 through 15 or (resid 16 and (nam \ e N or name CA or name C or name O or name CB )) or resid 17 through 24 or (resi \ d 25 and (name N or name CA or name C or name O or name CB )) or resid 26 or (re \ sid 27 through 28 and (name N or name CA or name C or name O or name CB )) or re \ sid 29 through 31 or (resid 32 through 33 and (name N or name CA or name C or na \ me O or name CB )) or resid 34 through 54 or (resid 55 through 60 and (name N or \ name CA or name C or name O or name CB )) or resid 61 through 64 or (resid 65 a \ nd (name N or name CA or name C or name O or name CB )) or resid 66 through 72 o \ r (resid 73 through 77 and (name N or name CA or name C or name O or name CB )) \ or resid 78 through 99 or (resid 100 through 106 and (name N or name CA or name \ C or name O or name CB )) or resid 107 or (resid 108 and (name N or name CA or n \ ame C or name O or name CB )) or resid 109 through 120)) selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 26 or (resid 27 through \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 31 or (resid 32 and (name N or name CA or name C or name O or name CB )) or res \ id 33 through 91 or (resid 92 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'L' and (resid 2 through 8 or resid 15 through 92)) selection = (chain 'W' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 26 or (resid 27 through \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 31 or (resid 32 and (name N or name CA or name C or name O or name CB )) or res \ id 33 through 91 or (resid 92 and (name N or name CA or name C or name O or name \ CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.250 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 78.700 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.150 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:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5282 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 : 0.004 0.147 28009 Z= 0.262 Angle : 0.694 14.397 38084 Z= 0.370 Chirality : 0.049 0.738 4422 Planarity : 0.005 0.096 4872 Dihedral : 14.260 109.215 10453 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.92 (0.14), residues: 3407 helix: -0.80 (0.19), residues: 653 sheet: -1.22 (0.21), residues: 655 loop : -1.47 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 886 HIS 0.021 0.001 HIS B1048 PHE 0.035 0.001 PHE C 906 TYR 0.022 0.001 TYR A 873 ARG 0.007 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.0484 (mtm) cc_final: 0.0270 (tmt) REVERT: A 902 MET cc_start: 0.5852 (tpt) cc_final: 0.5516 (mmm) REVERT: C 912 THR cc_start: 0.5915 (t) cc_final: 0.5590 (m) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 1.0021 time to fit residues: 311.9471 Evaluate side-chains 168 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 3.9990 chunk 260 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 175 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 317 ASN B 501 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5512 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 28009 Z= 0.399 Angle : 0.743 9.529 38084 Z= 0.383 Chirality : 0.049 0.278 4422 Planarity : 0.005 0.058 4872 Dihedral : 8.325 92.941 4388 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.52 % Favored : 93.43 % Rotamer: Outliers : 2.11 % Allowed : 8.83 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 3407 helix: -0.86 (0.19), residues: 656 sheet: -1.37 (0.20), residues: 686 loop : -1.55 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 886 HIS 0.006 0.002 HIS C 207 PHE 0.034 0.002 PHE C 906 TYR 0.031 0.002 TYR C1067 ARG 0.008 0.001 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 187 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: 0.0265 (ptt) cc_final: -0.1311 (mpt) REVERT: G 40 MET cc_start: 0.1920 (pmm) cc_final: 0.1040 (ptt) REVERT: L 4 MET cc_start: 0.0571 (mtm) cc_final: -0.1017 (tpt) REVERT: A 902 MET cc_start: 0.6161 (tpt) cc_final: 0.5901 (mmt) REVERT: A 1001 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7762 (tt) REVERT: C 861 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7337 (pt) REVERT: C 873 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.6576 (m-10) outliers start: 63 outliers final: 31 residues processed: 228 average time/residue: 0.9421 time to fit residues: 267.3144 Evaluate side-chains 198 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 0.5980 chunk 96 optimal weight: 50.0000 chunk 259 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 86 optimal weight: 30.0000 chunk 312 optimal weight: 2.9990 chunk 338 optimal weight: 0.0570 chunk 278 optimal weight: 7.9990 chunk 310 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 251 optimal weight: 9.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 762 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1023 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 196 ASN B 317 ASN B 762 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28009 Z= 0.199 Angle : 0.588 11.354 38084 Z= 0.302 Chirality : 0.044 0.267 4422 Planarity : 0.004 0.062 4872 Dihedral : 7.462 86.800 4388 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 2.21 % Allowed : 11.91 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.77 (0.14), residues: 3407 helix: -0.43 (0.19), residues: 657 sheet: -1.21 (0.21), residues: 649 loop : -1.43 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 886 HIS 0.004 0.001 HIS B1048 PHE 0.021 0.001 PHE A 65 TYR 0.020 0.001 TYR A 789 ARG 0.005 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 194 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: 0.0406 (ptt) cc_final: -0.1277 (mpt) REVERT: L 29 ILE cc_start: 0.0688 (OUTLIER) cc_final: 0.0488 (tt) REVERT: A 567 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.5431 (mpp80) REVERT: A 740 MET cc_start: 0.5611 (OUTLIER) cc_final: 0.4830 (mtp) REVERT: A 969 ASN cc_start: 0.6453 (OUTLIER) cc_final: 0.6210 (m-40) REVERT: A 1001 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7587 (tt) REVERT: B 275 PHE cc_start: 0.5828 (OUTLIER) cc_final: 0.5228 (t80) REVERT: C 926 GLN cc_start: 0.5991 (tm130) cc_final: 0.5752 (tm130) outliers start: 66 outliers final: 25 residues processed: 242 average time/residue: 0.9151 time to fit residues: 277.3915 Evaluate side-chains 195 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 3.9990 chunk 235 optimal weight: 0.3980 chunk 162 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 314 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 164 optimal weight: 20.0000 chunk 297 optimal weight: 0.0670 chunk 89 optimal weight: 50.0000 overall best weight: 1.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 6 GLN ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A1023 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 762 GLN B 919 ASN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5495 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28009 Z= 0.321 Angle : 0.664 9.693 38084 Z= 0.341 Chirality : 0.047 0.250 4422 Planarity : 0.005 0.058 4872 Dihedral : 7.263 81.341 4388 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.57 % Favored : 93.37 % Rotamer: Outliers : 3.46 % Allowed : 13.09 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 3407 helix: -0.52 (0.19), residues: 657 sheet: -1.36 (0.20), residues: 665 loop : -1.47 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.004 0.001 HIS B1058 PHE 0.018 0.002 PHE B 238 TYR 0.025 0.002 TYR C1067 ARG 0.004 0.000 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 179 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: 0.0389 (ptt) cc_final: -0.1276 (mpt) REVERT: G 40 MET cc_start: 0.2237 (pmm) cc_final: 0.1055 (ptt) REVERT: I 4 MET cc_start: 0.1621 (mmm) cc_final: 0.1371 (mmm) REVERT: L 4 MET cc_start: -0.0025 (mmm) cc_final: -0.0830 (tmt) REVERT: A 567 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.5551 (mpp80) REVERT: A 740 MET cc_start: 0.5861 (OUTLIER) cc_final: 0.4987 (mtp) REVERT: A 878 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7047 (tt) REVERT: A 984 LEU cc_start: 0.2187 (OUTLIER) cc_final: 0.1579 (mp) REVERT: A 1001 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7766 (tt) REVERT: C 873 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.6714 (m-10) outliers start: 103 outliers final: 49 residues processed: 257 average time/residue: 0.9149 time to fit residues: 294.8630 Evaluate side-chains 214 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 159 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 30.0000 chunk 188 optimal weight: 30.0000 chunk 4 optimal weight: 4.9990 chunk 247 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 283 optimal weight: 30.0000 chunk 229 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 169 optimal weight: 0.8980 chunk 298 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 675 GLN B 762 GLN B 919 ASN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28009 Z= 0.277 Angle : 0.629 9.637 38084 Z= 0.322 Chirality : 0.046 0.248 4422 Planarity : 0.004 0.059 4872 Dihedral : 6.958 75.866 4388 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.28 % Favored : 94.66 % Rotamer: Outliers : 3.46 % Allowed : 14.19 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.84 (0.14), residues: 3407 helix: -0.44 (0.19), residues: 653 sheet: -1.35 (0.20), residues: 656 loop : -1.46 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.004 0.001 HIS C 207 PHE 0.017 0.002 PHE C 927 TYR 0.024 0.002 TYR C1067 ARG 0.003 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 175 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: 0.0427 (ptt) cc_final: -0.1185 (mpt) REVERT: H 93 MET cc_start: 0.1144 (mtt) cc_final: -0.1101 (tmm) REVERT: L 4 MET cc_start: 0.0101 (mmm) cc_final: -0.0704 (tmt) REVERT: A 567 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.5701 (mpp80) REVERT: A 740 MET cc_start: 0.5771 (OUTLIER) cc_final: 0.4824 (mtp) REVERT: A 878 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7047 (tt) REVERT: A 1001 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7692 (tt) REVERT: B 740 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5188 (mtp) REVERT: B 858 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.5368 (pt) REVERT: C 926 GLN cc_start: 0.6102 (tm130) cc_final: 0.5855 (tm130) outliers start: 103 outliers final: 50 residues processed: 254 average time/residue: 0.9118 time to fit residues: 290.6143 Evaluate side-chains 220 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 164 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 chunk 65 optimal weight: 0.0770 chunk 195 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 332 optimal weight: 0.7980 chunk 276 optimal weight: 30.0000 chunk 154 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 110 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 675 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 762 GLN B 919 ASN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5414 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28009 Z= 0.218 Angle : 0.596 14.786 38084 Z= 0.302 Chirality : 0.044 0.247 4422 Planarity : 0.004 0.059 4872 Dihedral : 6.685 71.179 4388 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.17 % Favored : 94.78 % Rotamer: Outliers : 3.39 % Allowed : 15.34 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.72 (0.14), residues: 3407 helix: -0.32 (0.19), residues: 659 sheet: -1.27 (0.20), residues: 651 loop : -1.38 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.004 0.001 HIS B1058 PHE 0.026 0.001 PHE B 194 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 178 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 40 MET cc_start: 0.1410 (tpp) cc_final: 0.0683 (tpp) REVERT: W 4 MET cc_start: 0.0397 (ptt) cc_final: -0.1187 (mpt) REVERT: H 93 MET cc_start: 0.0881 (mtt) cc_final: -0.1133 (tmm) REVERT: L 4 MET cc_start: 0.0026 (mmm) cc_final: -0.0720 (tmt) REVERT: A 567 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.5548 (mpp80) REVERT: A 740 MET cc_start: 0.5691 (OUTLIER) cc_final: 0.5350 (mtp) REVERT: A 878 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7071 (tt) REVERT: A 1001 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7611 (tt) REVERT: B 740 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.5112 (mtp) REVERT: C 865 LEU cc_start: 0.6286 (OUTLIER) cc_final: 0.6038 (mp) outliers start: 101 outliers final: 50 residues processed: 256 average time/residue: 0.8874 time to fit residues: 288.9675 Evaluate side-chains 216 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 160 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 189 optimal weight: 40.0000 chunk 243 optimal weight: 0.9980 chunk 188 optimal weight: 30.0000 chunk 280 optimal weight: 0.3980 chunk 185 optimal weight: 6.9990 chunk 331 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 675 GLN A 762 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 762 GLN B 919 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5378 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28009 Z= 0.197 Angle : 0.580 12.268 38084 Z= 0.294 Chirality : 0.044 0.246 4422 Planarity : 0.004 0.058 4872 Dihedral : 6.438 66.978 4388 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.32 % Allowed : 16.24 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.61 (0.14), residues: 3407 helix: -0.18 (0.20), residues: 653 sheet: -1.23 (0.20), residues: 669 loop : -1.32 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.004 0.001 HIS A1048 PHE 0.015 0.001 PHE C 927 TYR 0.019 0.001 TYR B 369 ARG 0.002 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 178 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 40 MET cc_start: 0.1516 (tpp) cc_final: 0.0846 (tpp) REVERT: W 4 MET cc_start: 0.0373 (ptt) cc_final: -0.1226 (mpt) REVERT: H 93 MET cc_start: 0.0777 (mtt) cc_final: -0.1165 (tmm) REVERT: L 4 MET cc_start: 0.0149 (mmm) cc_final: -0.0614 (tmt) REVERT: A 567 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.5595 (mpp80) REVERT: A 740 MET cc_start: 0.5725 (OUTLIER) cc_final: 0.5382 (mtp) REVERT: A 878 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7071 (tt) REVERT: A 1001 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7576 (tt) REVERT: B 858 LEU cc_start: 0.5685 (OUTLIER) cc_final: 0.5441 (pt) REVERT: B 1058 HIS cc_start: 0.6148 (OUTLIER) cc_final: 0.5740 (m-70) outliers start: 99 outliers final: 54 residues processed: 255 average time/residue: 0.8207 time to fit residues: 267.9194 Evaluate side-chains 226 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 166 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.0970 chunk 210 optimal weight: 0.9980 chunk 225 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 260 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 196 ASN B 317 ASN B 762 GLN B 919 ASN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5373 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28009 Z= 0.201 Angle : 0.581 11.991 38084 Z= 0.294 Chirality : 0.044 0.264 4422 Planarity : 0.004 0.059 4872 Dihedral : 6.302 63.105 4388 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.12 % Allowed : 16.58 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.57 (0.14), residues: 3407 helix: -0.13 (0.20), residues: 653 sheet: -1.20 (0.20), residues: 685 loop : -1.29 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.017 0.001 HIS B1058 PHE 0.032 0.001 PHE B 168 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 172 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 48 MET cc_start: 0.4606 (OUTLIER) cc_final: 0.2962 (pmm) REVERT: W 4 MET cc_start: 0.0392 (ptt) cc_final: -0.1199 (mpt) REVERT: H 93 MET cc_start: 0.0908 (mtt) cc_final: -0.0950 (tmm) REVERT: L 4 MET cc_start: 0.0136 (mmm) cc_final: -0.0647 (tmt) REVERT: A 141 LEU cc_start: 0.0322 (OUTLIER) cc_final: -0.0195 (pp) REVERT: A 567 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.5638 (mpp80) REVERT: A 878 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7066 (tt) REVERT: A 1001 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7530 (tt) REVERT: B 740 MET cc_start: 0.5787 (OUTLIER) cc_final: 0.4792 (mtp) REVERT: B 858 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5565 (pt) REVERT: C 926 GLN cc_start: 0.6084 (tm130) cc_final: 0.5767 (tm130) outliers start: 93 outliers final: 59 residues processed: 241 average time/residue: 0.7928 time to fit residues: 247.8903 Evaluate side-chains 230 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 164 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1048 HIS Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 8.9990 chunk 317 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 308 optimal weight: 0.8980 chunk 185 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 94 optimal weight: 0.2980 chunk 279 optimal weight: 5.9990 chunk 292 optimal weight: 0.0070 chunk 307 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 114 GLN A 564 GLN A 762 GLN A1054 GLN A1113 GLN B 196 ASN B 317 ASN B 762 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5340 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28009 Z= 0.185 Angle : 0.571 11.706 38084 Z= 0.290 Chirality : 0.044 0.243 4422 Planarity : 0.004 0.060 4872 Dihedral : 6.092 59.923 4388 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.85 % Allowed : 17.05 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.49 (0.14), residues: 3407 helix: -0.03 (0.20), residues: 653 sheet: -1.21 (0.20), residues: 688 loop : -1.23 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.004 0.001 HIS B1058 PHE 0.027 0.001 PHE B 168 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 173 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 48 MET cc_start: 0.4641 (OUTLIER) cc_final: 0.3072 (pmm) REVERT: W 4 MET cc_start: 0.0327 (ptt) cc_final: -0.1230 (mpt) REVERT: H 93 MET cc_start: 0.0865 (mtt) cc_final: -0.0898 (tmm) REVERT: L 4 MET cc_start: 0.0029 (mmm) cc_final: -0.0710 (tmt) REVERT: A 141 LEU cc_start: 0.0437 (OUTLIER) cc_final: -0.0118 (pp) REVERT: A 567 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.5702 (mpp80) REVERT: A 878 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7040 (tt) REVERT: A 1001 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7387 (tt) REVERT: B 1058 HIS cc_start: 0.5997 (OUTLIER) cc_final: 0.5666 (m170) REVERT: C 34 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.6195 (mpt90) REVERT: C 926 GLN cc_start: 0.6129 (tm130) cc_final: 0.5907 (tm130) REVERT: C 1001 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7690 (tt) outliers start: 85 outliers final: 55 residues processed: 241 average time/residue: 0.8064 time to fit residues: 253.8203 Evaluate side-chains 229 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 166 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 5.9990 chunk 326 optimal weight: 0.5980 chunk 199 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 227 optimal weight: 0.8980 chunk 342 optimal weight: 0.0870 chunk 315 optimal weight: 7.9990 chunk 272 optimal weight: 0.0370 chunk 28 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 762 GLN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5322 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28009 Z= 0.181 Angle : 0.571 13.080 38084 Z= 0.290 Chirality : 0.044 0.243 4422 Planarity : 0.004 0.062 4872 Dihedral : 5.967 59.043 4388 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.32 % Allowed : 17.82 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.43 (0.14), residues: 3407 helix: -0.01 (0.20), residues: 653 sheet: -1.16 (0.20), residues: 688 loop : -1.18 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.019 0.001 HIS B1058 PHE 0.026 0.001 PHE B 168 TYR 0.021 0.001 TYR C1067 ARG 0.002 0.000 ARG A1000 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 178 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 40 MET cc_start: 0.1182 (tpp) cc_final: 0.0735 (tpp) REVERT: F 48 MET cc_start: 0.4646 (OUTLIER) cc_final: 0.3090 (pmm) REVERT: W 4 MET cc_start: 0.0308 (ptt) cc_final: -0.1261 (mpt) REVERT: H 93 MET cc_start: 0.0829 (mtt) cc_final: -0.0879 (tmm) REVERT: L 4 MET cc_start: -0.0231 (mmm) cc_final: -0.1915 (tpt) REVERT: A 141 LEU cc_start: 0.0426 (OUTLIER) cc_final: -0.0150 (pp) REVERT: A 567 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.5713 (mpp80) REVERT: A 878 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7040 (tt) REVERT: A 1001 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7306 (tt) REVERT: C 34 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.5907 (mpt90) REVERT: C 926 GLN cc_start: 0.6089 (tm130) cc_final: 0.5880 (tm130) REVERT: C 1001 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7648 (tt) outliers start: 69 outliers final: 47 residues processed: 232 average time/residue: 0.8380 time to fit residues: 248.4536 Evaluate side-chains 221 residues out of total 3031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 167 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 chunk 251 optimal weight: 9.9990 chunk 40 optimal weight: 0.3980 chunk 75 optimal weight: 9.9990 chunk 273 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 34 optimal weight: 30.0000 chunk 50 optimal weight: 7.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 675 GLN B 762 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.264619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.234210 restraints weight = 36119.244| |-----------------------------------------------------------------------------| r_work (start): 0.4763 rms_B_bonded: 1.98 r_work: 0.4587 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 28009 Z= 0.450 Angle : 0.766 11.977 38084 Z= 0.391 Chirality : 0.049 0.266 4422 Planarity : 0.005 0.062 4872 Dihedral : 6.590 58.442 4388 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 2.52 % Allowed : 18.02 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.87 (0.14), residues: 3407 helix: -0.61 (0.19), residues: 647 sheet: -1.36 (0.20), residues: 674 loop : -1.41 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 104 HIS 0.009 0.002 HIS B1058 PHE 0.039 0.003 PHE C 718 TYR 0.023 0.002 TYR A1067 ARG 0.005 0.001 ARG C1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6690.16 seconds wall clock time: 120 minutes 37.83 seconds (7237.83 seconds total)